Origins and Science

Arik Soong said:

I doubt you (or most atheists or agnostics) will convert to Christianity when (I do not know if the event described by Shapiro will occur) that day arrives too.

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In other words, and this has been my only position so far, your only position is an argument from ignorance combined with a false dichotomy.

Hmm...argument from ignorance. Perphaps you are correct about that but my position is skepticism of the vogue origin of life scenarios such as the RNA World (an example of a major flaw in this scenario is that there is currently little reason to actually believe D-beta ribonucleotides will form in the need quantities on the prebiotic Earth and a plethora of reasons to believe the contrary.)

About the "false dichotomy." Well, I only mentioned Christianity as it is a major world religion and I guess including Islam, Hare Krishna, or Judaism will suffice too.

BTW, anyone want to defend the notion of peptide bond formation being a downhill process?

Arik Soong said:

Hmm...argument from ignorance. Perphaps you are correct about that but my position is skepticism of the vogue origin of life scenarios such as the RNA World (an example of a major flaw in this scenario is that there is currently little reason to actually believe D-beta ribonucleotides will form in the need quantities on the prebiotic Earth and a plethora of reasons to believe the contrary.)

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Skepticism is ok. I'll certainly agree with you that current abiogenesis models are underdeveloped and that we know too little about how life would have formed. So when pressed, I'll agree that we don't know whether abiogenesis happened. That is skepticism.

You want to take the don't know and claim that because we don't know, we should accept God as an answer. I see no reason to brand that as skepticism.

About the "false dichotomy." Well, I only mentioned Christianity as it is a major world religion and I guess including Islam, Hare Krishna, or Judaism will suffice too.

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We don't know, so the answer must be God. Still a false dichotomy. You want to say that one model is correct because the other is incorrect. That is the basic logical structure of your argument. But it is a invalid logic.

BTW, anyone want to defend the notion of peptide bond formation being a downhill process?

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At present, I couldn't care less. You'll need to talk to a biochemist, which I'm not. Whether it is uphill or downhill doesn't tell us much however, since energy supply is everywhere (either in hydrothermal vents or through the sun). So energy is around to get the process going if it wouldn't occur spontaneously.

I explicitly mentioned that I would believe in a naturalistic origin of life even IF all the evidence is against it so how could one say that I am advocating the theistic option when all naturalistic explanations fail?

I also acknowledged early in this thread that heating could provide the energy to overcome the thermodynamic barrier for peptide bond formation in addition to condensing agents. One look at Wachtershauser 1998 for hydrothermal polymerization (all you have to do is register at www.sciencemag.org for free to read it.) Also I think light (especially UV light) could also provide the energy to cleave the peptide bonds too. Remember, photosynthetic organisms (I do not know much about the photosynthesis in prokaryotes though) have an intricate system involving a myriad of pigments and membrane proteins for converting solar energy to ATP and NADPH.

Arik Soong said:

I explicitly mentioned that I would believe in a naturalistic origin of life even IF all the evidence is against it so how could one say that I am advocating the theistic option when all naturalistic explanations fail?

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Fair enough. Reading back that seems to be the case. But then I'm really off on what you are arguing.

I also acknowledged early in this thread that heating could provide the energy to overcome the thermodynamic barrier for peptide bond formation in addition to condensing agents. One look at Wachtershauser 1998 for hydrothermal polymerization (all you have to do is register at www.sciencemag.org for free to read it.) Also I think light (especially UV light) could also provide the energy to cleave the peptide bonds too. Remember, photosynthetic organisms (I do not know much about the photosynthesis in prokaryotes though) have an intricate system involving a myriad of pigments and membrane proteins for converting solar energy to ATP and NADPH.

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Then I don't really see your problem with it. I guess I'm just unclear on what you're arguing specifically. You direct your post at USIncognito and me, two persons who have specifically stated to not know how life arose. US certainly hasn't even provided a preference for any model.

