Freethought & Rationalism Archive

Reldas of Melchezidec · 12-01-2002, 11:22 PM

Greetings all,
Even after several years of hard schoolin' and keeping up with the interestiing threads on science forums, i'm not quite able to accurately describe theorectical evolutionary mechanisms. I am certain you, yes you can help me. We all like logic puzzels, so heres 1 that I hope you haven't already gotten board with:
1) The enzyme paradox- this one confused me for a short time, as it is barely within my cognitivwe grasp. Enzymes are crucial proteins for life as we know it. They catalyse reactions that would normaly take much longer- even a milisecond longer would be way too long on a microscale. Millions and millions of enzyme catalysed reactions are happening at any given moment inside even the simplist cell known. However, enzymes, like other proteins, are synthesized from a DNA/RNA recipe! So how can something that is so incredibly crucial to the existence and function of genetic material be created exclusively by that same material(at least in our present atmoshere)?? The best answer so far is that RNA actually catalyses the production of itself. I'm skeptical- can anyone provide sources?

Dr.GH · 12-02-2002, 09:06 AM

Here is a fairly good review:

<a href="http://www.chemsoc.org/chembytes/ezine/2000/evans_may00.htm" target="_blank">Its alive, isn't it?</a>

Doubting Didymus · 12-02-2002, 02:16 PM

I think the problem you are having is that it is difficult for you to conceive of an irreducibly complex structure being formed in several steps.

What you are looking at (a simple cell) is generally known as an 'irreducibly complex' system. Behe build an entire lucrative career out of screaming about it, which was silly of him, because practically everyone saw through it straight off.

DNA and its neccessary enzymes, each required for the production of the other, is indeed 'irreducibly' complex. BUT, can evolution create such structures? the answer is a resounding 'yes'. This site demonstrates a theoretical evolutionary pathway that leads to an irreducible mousetrap: <a href="http://udel.edu/~mcdonald/mousetrap.html" target="_blank">Here.</a>

Imagine the trap as a simple cell, imagine the catch an an enzyme, and the bar as DNA. As in a cell, neither can work without the other, yet the end product has been built up from a simple loop of wire in small steps.

That is how it works in theory, which I think is what you most needed to know. In reality, we don't know for absolute certain what the first replicator wsa, of what forms it took before it was RNA, nor exactly how it progressed to DNA. There is a lot of research going on there, however. What we do know is that there are no theoretical barriers.

Run a search for 'abiogenesis'. There are a few threads around here as well, that might give you an insight, but I have never gotten the hang of serching these archives.

Reldas of Melchezidec · 12-09-2002, 07:07 PM

Greetings Doc and Didymus,

My thanks for a prompt and informative reply, and apologies for my belated ones. I'm still rummaging through the material, but so far it has helped with my conceptual logistics. The theoretical path for ribozymes to RNA to DNA is not such a big stretch to my noggin given the reducible moustrap thingy- I don't pretend to really understand it in any �better� fashion other than previously theoretisized, or even believe all of it for that matter. Its just that many people throw around these concepts as if they are conceivable, and I want to verify it with my own noggin�.

The reducible mousetrap is good for basics- I am okay with that aspect of evolution. I don�t have much of a problem with it in the context of a cell. But thanks anyway Didymous, for that examplimous reducible death-to mouse that is analogous to my inquiring foment of fuss.

However, as long as I am using my creative capacities to generate a hypothetical chain of molecular events taking place over time within a micelle or clay or some other precellular substrate, I cannot make the leap involved when abiotic molecules react to form nucleotides outside of a protective nurturing cell! Without a bilipid membrane enclosing the necessary ingredients and gradients within, and a selective means of extracting it from the environment, it seems that any sequences formed in chaotic nature would be ever so fleeting.

Part of uniformitarianism is that the same processes shape the earth today as a while ago, but this is not entirely true because the presence of life changed the atmosphere and sculpted the biome into what it is today. Early prospectfull life didn�t have the conditions we have today, so doesn�t this mean that early life was bombarded with UV radiation- all 3 or 4 types at once? Nucleotides forming in primordial soup literally better do it over night, not over �long periods of time�. Am I overplaying the destructiveness of radiation and chaotic weather conditions on simple free-floating nucleotide sequences?

How many different types of short-lived ribosymes would have to be captured inside the same micelle with plenty of substrate, and building blocks, and energy before it could replicate? I know this is a question we are not ready to answer, but with all of my knowledge of organic chemistry, I am skeptical of the current theories. Maybe it was some other sort of semipermiable membrane that allowed enough building blocks to enter within to give prospectful life a fighting chance. I should like to look into the stereochemical mechanisms that ribosymes catalyze to see what sort of temperatures, concentrations, and solvents are needed for some replicative action.

