Thermodynamics, Abiogenesis and Evolution

The second law of thermodynamics poses no problem at all for evolution: abiogenesis is a different story. Why?Because for existing life - and therefore evolution - we can give a full account of how energy enters organisms and how it is then used to maintain the high degree of order of the organism, and to even increase the organism's complexity (same goes for higher levels, such as populations, communities, etc.).But we can't yet give such an explanation for the origin of life (we don't even know what the very first life could have actually been). Until some prebiotically plausible mechanism for capturing and channeling the available prebiotic energy into performing useful "biological" work is found, vague appeals to "open systems" just aren't sufficient ("open system thermodynamics" are necessary, but not sufficient).[This message has been edited by DNAunion, 04-12-2004]

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DNAunion: Until some prebiotically plausible mechanism for capturing and channeling the available prebiotic energy into performing useful "biological" work is found, vague appeals to "open systems" just aren't sufficient ("open system thermodynamics" are necessary, but not sufficient).

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JohnF: Er, you appear to have a serious misunderstanding of thermodynamics.

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No, you appear to have a serious misunderstanding of bioenergetics.

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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.

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Yeah, so what? You’re confused. You see, I am not talking about only thermodynamics: I am talking about thermodynamics as it applies to the origin of life — more than one field of science is involved here.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. Simply saying sufficient energy was available because the Earth is an open system is insufficient.

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JohnF: Therefore the idea of needing to know a mechanism (for the transition between states) in order to evaluate the thermodynamic possibilities is a red herring.

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No red herring...you're just confused.

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JohnF: What counts thermodynamically is the difference in entropy between the initial and final states, not how it got from one state to the other.

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And what counts in explaining the origin of life is explaining how things got from one state to another! This particular discussion does involve the origin of life...remember: it’s not about some simple thermodynamic process like a cup of hot tea cooling off.

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JohnF: However, what I am sure of is that you can't claim that the second law of thermodynamics poses any problem for any hypothesized event until you have calculated the change in entropy and demonstrated a spontaneous decrease.

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And I’d disagree. For example, we know that the change from free monomers to polymers involves a decrease in entropy (increase in order) and is endergonic (which is why OOL researchers preactivate their monomers). And we know this without having to know exact values. So polymer formation goes in the wrong direction and is thus a nonspontaneous process. Therefore, some sort of process or mechanism must be present in order for such an uphill process to occur (for example, cells couple endergonic reactions with exergonic reactions, usually using ATP as an energy intermediate). What was the prebiotic mechanism? Simply saying that sufficient energy was present is not a sufficient explanation. It's like trying to explain translation in extant cells by simply saying that cells have ATP at their disposal: insufficient explanation. Worse yet, even having sufficient ATP in a cell won't produce proteins if ribosomes - the cellular "machine" that makes proteins - are absent. So relying on just vauge appeals to "open system thermodynamics" for translation is insufficient in more than one way - same goes for OOL.[This message has been edited by DNAunion, 04-12-2004]

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

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

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No, that is not my point.Let me try an analogy. We see an antenna on the top of the Empire State building. Getting it up there is an uphill process and won't occur spontaneously. There's no problem explaining it though because we know how cranes, elevators, motors, etc. were used to get it up there (this is analogous to how cells make their uphill processes work today). But what about the pyramids? There were no cranes, elevators, motors, etc. so we can't use them to explain how the top blocks got up there - gravity poses a problem for the origin of pyramids (analogous to how the second law poses a problem for OOL). It is insufficient to say simply that there was sufficient free energy - volcanoes, wind storms, sunlight, etc.: that fails as an explanation for how the top blocks got up there. What is needed is some plausible, "pretechnology" mechanism that would allow those blocks to get up there and that is what several teams have attempted to explain.**********************************
PS: Please note that my use of a pyramid analogy does not mean I am saying that intelligence was required for OOL.

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

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

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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.

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

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

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

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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.

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

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JohnF: Until you realize and accept that...

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See, you’re 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 aren’t addressing what I am addressing, so... Yeah, so what?.

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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.

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

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

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

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No, you’ve 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.

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

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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.

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

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

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John, you’ve 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 don’t you tell us exactly what you (wrongly) think I said, then I’ll 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]

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

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Why don't you read what I say and try to understand it? Deja vu?For example, you next ask:

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

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

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

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DNAunion: No, that is not my point.

