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Author Topic:   Thermodynamics, Abiogenesis and Evolution
Percy
Member
Posts: 17325
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.1


Message 16 of 128 (99676)
04-13-2004 12:34 PM
Reply to: Message 14 by DNAunion
04-13-2004 9:54 AM


Hi, DNAunion!

Since we don't know how abiogenesis occurred, we can't know the thermodynamic implications. Abiogensis hypotheses might benefit from taking thermodynamic considerations into account, but we of course assume it followed the laws of physics, including the thermodynamic laws.

--Percy


This message is a reply to:
 Message 14 by DNAunion, posted 04-13-2004 9:54 AM DNAunion has not yet responded

    
JonF
Member
Posts: 4140
Joined: 06-23-2003
Member Rating: 1.7


Message 17 of 128 (99690)
04-13-2004 1:29 PM
Reply to: Message 14 by DNAunion
04-13-2004 9:54 AM


Let me try an analogy ... gravity poses a problem for the origin of pyramids (analogous to how the second law poses a problem for OOL).

You have made nothing but assertions. I (and, I believe, others) understand what you are saying and don't need your analogies ... what we are asking for is evidence for your unsupported assertion that "the second law poses a problem for OOL".

Thermodynamic calculations should be part of a comprehensive theory of abiogenesis (which theory we don't have yet). Only a fool would offer a hypothesis which requires flouting the second law. But until calculations are presented nobody, including you and me, knows whether or not "the second law poses a problem for OOL".

Present your calculations or accept that you do not know whether or not "the second law poses a problem for OOL".


This message is a reply to:
 Message 14 by DNAunion, posted 04-13-2004 9:54 AM DNAunion has not yet responded

  
RAZD
Member
Posts: 19509
From: the other end of the sidewalk
Joined: 03-14-2004
Member Rating: 2.3


Message 18 of 128 (99694)
04-13-2004 1:38 PM
Reply to: Message 15 by NosyNed
04-13-2004 11:55 AM


Re: agreeing to a point
There is another issue here as well, whether we are talking about getting from A to B to C and eventually to Z, or about getting from A to Z in one move (or A to Y and then to Z), the {energy \ information processing} requirements are different.

(canadian pennies are worth a penny in michigan ... perspectives ....)


we are limited in our ability to understand
by our ability to understand

RebelAAmerican.Zen[Deist
{{{Buddha walks off laughing with joy}}}


This message is a reply to:
 Message 15 by NosyNed, posted 04-13-2004 11:55 AM NosyNed has not yet responded

  
DNAunion
Inactive Member


Message 19 of 128 (99702)
04-13-2004 2:22 PM
Reply to: Message 15 by NosyNed
04-13-2004 11:55 AM


Re: agreeing
quote:
NosyNed: Now DNA, the discussion was thermodynamics and you did confuse the topic by bringing in something else.

But when I made my first post in this thread the title of the thread was "Thermodynamics & Abiogenesis".


This message is a reply to:
 Message 15 by NosyNed, posted 04-13-2004 11:55 AM NosyNed has responded

Replies to this message:
 Message 20 by NosyNed, posted 04-13-2004 2:27 PM DNAunion has responded

  
NosyNed
Member
Posts: 8807
From: Canada
Joined: 04-04-2003


Message 20 of 128 (99704)
04-13-2004 2:27 PM
Reply to: Message 19 by DNAunion
04-13-2004 2:22 PM


something else
But when I made my first post in this thread the title of the thread was "Thermodynamics & Abiogenesis".

But the issue of a mechanism for using free energy to locally decrease entropy isn't directly a thermodynamic question. I'm sure we all expect that the mechanism for OOL will have to be thermodynamically "uphill".

So the second law itself doesn't pose a problem. If you agree with that then bring the mechanism issue up in a separate thread not here.