Some people have provided a preference for metabolism-first scenario's. You disagree with them, based on criticism by Shapiro. That's all fine and dandy, but as I've stated in a previous post (#23), all current models have problems. There just is no full-proof model of abiogenesis yet, period. And the criticism by Shapiro may or may not be valid, I don't know, but that doesn't mean the metabolism-first cannot be the best current (ie, the most promising) model.

You see, the problem with your posts is that you seem to be arguing that a certain scenario is definitely false. But we cannot say that yet, as far as I can tell. Our best answer seems to be 'we don't know, but we have several theories, of which metabolism first has the least problems'. That doesn't mean it doesn't have it's weak points.

And if you were arguing that it does have it's weak points, sure, nobody could disagree. But you seem to be arguing that it is definitely false, and that does not seem to be a valid conclusion yet.

Arik Soong said:

I explicitly mentioned that I would believe in a naturalistic origin of life even IF all the evidence is against it so how could one say that I am advocating the theistic option when all naturalistic explanations fail?

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Since I was singled out in in both your response and Tom's I'm gong to reply to this specifically.

My reply to you was a general comment about abiogeneis vs. directed biogenesis and should have been taken within that context. After all, that is what the distilled argument of ID is all about right? My issue was with the OP and whether philosophy and logic could appropriately address the issue of "origins" or not. My contention is that "logic" cannot without being buttressed by scientific evidence... that was all.

The only positions I advocate is that while biogenesis might be the result of some supernatural or paranormal intervention on Earth, that does not logically preclude a natural or "normal" abiogenetic event being the source of life on Earth. I was sticking to the constraints of the OP. If you want to get into genetics, start a new thread.

Sorry to be getting back to this late. I've been busy these last several days.

Arik Soong said:

Hmm...how could I forget about this thread. Of course, letting it die would simply be the best option but how could nice it would be to people like Tom and USIncognito to believe in the nonsense that peptide bond formation is a energetically downhill process. But personally I doubt they would care.

Lol, spontaneous peptide formation is a nice description of your position. You explicitly state this and I am assailing your assertion. Moreover, the diagram that you invoked seems to agree with my position since it acknowledges that there is a GAIN in free energy with the formation of the peptide bond. You called me a "poser" when I tried to bring this to your attention.

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Actually, my earlier diagram was not about free energy at all. (If you only read carefully before you stuck your foot in your mouth!) It used bond dissociation energies (BDE's). A gain in BDE is a gain in stability (which means the reaction is downhill), because a bond dissociation energy is the energy expended to break a bond. Get it?

Admittedly, however, bond dissociation energies are not the best way to compute reaction profiles, although they are easier to find on the internet (I'm doing this from home and have no access to my books at work). So, I dug some more and found appropriate heats of formation and entropies for you:

At the bottom right is the computed heat of reaction and the free-energy change for the formation of an amide bond from an acid and an amine. (Just in case you don't get it, the heat of formation is the heat released upon forming a compound from its elements; subtracting the summed heats of formation of reactants from that of products provides the heat of reaction. A negative heat of reaction is energy released. A negative Gibb's free energy is indicative of a favourable, spontaneous, exergonic, downhill reaction.) As you can see, it's downhill by a little over 5.3 kcal/mol at room temperature. Your biochemistry lecture notes have the right number (about 22 kJ/mol) but the wrong sign.

In case you don't believe me, you can go to a nice little site (www.srdata.nist.gov/cccbdb and click on "Section XIV") where there is a calculator of reaction enthalpies, and you can check that the reaction is indeed exergonic (the value, -0.5 kcal/mol, is different than what I have above because all of the heats of formation that this calculator uses are gas-phase and so do not include heats of vaporization).

Arik Soong said:

Since peptide bond formation is uphill, it also explains why aminoacyl tRNA synthetases expend ATP when attaching the carboxyl group of an amino acid to the 3' terminus of the appropriate tRNA. (Yes, I do know what I am talking about here!)