Supposing that conditions provided enough primordial soup to make a chain of the minimum needed 50 nucleotide sequences.(sounds feasible if I say it fast) Assuming that you need other abiotic organic compounds to use to self replicate, these building blocks must be readily available for the RNA strand to start cloning itself.(It is that theorectical Super RNA type that can perform all of the myriad of different functions that must be carried out within milliseconds for RNA to replicate itself) Now that all these assumptions are met, it sounds like a more probable cenancestor than what I�ve been bogged down with before- that is if this renegade super mutant ninja RNA can replicate the crap out of itself. Keep in mind that this cannot happen without a bunch of nearby nucleotides volunteering for it�s life�s cause (forgive the pun). And then after the prolific self-replicating sessions, a micelle could come along and make a cell out of some of it! Just like that!

Now it makes more sense if by some natural process a mega-plethora of nucleotides were spontaneously generated in one area from abiotic material- its bound to happen once or twice over a few billion years, right? Then, (nearing climax!) a lipid layer formed over the surface of this material (just like what I stepped in earlier), protecting it a little from entropy as it randomly combines in the murky depths below. Now something truly crucial must take place! Energy in the form of sound waves are generated, (perhaps from lightning or seismic activity), that featured the exact frequencies heard in the music of our modern day �Righteous Brothers�! Subsequently, RNA is no longer free-floating- MEMBRANOUS LIFE IS SYNTHESIZED!!!!!!! One likes this hypothesis better than most because it conforms with similar trends in reproductive processes we see amongst Humans today.

One likes the pre-RNA theories better- RNA isn�t stable enough to support the RNA-world hypothesis but a more stable molecule might suffice. Then arises the question of how RNA usurped it. Also, was there a pre-pre RNA world? There are lots of questions in this new area, I just thought it would be fun to mull them around a little and see what comes up...

�Scientists interested in the origins of life seem to divide neatly into two classes. The first, usually but not always molecular biologists, believe that RNA must have been the first replicating molecule and that chemists are exaggerating the difficulties of nucleotide synthesis. The second group of scientists are much more pessimistic. They believe that the de novo appearance of oligonucleotides on the primitive Earth would have been a near miracle. Time will tell which is correct.�

I hope Doc and Didymous at least will disagree with some of this stuff, if only for giggles.

Anyone else notice that the more that scientists uncover about nature, the more questions arise? I bet there�s enough stuff out there to keep inquiring minds satiated until Adam extinction!

Reldas of Arelius

Dr.GH · 12-10-2002, 09:33 AM

I am giving finals this week, and submiting grades next week. I'll try to respond somewhat later.

I hope that some others can help you on this in the meantime.

ps418 · 12-10-2002, 01:47 PM

Quote:

RoM: Anyone else notice that the more that scientists uncover about nature, the more questions arise?

Knowledge is like a sphere. As its radius increases, its surface area increases also.

hmm. . . what is the relationship between the radius of a sphere and its surface area again?

Doubting Didymus · 12-10-2002, 01:53 PM

Sorry, reldas. I can't really go into depth on this one with you. You seem to want to go quite deep into biochemistry, which I do not hold much knowledge about (spherical or no). If no-one else can help you, you might look through some old threads by searching this forum for 'abiogenesis'.

Where it that thread with the really good abiogenesis summary that camaban linked to? I can't find it...

Reldas of Melchezidec · 12-10-2002, 03:03 PM

Greetings Doc, 418, and Didy',
Is ok.
The topic of this forum is "Swizzy my Nizzy"
And I feel that my nizzy has been pretty well swizzied thus far, thanks to the input and urls provided.

Human knowledge is also like a living entity. When nurtured by each individual, contributeing with thier particular insights, it grows. However most of its constituents cannot see the whole creature that they make, complete with its goodness and vices, and so only the knowledge that can be conceived of by an individual is employed and subsequently passed on to the next generation. Knowledge is knowledge, whether "right" or "wrong", or conforming with "reality" or not conforming with reality, it is still knowledge.

And I like knowledge. Its fun and even practical sometimes!