This message is a reply to:
 Message 19 by DNAunion, posted 04-13-2004 2:22 PM DNAunion has responded

Replies to this message:
 Message 27 by DNAunion, posted 04-13-2004 8:22 PM NosyNed has responded

  
DNAunion
Inactive Member


Message 21 of 128 (99706)
04-13-2004 2:48 PM
Reply to: Message 13 by JonF
04-13-2004 8:48 AM


quote:
JohnF: The second law deals with entropy, and entropy is a property; that's a technical term that means its value depends only on the current state of the system and not in any way how the system got to that state.

quote:
DNAunion: Yeah, so what? Youíre confused. You see, I am not talking about only thermodynamics: I am talking about thermodynamics as it applies to the origin of life Ė more than one field of science is involved here.

quote:
JohnF: It doesn't matter how many fields of science you are talking about ...

Sure it does. That's how additional concepts get folded into the discussion.

quote:
JohnF: Entropy is a property and its value depends only on the current state of the system and not in any way how the system got to that state.

Yeah, so what? Iím not talking about just entropy: Iím also talking about the origin of life (see, thatís the part where multiple fields of science brings in additional concepts).

quote:
JohnF: Until you realize and accept that...

See, youíre all confused again John. I already made it clear that I realize and accept that. Of course I understand that what you are saying is correct, but you arenít addressing what I am addressing, so... ďYeah, so what?Ē.

quote:
DNAunion: Explaining how life could arise from nonlife requires explaining the mechanism by which a decrease in entropy - associated with the formation of biological polymers and systems of such polymers - could have plausibly occurred in a prebiotic context.

quote:
JohnF: From the point of view of thermodynamics, absolutely not.

So what? I am not talking about only thermodynamics. Iíve already explained that to you.

quote:
JohnF: If you wish to claim (as you have) that there is a thermodynamic problem with abiogenesis, ...

No, youíve misunderstood me. Let me try to explain using the analogy again.

The second law of thermodynamics poses a problem for abiogenesis in a manner similar to how gravity poses a problem for pyramid builders. Both processes are "uphill" and so are nonspontaneous (i.e., are endergonic). There's the problem imposed by the law. Now, the overcoming of the problem involves plausible mechanism(s) and steps, even though such concepts are not part of the law itself.

It's kind of like me saying that gravity poses a problem for pyramid builders and asking for the steps they used to get the top blocks up there, such as using inclined planes and logs as rollers, and you replying that inclined planes are not part of Newton's law of universal gravitation. Yeah, so what? I'm not talking about just gravity.

quote:
JohnF: ... the only way you can support that statement is with calculations that demonstrate an overall decrease in entropy.

I already pointed out that going from free monomers to polymers involves a decrease in entropy: the fact is there whether I provide any calculations or not. Do you need me to support that statement with quotes? I can.

quote:
DNAunion: Simply saying sufficient energy was available because the Earth is an open system is insufficient.

quote:
JohnF: Agreed, but irrelevant to your claim of a thermodynamic problem.

John, youíve clearly misunderstood me. And it is pointless for me to point out, error by error, every error you made based on that misunderstanding. So...

Tell you what, why donít you tell us exactly what you (wrongly) think I said, then Iíll point out where your problem lies. That way, it will take just one post to prevent you from making dozens of additional errors.

[This message has been edited by DNAunion, 04-13-2004]


This message is a reply to:
 Message 13 by JonF, posted 04-13-2004 8:48 AM JonF has responded

Replies to this message:
 Message 22 by Loudmouth, posted 04-13-2004 2:59 PM DNAunion has responded
 Message 23 by Percy, posted 04-13-2004 3:27 PM DNAunion has responded
 Message 24 by JonF, posted 04-13-2004 3:35 PM DNAunion has responded

  
Loudmouth
Inactive Member


Message 22 of 128 (99709)
04-13-2004 2:59 PM
Reply to: Message 21 by DNAunion
04-13-2004 2:48 PM


quote:
No, youíve misunderstood me. Let me try to explain using the analogy again. The second law of thermodynamics poses a problem for abiogenesis in a manner similar to how gravity poses a problem for pyramid builders. Both processes are nonspontaneous (i.e., are endergonic). Therefore, both require some mechanism in order to occur.