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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]

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

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

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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?

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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.

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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?

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

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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]

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DNAunion: No, you’ve 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.

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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.

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

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

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

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

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

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

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BINGO!

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

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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.

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

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

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

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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.

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.

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"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)

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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.

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"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))

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"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)

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"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)

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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.

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"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)

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"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)

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" 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)

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"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)

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"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)

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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."

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"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)

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Percy: 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.

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Hold on Percy. Before you start targetting me, let's all note exactly who started the posturing in this thread: JohnF.

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JohnF: Er, you appear to have a serious misunderstanding of thermodynamics.

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... Therefore the idea of needing to know a mechanism (for the transition between states) in order to evaluate the thermodynamic possibilities is a red herring.

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Gee, I guess I'm pretty stupid and underhanded, huh? So, are we all straight on who lit the first match in this thread?Second point Percy. Not everyone is confused. For example:

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NosyNed: DNA has a clear point. The free energy is available but there must be some mechanism for allowing it to perform the work. That is all he is saying and it is the basic issue of abilogenesis.

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I don't know why others - such as you - are incapable of understanding me. If I must speak in words no longer than 4-letters just let me know and I will try to oblige.Third point Percy, regarding...

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Percy: 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?

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Since NosyNed agreed with me, are you insinuating that he too is some sort of Creationist? Must be, if he agrees with my position, and it is (supposedly) some form of Creationist argument.All in all, a fine post Percy! You pointed the finger at the wrong person, tried to claim that I was the problem of the confusion even though NosyNed was easily able to see what I was saying, and implicitly labeled NosyNed as some kind of Creationist. Keep up the good work![This message has been edited by DNAunion, 04-13-2004]

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DNAunion: Tell you what, why don’t you tell us exactly what you (wrongly) think I said ...

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JohnF: I thought you said:

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

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

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

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

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Uhm, if the last statement is correct, how could the others not be correct? If (3) is correct, then (2) must be correct. If (3) is correct, then (1) must be correct. So in other words, what you really meant to say was:"DNAunion, all of your above statements are likely correct..."[This message has been edited by DNAunion, 04-13-2004]

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JohnF: It appears to me that you are claiming that we know that abiogenesis is impossible because it violates the second law.

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Another person who can’t read.Look, I already stated that such is NOT my position. Here, let me show you also:

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

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DNAunion: No, that is not my point.

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So gee whiz Percy, who really is the problem for the misunderstandings here? Not me. NosyNed understood me, and at least two of those who just can’t seem to understand what I am saying - JohnF and wj — can’t even understand English: which isn’t my fault.

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JohnF: 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.

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Really now? You know, you would be right if I had said "the second law of thermodynamics prohibits abiogenesis"...but guess what...I didn't say that. I said it posed a problem for abiogenesis.Do you really equate the words "problem" and "impossible"? You shouldn't - problems can be overcome: impossibilities can't. Two very different things.[This message has been edited by DNAunion, 04-13-2004]

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Percy: Yes, yes, we know, you're once again the center of turmoil and completely blameless...

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Finally, you said something that's right! :-)However, note that I have not said that I was blameless, just that I wasn't the person who STARTED the posturing. And guess what? That's a provable fact.

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Percy: [you're] the only one in the discussion with the intellect to comprehend your spectacular insights.

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No, NosyNed understood my point early on. The problem lies with those who don't try to understand - those, like you, who wrongly try to interpret my statements as if I were a Creationist. As soon as you and the others stop making that silly mistake the confusion will vanish.

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Percy: At best your difficult to decipher claims...

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I'm sorry, you mean my crystal clear claims that some people completely mangled, right?

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Percy: ... boil down to abiogenesis having to obey 2LOT, which I don't think comes as a particular revelation to anyone.

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Hmmm, where did I claim to be making a revelation of any kind? I guess you're more confused than I thought.

Ah, but there was a point. There is a problem that has yet to be fully solved. Furthermore, anyone who tries to pretend that there is no problem by relying only on vague appeals to "open system thermodynamics" is solving nothing: sufficient free energy is a necessary, but insufficient, precondition for abiogenesis.I guess all of that got lost in the distortions and posturings the others employed.[This message has been edited by DNAunion, 04-13-2004]