Since peptide bond formation is "endergonic" that is it absorbs energy to form, it does not occur spontaneously and the exergonic reverse reaction (hydrolysis) is favored in aqueous solution.

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Which, as I have shown, is wrong.

And nature uses ATP-dependent synthetases because the reaction is kinetically difficult, not because it's not favourable. In the lab, heat is what's needed to overcome the kinetic barrier. Otherwise, people use activating agents of all kinds (DCC, CDI, etc.) to convert the relatively unreactinve carboxyl group into a better one.

I asked you some time ago the following question:
Can you name any non-protein amide polymer? and does it decompose in water?
This is a question you've repeatedly passed over. Maybe you can't answer it, or maybe you don't want to. So I will.
Nylon is a non-protein amide polymer. And, no, it doesn't decompose in water. Nylon exemplifies the extraordinary stability of peptide bonds. Proteins in hair and finger nails and lobster shells all attest to the robustness of the peptide bond.

Even if I had been wrong about the downhill thermodynamics, I also asked you another pertinent question:
Can you imagine any scenario where a thermodynamically uphill polymerization can occur?
Again, you've dutifully ignored this so, again, I'll answer it.
A thermodynamically uphill polymerization can occur spontaneously if you remove one of the products. Imagine, if you will, a pool of amino acids drying up in the hot sun. Not only is the water getting warmed by the sun and thus providing energy to drive reactions, but the concentration of reactants is increasing as the pool shrinks in volume by evaporation. This increases the rates of reaction further. Then, when the pool is dry and there is no water remaining, any water formed by a condensation polymerization is removed by evaporation, and the reaction equilibrium is driven toward the products. So, even if a reaction is unfavourable, it is not difficult to imagine how reactions can take place nevertheless. When the rain then falls and the product redissolves, the equilibrium could of course shift back toward the starting materials but, in the case of peptides at least, as exemplified by nylon, chitin, keratin and numerous other examples, that is kinetically very, very slow.

Arik Soong said:

I'll admit I read some of the responses of this thread in a cursory manner [...]

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That has been the source of some of your trouble, yes. I take some care in formulating answers. I expect to be read as carefully.

Arik Soong said:

[...]but I am questioning the notion that peptide bond formation is spontaneous. If this is not true, an advantage in your origin of life scenario is rendered invalid.

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But it's true.

Arik Soong said:

If you could not comprehend a simple chemistry fact correctly (e.g. Peptide bond formation is uphill), then what right do you have for criticizing me for trivial spelling errors?

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Oh, but I do comprehend chemistry.*
And because I do gives me just as much right to point out spelling mistakes as if I didn't.

* I don't think you can say the same.

HairlessSimian said:

Sorry to be getting back to this late. I've been busy these last several days.



Actually, my earlier diagram was not about free energy at all. (If you only read carefully before you stuck your foot in your mouth!) It used bond dissociation energies (BDE's). A gain in BDE is a gain in stability (which means the reaction is downhill), because a bond dissociation energy is the energy expended to break a bond. Get it?

Admittedly, however, bond dissociation energies are not the best way to compute reaction profiles, although they are easier to find on the internet (I'm doing this from home and have no access to my books at work). So, I dug some more and found appropriate heats of formation and entropies for you:

At the bottom right is the computed heat of reaction and the free-energy change for the formation of an amide bond from an acid and an amine. (Just in case you don't get it, the heat of formation is the heat released upon forming a compound from its elements; subtracting the summed heats of formation of reactants from that of products provides the heat of reaction. A negative heat of reaction is energy released. A negative Gibb's free energy is indicative of a favourable, spontaneous, exergonic, downhill reaction.) As you can see, it's downhill by a little over 5.3 kcal/mol at room temperature. Your biochemistry lecture notes have the right number (about 22 kJ/mol) but the wrong sign.