There are naturally occuring pyramids, well sort of. At the bottom of mountains there are piles of debris that stack themselves just like a pyramid. There is your mechanism. Reactants at a higher energy go DOWNHILL to form polymers. The second law of thermo is the mechanism, since reactants with higher energy will go to a lower energy state in the form of the polymer. The problem with your pyramid analogy is that you are starting from a lower energy state and moving towards a higher energy state. For example, DNA nucleotides without their phosphate groups will not spontaneously bind. However, if the high energy phosphates are included, then the nucleotides will spontaneously polymerize. I don't know if you are familiar with plasmid ligation, but to keep a cut plasmid from going back to its circular configuration you use calf intestine phosphatase to remove the phosphates from the nicked ends. If you don't remove the phosphates the plasmid will self ligate, or reform the complete circular formation.

I guess my point is this. There is no reason polymerization has to be an uphill event with respect to entropy, given that the polymerization units are at a higher energy state. Therefore, your pyramide analogy isn't accurate.

Added in edit: Instead of pyramids, maybe you should explain why mountain formation is non-spontaneous because it goes against gravity.

[This message has been edited by Loudmouth, 04-13-2004]


This message is a reply to:
 Message 21 by DNAunion, posted 04-13-2004 2:48 PM DNAunion has responded

Replies to this message:
 Message 29 by DNAunion, posted 04-13-2004 8:51 PM Loudmouth has not yet responded
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Percy
Member
Posts: 17325
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.1


Message 23 of 128 (99714)
04-13-2004 3:27 PM
Reply to: Message 21 by DNAunion
04-13-2004 2:48 PM


Let Confusion Reign
Hi, DNAunion!

This discussion has a similar feel to it. Nobody can figure out what point is being made, clarifications only introduce more confusion, an argument breaks out anyway, and in the center of the melee is...DNAunion.

2LOT, the other thermodynamic laws, the other laws of physics, govern all that happens in the natural universe. Abiogenesis happened in the natural universe, therefore it followed the laws of physics. Beyond that, we don't know much. There will be many scenarios we may be able to rule out because they violate one of more laws of physics, 2LOT perhaps among them, and in that sense 2LOT may be helpful to in constraining and helping to decipher the story.

It provides a nice sense of balance to know that the evolutionist side has its own Stephen ben Yeshua's and WillowTree's. So what Creationist position will you faux imitate next?

--Percy


This message is a reply to:
 Message 21 by DNAunion, posted 04-13-2004 2:48 PM DNAunion has responded

Replies to this message:
 Message 31 by DNAunion, posted 04-13-2004 9:10 PM Percy has responded

    
JonF
Member
Posts: 4140
Joined: 06-23-2003
Member Rating: 1.7


Message 24 of 128 (99715)
04-13-2004 3:35 PM
Reply to: Message 21 by DNAunion
04-13-2004 2:48 PM


Tell you what, why donít you tell us exactly what you (wrongly) think I said

I thought you said:

"The second law of thermodynamics poses no problem at all for evolution: abiogenesis is a different story."

and "... the second law poses a problem for OOL"

and "The second law of thermodynamics poses a problem for abiogenesis in a manner similar to how gravity poses a problem for pyramid builders."

The last statement is likely to be correct, but all are unsupported assertions.

It appears to me that you are claiming that we know that abiogenesis is impossible because it violates the second law. That claim is absolutely untrue; it is possible that there is no scenario of abiogenesis that violates the second law (actually, I think that this has been ruled out already, but I'll admit the possibility because I'm not sure), but we don't know that abiogenesis violates the second law.

Now, if you said that the 2LoT must be consisdered in any sufficiently advanced theory of abiogenesis I would agree. If you want to argue that thermodynamics might pose a problem for abiogenesis, I could go along with that. But you said that "the second law poses a problem for OOL", which means either that you are just blathering or you think you have a thermodynamic calculation which demonstrates that a first self-replicator arising from primordial conditions must violate the second law of thermodynamics.

I already pointed out that going from free monomers to polymers involves a decrease in entropy: the fact is there whether I provide any calculations or not. Do you need me to support that statement with quotes? I can.