Reldas of ambiguous poeticism

[ December 10, 2002: Message edited by: Reldas of Melchezidec ]</p>

12-01-2002, 11:22 PM	#1
Reldas of Melchezidec Regular Member Join Date: Sep 2002 Location: "Wherever the body is, there the vultures gather..." Posts: 106	Swizzy my Nizzy Greetings all, Even after several years of hard schoolin' and keeping up with the interestiing threads on science forums, i'm not quite able to accurately describe theorectical evolutionary mechanisms. I am certain you, yes you can help me. We all like logic puzzels, so heres 1 that I hope you haven't already gotten board with: 1) The enzyme paradox- this one confused me for a short time, as it is barely within my cognitivwe grasp. Enzymes are crucial proteins for life as we know it. They catalyse reactions that would normaly take much longer- even a milisecond longer would be way too long on a microscale. Millions and millions of enzyme catalysed reactions are happening at any given moment inside even the simplist cell known. However, enzymes, like other proteins, are synthesized from a DNA/RNA recipe! So how can something that is so incredibly crucial to the existence and function of genetic material be created exclusively by that same material(at least in our present atmoshere)?? The best answer so far is that RNA actually catalyses the production of itself. I'm skeptical- can anyone provide sources?

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12-02-2002, 09:06 AM	#2
Dr.GH Veteran Member Join Date: Jul 2001 Location: Dana Point, Ca, USA Posts: 2,115	Here is a fairly good review: <a href="http://www.chemsoc.org/chembytes/ezine/2000/evans_may00.htm" target="_blank">Its alive, isn't it?</a>

12-02-2002, 02:16 PM	#3
Doubting Didymus Veteran Member Join Date: Jul 2002 Location: East Coast. Australia. Posts: 5,455	I think the problem you are having is that it is difficult for you to conceive of an irreducibly complex structure being formed in several steps. What you are looking at (a simple cell) is generally known as an 'irreducibly complex' system. Behe build an entire lucrative career out of screaming about it, which was silly of him, because practically everyone saw through it straight off. DNA and its neccessary enzymes, each required for the production of the other, is indeed 'irreducibly' complex. BUT, can evolution create such structures? the answer is a resounding 'yes'. This site demonstrates a theoretical evolutionary pathway that leads to an irreducible mousetrap: <a href="http://udel.edu/~mcdonald/mousetrap.html" target="_blank">Here.</a> Imagine the trap as a simple cell, imagine the catch an an enzyme, and the bar as DNA. As in a cell, neither can work without the other, yet the end product has been built up from a simple loop of wire in small steps. That is how it works in theory, which I think is what you most needed to know. In reality, we don't know for absolute certain what the first replicator wsa, of what forms it took before it was RNA, nor exactly how it progressed to DNA. There is a lot of research going on there, however. What we do know is that there are no theoretical barriers. Run a search for 'abiogenesis'. There are a few threads around here as well, that might give you an insight, but I have never gotten the hang of serching these archives.