I believe you could. The fact that entropy decreases in a portion of a particular system does not mean that the second law is violated. Hell, I'll even accept without proof that those studies going from monomers to polymers is relevant to all possible modes of abiogenesis. So what?

What you need to provide to support your claim is a calculation that shows that the second law of thermodyanamics prohibits a self-replicator from arising.


This message is a reply to:
 Message 21 by DNAunion, posted 04-13-2004 2:48 PM DNAunion has responded

Replies to this message:
 Message 32 by DNAunion, posted 04-13-2004 9:27 PM JonF has not yet responded
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 Message 34 by DNAunion, posted 04-13-2004 9:38 PM JonF has responded

  
wj
Inactive Member


Message 25 of 128 (99754)
04-13-2004 8:03 PM


DNA, why don't you try and clarify your position rather than continually claiming that you are being misreprersented? Deja vu?

Do you assert that abiogenesis is impossible because of the 2LOT? Or do you assert that any proposed mechanism for abiogenesis must be consistent with the 2LOT?

"poses a problem" is rather vague.


Replies to this message:
 Message 26 by DNAunion, posted 04-13-2004 8:09 PM wj has responded

  
DNAunion
Inactive Member


Message 26 of 128 (99755)
04-13-2004 8:09 PM
Reply to: Message 25 by wj
04-13-2004 8:03 PM


quote:
DNA, why don't you try and clarify your position rather than continually claiming that you are being misreprersented? Deja vu?

Why don't you read what I say and try to understand it? Deja vu?

For example, you next ask:

quote:
Do you assert that abiogenesis is impossible because of the 2LOT?

That question was already asked to me and I already gave a crystal clear answer. Here let me show you:

quote:
BerBerry: Are you saying that abiogenesis could not have happened because it is made impossible by the 2nd law?

quote:
DNAunion: No, that is not my point.

How silly of you to try to blame me for your not being able to understand my position when you don't even know what I've said!

[This message has been edited by DNAunion, 04-13-2004]


This message is a reply to:
 Message 25 by wj, posted 04-13-2004 8:03 PM wj has responded

Replies to this message:
 Message 41 by wj, posted 04-13-2004 11:32 PM DNAunion has not yet responded

  
DNAunion
Inactive Member


Message 27 of 128 (99760)
04-13-2004 8:22 PM
Reply to: Message 20 by NosyNed
04-13-2004 2:27 PM


Re: something else
quote:
DNAunion: But when I made my first post in this thread the title of the thread was "Thermodynamics & Abiogenesis".

quote:
NosyNed: But the issue of a mechanism for using free energy to locally decrease entropy isn't directly a thermodynamic question.

So what? It is directly related to abiogenesis, and, the thread was not called just Thermodynamics when I made the first reply, it was called Thermodynamics & ABIOGENESIS. Even now it is called Thermodynamics, ABIOGENESIS, and Evolution.

I still don't understand how you people can honestly raise your objections. It's like me talking about finding the volume of a box by using math - multiplying the measures of its three dimensions - then you guys saying boxes aren't part of math! Yeah, so what?

quote:
NosyNed: I'm sure we all expect that the mechanism for OOL will have to be thermodynamically "uphill". So the second law itself doesn't pose a problem.

Uhm, if something is a thermodynamically uphill process IT WILL NOT OCCUR. Going by what you said, the second law poses such a problem for abiogenesis that it can't occur.

An uphill process can occur if coupled to a downhill process. But how is that accomplished prebiotically? How is the problem posed by the second law overcome? What steps and mechanisms are involved in the solution?

quote:
NosyNed: If you agree with that then bring the mechanism issue up in a separate thread not here.

Why? Is this thread about nothing but thermodynamics? Then take the words abiogeneis and evolution out of the title. As long as they are there, this thread is about more than just thermodynamics.

[This message has been edited by DNAunion, 04-13-2004]


This message is a reply to:
 Message 20 by NosyNed, posted 04-13-2004 2:27 PM NosyNed has responded

Replies to this message:
 Message 28 by NosyNed, posted 04-13-2004 8:34 PM DNAunion has not yet responded

  
NosyNed
Member
Posts: 8807
From: Canada
Joined: 04-04-2003


Message 28 of 128 (99763)
04-13-2004 8:34 PM
Reply to: Message 27 by DNAunion
04-13-2004 8:22 PM


Re: something else
Fine but then be careful to note when you are and are not talking about the 2nd law.

Yes, you are correct with your comment about my uphill comment. Some parts of the OOL must have been downhill to get to the right place. Then we need some mechanism to handle any uphill parts.


This message is a reply to:
 Message 27 by DNAunion, posted 04-13-2004 8:22 PM DNAunion has not yet responded

  
DNAunion
Inactive Member


Message 29 of 128 (99766)
04-13-2004 8:51 PM
Reply to: Message 22 by Loudmouth
04-13-2004 2:59 PM


quote:
DNAunion: No, youíve misunderstood me. Let me try to explain using the analogy again. The second law of thermodynamics poses a problem for abiogenesis in a manner similar to how gravity poses a problem for pyramid builders. Both processes are nonspontaneous (i.e., are endergonic). Therefore, both require some mechanism in order to occur.

quote:
Loudmouth: There are naturally occuring pyramids, well sort of. At the bottom of mountains there are piles of debris that stack themselves just like a pyramid. There is your mechanism.

So the (Egyptian) pyramids were built by debris piling up at the bottom of a mountain? Gee, I've never heard that theory before.

quote:
Loudmouth: Reactants at a higher energy go DOWNHILL to form polymers.

Which would require them to first be RAISED ABOVE the energy level needed for polymer formation.

quote:
Loudmouth: The problem with your pyramid analogy is that you are starting from a lower energy state and moving towards a higher energy state.

No, that's what's right about my analogy.

quote:
Loudmouth: For example, DNA nucleotides without their phosphate groups will not spontaneously bind.

BINGO!

quote:
Loudmouth: However, if the high energy phosphates are included, then the nucleotides will spontaneously polymerize.

And attaching the high energy triphosphates is an uphill process and requires an input of energy (and in cells, uses enzymes too). You're changing which process is uphill, not making the "uphillness" disappear.

quote:
Loudmouth: I guess my point is this. There is no reason polymerization has to be an uphill event with respect to entropy,...

Wrong. Polymerization of free monomers always involves a reduction in their entropy. Remember, entropy and free energy are not the same.

quote:
Added in edit: Instead of pyramids, maybe you should explain why mountain formation is non-spontaneous because it goes against gravity.

Gravity DOES pose a problem for mountain building: do you disagree???? Enormous amounts of mass must be lifted high and a multi-ton mass of rocks will not just spontaneously rise to form a mountain: some mechanism sufficient to overcome the problem posed by gravity must be operating. In fact, even once mountains are built gravity still poses problems for them: it's called mass wasting.


This message is a reply to:
 Message 22 by Loudmouth, posted 04-13-2004 2:59 PM Loudmouth has not yet responded

  
DNAunion
Inactive Member


Message 30 of 128 (99767)
04-13-2004 8:58 PM
Reply to: Message 22 by Loudmouth
04-13-2004 2:59 PM


It seems one of the main points of contention is whether or not the formation of polymers from free monomers is an uphill process, particularly in a prebiotic context. If it's not, then my pyramid analogy does fail as does the rest of what I am saying. Lucky for me it is uphill :-)

First, it does involve an increase in order and so a decrease in entropy: this alone points towards the process being uphill (but does not necessitate that it is, since changes in entropy and changes in free energy can move in opposite directions). A single quote should suffice here.

quote:
"This is a general reaction describing the dehydration-condensation of, for instance, proteins from amino acids, polysaccharides from sugars, and nucleic acids from mononucleotides (whose constituents are pentoses, bases, and phosphates). These biosynthetic reactions result in a decrease in entropy. For example, when amino acids are linked to produce a peptide, they lose much of their freedom of movement in the solution. The formation of a peptide, a rather rigid and ordered molecule, imposes restrictions on the free movements of its building blocks. These restrictions are associated with an increase in the order of the system or a decrease in entropy." (Noam Lahav, Biogenesis: Theories of Life's Origins, Oxford University Press, 1999, p90)