12-09-2002, 07:07 PM	#4
Reldas of Melchezidec Regular Member Join Date: Sep 2002 Location: "Wherever the body is, there the vultures gather..." Posts: 106	Greetings Doc and Didymus, My thanks for a prompt and informative reply, and apologies for my belated ones. I'm still rummaging through the material, but so far it has helped with my conceptual logistics. The theoretical path for ribozymes to RNA to DNA is not such a big stretch to my noggin given the reducible moustrap thingy- I don't pretend to really understand it in any �better� fashion other than previously theoretisized, or even believe all of it for that matter. Its just that many people throw around these concepts as if they are conceivable, and I want to verify it with my own noggin�. The reducible mousetrap is good for basics- I am okay with that aspect of evolution. I don�t have much of a problem with it in the context of a cell. But thanks anyway Didymous, for that examplimous reducible death-to mouse that is analogous to my inquiring foment of fuss. However, as long as I am using my creative capacities to generate a hypothetical chain of molecular events taking place over time within a micelle or clay or some other precellular substrate, I cannot make the leap involved when abiotic molecules react to form nucleotides outside of a protective nurturing cell! Without a bilipid membrane enclosing the necessary ingredients and gradients within, and a selective means of extracting it from the environment, it seems that any sequences formed in chaotic nature would be ever so fleeting. Part of uniformitarianism is that the same processes shape the earth today as a while ago, but this is not entirely true because the presence of life changed the atmosphere and sculpted the biome into what it is today. Early prospectfull life didn�t have the conditions we have today, so doesn�t this mean that early life was bombarded with UV radiation- all 3 or 4 types at once? Nucleotides forming in primordial soup literally better do it over night, not over �long periods of time�. Am I overplaying the destructiveness of radiation and chaotic weather conditions on simple free-floating nucleotide sequences? How many different types of short-lived ribosymes would have to be captured inside the same micelle with plenty of substrate, and building blocks, and energy before it could replicate? I know this is a question we are not ready to answer, but with all of my knowledge of organic chemistry, I am skeptical of the current theories. Maybe it was some other sort of semipermiable membrane that allowed enough building blocks to enter within to give prospectful life a fighting chance. I should like to look into the stereochemical mechanisms that ribosymes catalyze to see what sort of temperatures, concentrations, and solvents are needed for some replicative action. Supposing that conditions provided enough primordial soup to make a chain of the minimum needed 50 nucleotide sequences.(sounds feasible if I say it fast) Assuming that you need other abiotic organic compounds to use to self replicate, these building blocks must be readily available for the RNA strand to start cloning itself.(It is that theorectical Super RNA type that can perform all of the myriad of different functions that must be carried out within milliseconds for RNA to replicate itself) Now that all these assumptions are met, it sounds like a more probable cenancestor than what I�ve been bogged down with before- that is if this renegade super mutant ninja RNA can replicate the crap out of itself. Keep in mind that this cannot happen without a bunch of nearby nucleotides volunteering for it�s life�s cause (forgive the pun). And then after the prolific self-replicating sessions, a micelle could come along and make a cell out of some of it! Just like that! Now it makes more sense if by some natural process a mega-plethora of nucleotides were spontaneously generated in one area from abiotic material- its bound to happen once or twice over a few billion years, right? Then, (nearing climax!) a lipid layer formed over the surface of this material (just like what I stepped in earlier), protecting it a little from entropy as it randomly combines in the murky depths below. Now something truly crucial must take place! Energy in the form of sound waves are generated, (perhaps from lightning or seismic activity), that featured the exact frequencies heard in the music of our modern day �Righteous Brothers�! Subsequently, RNA is no longer free-floating- MEMBRANOUS LIFE IS SYNTHESIZED!!!!!!! One likes this hypothesis better than most because it conforms with similar trends in reproductive processes we see amongst Humans today. One likes the pre-RNA theories better- RNA isn�t stable enough to support the RNA-world hypothesis but a more stable molecule might suffice. Then arises the question of how RNA usurped it. Also, was there a pre-pre RNA world? There are lots of questions in this new area, I just thought it would be fun to mull them around a little and see what comes up... �Scientists interested in the origins of life seem to divide neatly into two classes. The first, usually but not always molecular biologists, believe that RNA must have been the first replicating molecule and that chemists are exaggerating the difficulties of nucleotide synthesis. The second group of scientists are much more pessimistic. They believe that the de novo appearance of oligonucleotides on the primitive Earth would have been a near miracle. Time will tell which is correct.� I hope Doc and Didymous at least will disagree with some of this stuff, if only for giggles. Anyone else notice that the more that scientists uncover about nature, the more questions arise? I bet there�s enough stuff out there to keep inquiring minds satiated until Adam extinction! Reldas of Arelius

12-10-2002, 09:33 AM	#5
Dr.GH Veteran Member Join Date: Jul 2001 Location: Dana Point, Ca, USA Posts: 2,115	I am giving finals this week, and submiting grades next week. I'll try to respond somewhat later. I hope that some others can help you on this in the meantime.

12-10-2002, 01:53 PM	#7
Doubting Didymus Veteran Member Join Date: Jul 2002 Location: East Coast. Australia. Posts: 5,455	Sorry, reldas. I can't really go into depth on this one with you. You seem to want to go quite deep into biochemistry, which I do not hold much knowledge about (spherical or no). If no-one else can help you, you might look through some old threads by searching this forum for 'abiogenesis'. Where it that thread with the really good abiogenesis summary that camaban linked to? I can't find it...

12-10-2002, 03:03 PM	#8
Reldas of Melchezidec Regular Member Join Date: Sep 2002 Location: "Wherever the body is, there the vultures gather..." Posts: 106	Greetings Doc, 418, and Didy', Is ok. The topic of this forum is "Swizzy my Nizzy" And I feel that my nizzy has been pretty well swizzied thus far, thanks to the input and urls provided. Human knowledge is also like a living entity. When nurtured by each individual, contributeing with thier particular insights, it grows. However most of its constituents cannot see the whole creature that they make, complete with its goodness and vices, and so only the knowledge that can be conceived of by an individual is employed and subsequently passed on to the next generation. Knowledge is knowledge, whether "right" or "wrong", or conforming with "reality" or not conforming with reality, it is still knowledge. And I like knowledge. Its fun and even practical sometimes! Reldas of ambiguous poeticism [ December 10, 2002: Message edited by: Reldas of Melchezidec ]</p>

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