Second, formation of polymers from monomers is uphill overall (i.e., endergonic) because it requires an input of energy: this is why OOL researchers preactivate their monomers. Loudmouth even acknowledges (at least implicitly) that an input of energy is needed for formation of polymers, but tries to get around it by starting with preactivated monomers, such as dNTPs - the nucleoside triphosphates used by cells to produce DNA. But he's trying to avoid the problem by pushing it off elsewhere - that doesn't make it go away. Besides, we know what mechanisms cells use today to preactivate the monomers used in polymerization, that's not the question: how would monomers have been preactivated in a prebiotic context? First of all, note that the fact the they have to preactivated alone wins me the point!

Let's start with the activation process used by cells, and the one Loudmouth mentioned: triphosphates. It is unlikely that triphosphates were the prebiotic activating agents for nucleosides.

quote:
"Even with plenty of time, ribose would have trouble hooking up with phosphate. Organisms today have enzymes to grab phosphate out of their environment and link it with sugars, but those enzymes would not have been available in the primordial soup - and phosphate on its own, it turns out, is not very reactive. Tony Keefe, a postdoc with [Stanley] Miller, tried dozens of experiments and couldn't make an RNA backbone with phosphate. Even if such a backbone could have formed on the early Earth, Miller argues, it wouldn't have lasted long enough to begin acting like life: ribose and phosphate are linked by the same weak carbon-oxygen bond that makes ribose itself so fragile." (Carl Zimmer, Life Takes Backbone, Discover, Dec 1995, v16 n12 p38(2))

quote:
"The many laboratory experiments carried out by Orgel's school have shown that template-directed condensation of mononucleotides on RNA strands in the absence of enzymes did not occur. Apparently, the universal natural activating agent of nucleotides, the triphosphate ion, is not active enough for the condensation reaction of the mononucleotides to take place on the RNA strand in the absence of a catalyst." (Biogenesis: Theories of Life's Origin, Noam Lahav, Oxford University Press, 1999, p205)

quote:
"Not only RNA's (or an alternative's) potential for nonenzymatic replication, but also its chances for formation in an abiotic natural environment remain open to question. Whereas there is a consensus on the notion that the building blocks of RNA (sugars, purines, and pyrimidines) potentially are of prebiotic origin and whereas the broad chemical contours of an assembly of the RNA structure from such building blocks seem clear, convincing experimental evidence that such a process can in fact occur under potentially natural conditions is still lacking; this is particularly true with regard to such crucial steps as nucleotide formation and phosphate activation." (Chemical Etiology of Nucleic Acid Structure, Albert Eschenmoser, Science, Volume 284, Number 5423 Issue of 25 Jun 1999, pp. 2118 - 2124)

Since what cells use today - triphosphates - didn't hold much promise for prebiotic chemistry, researchers turned to other activating agents, such as imidazolides. However, the alternative activating agents' prebiotic plausibility is either rejected or doubted, or, they turn out also to be only marginally effective.

quote:
"All this seems almost too good to be true. And it is. First, .... Second, the subunits used in these experiments must be "activated" beforehand in order for them to polymerize. Orgel and others have used nasty-sounding compounds such as methylimidazolide and carbonyldiimidizole as the activation reagents. These reagents would certainly not have been present in the primordial soup." (Christopher Wills and Jeffrey Bada, The Spark of Life: Darwin and the Primordial Soup, Perseus Publishing, 2000, p102-103)

quote:
"Most attempts to study nonenzymatic polymerization of nucleotides in the context of prebiotic chemistry have used nucleoside 5'-phosphorimidazolides. Although phosphorimidazolides can be formed from imidazoles and nucleoside 5'-polyphosphates (Lohrmann 1977), they are only marginally plausible as prebiotic molecules. They were chosen because they are prepared easily and react at a convenient rate in aqueous solution." (Prospects for Understanding the Origin of the RNA World, Gerald F. Joyce & Leslie E. Orgel, p50-51, chapter 2 of The RNA World: Second Edition, Cold Springs Harbor Laboratory Press, 1999)

quote:
" A template-directed reaction did take place, however, in certain systems where the mononucleotide building blocks were preactivated by reactive chemical groups that are more effective than the triphosphate. The result was a complementary strand on the RNA template under study. The most powerful activating agent in these reactions were imidazolides such as phosphorimidazolide of adenine (ImpA) and guanosine 5'-phospho-2-methyl-imidazolide (2-MeImPG). Imidazole is considered by some researchers to be a reasonable prebiotic compound, since it can be readily prepared under prebiotic conditions. However, because of its high chemical reactivity, its accumulation in prebiotic environments such as the prebiotic sea is still not clear." (Biogenesis: Theories of Life's Origin, Noam Lahav, Oxford University Press, 1999, p205)

quote:
"Imidazolides are generally much easier to prepare and are more stable than amino-acid adenylates. Nevertheless, their availability on the primitive Earth in sufficient purity is open to question. Glycoaldehyde phosphate is a starting material for which a prebiotic synthesis has yet to be devised, and the synthesis would have to be efficient indeed to produce pure solutions of this reactive compound." (Alan W. Schwartz, Did Minerals Perform Prebiotic Combinatorial Chemistry?, Chemistry & Biology, vol. 3, No. 7, July 1996, p515-518)

quote:
"In a different approach to the activation of nucleotides, the isolation of an activated intermediate is avoided by employing a condensing agent such as a carbodiimide (Khorana 1961). This is a popular method in organic synthesis, but its application to prebiotic chemistry is problematic. Potentially prebiotic molecules such as cyanamide and cyanoacetylene activate nucleotides in aqueous solution, but the subsequent condensation reactions are inefficient (Lohrmann and Orgel 1973)." (Prospects for Understanding the Origin of the RNA World, Gerald F. Joyce & Leslie E. Orgel, p50-51, chapter 2 of The RNA World: Second Edition, Cold Springs Harbor Laboratory Press, 1999)

Note all of these methods of preactivating monomers for "prebiotic" experiments. Why is this needed? Because polymer formation from free monomers is energetically uphill. Sure, once you've preactivated the molecules, THEN the process is downhill. But starting with preactivated monomers still leaves open the question of what mechanism preactivated them.

Let's bring this back to the pyramid analogy. Loudmouth's counter to me is like saying the Egyptians built the pyramids by first building some sort of scaffolding that was even higher than the pyramids would end up being, then drug the huge stone blocks up to the top of the scaffolding, then slid them down so they stacked onto each other to form the pyramid. Sure, if they did that the process of actually placing the top blocks onto the the pyramid would be downhill. But how would that get around the problem that gravity poses for pyramid building? It doesn't. The blocks still had to be carried uphill, here, to the top of the even higher scaffolding.

*********************************
One final point that JohnF might really enjoy :-)

Let us assume that we have taken our uphill process and somehow made it a downhill process - will it now occur at a sufficient rate? Not necessarily. Why not? It's actually occurring "depends ... also on the availability of a mechanism or pathway to get from the initial state to the final state."

quote:
"Thus, [delta] G can really tell us only whether a reaction or process is thermodynamically possible - whether it has the potential for occurring. Whether an exergonic reaction will in fact proceed depends not only on its favorable (negative) [delta] G but also on the availability of a mechanism or pathway to get from the initial state to the final state. ... Thermodynamic spontaneity is therefore a necessary but insufficient criterion for determining whether a reaction will actually occur." (The World of the Cell: Third Edition, Wayne M. Becker, Jane B. Reece, Martin F. Poenie, Benjamin/Cummings Publishing Co., 1996, p128)

This message is a reply to:
 Message 22 by Loudmouth, posted 04-13-2004 2:59 PM Loudmouth has not yet responded

Replies to this message:
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