In case you don't believe me, you can go to a nice little site (www.srdata.nist.gov/cccbdb and click on "Section XIV") where there is a calculator of reaction enthalpies, and you can check that the reaction is indeed exergonic (the value, -0.5 kcal/mol, is different than what I have above because all of the heats of formation that this calculator uses are gas-phase and so do not include heats of vaporization).



Which, as I have shown, is wrong.

And nature uses ATP-dependent synthetases because the reaction is kinetically difficult, not because it's not favourable. In the lab, heat is what's needed to overcome the kinetic barrier. Otherwise, people use activating agents of all kinds (DCC, CDI, etc.) to convert the relatively unreactinve carboxyl group into a better one.

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Excellent elucidation.

I asked you some time ago the following question:

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Can you name any non-protein amide polymer? and does it decompose in water?
This is a question you've repeatedly passed over. Maybe you can't answer it, or maybe you don't want to. So I will.
Nylon is a non-protein amide polymer. And, no, it doesn't decompose in water. Nylon exemplifies the extraordinary stability of peptide bonds. Proteins in hair and finger nails and lobster shells all attest to the robustness of the peptide bond.

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It does but it is really slow for reasons like you mentioned like resonance (http://www.chemguide.co.uk/organicprops/amides/hydrolysis.html). I am sure that in the presence of a catalyst like nylonase (an enzyme which evolved in some bacteria), one would achieve appreciable hydrolysis. Of course, the properties of the polymer also determine the rate of hydrolysis, for example, kevlar is more resistant to hydrolysis compared to nylon.I did not try to say peptide bond hydrolysis was instantaneous but rather inevitable.

Ev

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en if I had been wrong about the downhill thermodynamics, I also asked you another pertinent question:
Can you imagine any scenario where a thermodynamically uphill polymerization can occur?
Again, you've dutifully ignored this so, again, I'll answer it.
A thermodynamically uphill polymerization can occur spontaneously if you remove one of the products. Imagine, if you will, a pool of amino acids drying up in the hot sun. Not only is the water getting warmed by the sun and thus providing energy to drive reactions, but the concentration of reactants is increasing as the pool shrinks in volume by evaporation. This increases the rates of reaction further. Then, when the pool is dry and there is no water remaining, any water formed by a condensation polymerization is removed by evaporation, and the reaction equilibrium is driven toward the products. So, even if a reaction is unfavourable, it is not difficult to imagine how reactions can take place nevertheless. When the rain then falls and the product redissolves, the equilibrium could of course shift back toward the starting materials but, in the case of peptides at least, as exemplified by nylon, chitin, keratin and numerous other examples, that is kinetically very, very slow.

That has been the source of some of your trouble, yes. I take some care in formulating answers. I expect to be read as carefully.

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I already answered that question by saying thermodynamically upill reactions occur (using enzyme catalyzed nucleic acid synthesis as my example) but I acknowledged that energy required to drive the polymerization when pyrophosphate of the (d)NTP were released. Implicitly implied in this demonstration was doubt that a nucleic acid polymerase would not be able to synthesize a complementary nucleic acid strand if (d)NMPs were used as substrates for the reaction rather than (d)NTPs as I see no reason for this scenario to occur.

BTW, chitin is a polysaccharide (so it is a bad example to demonstate the metastability of the peptide bond) but I do understand the metastability of peptide bond which was you were attempting to convey. It is correct chitin has an amide group but amide linkages do not link the monosaccharides together but rather a beta 1,4 glycosidic bond.

I do not dispute dry-phase synthesis as a method to form peptide bonds nor was I attempting to in previous posts.

But it's true.

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You have demonstrate that you are correct as my skeptism of your assertion was based on a personal misunderstanding but I will still assail the notion that it is favored in aqueous solution though. Although, you did not say this nonsense explicitly, I thought it was implied when you mentioned amide bond formation was spontaneous. Of course, the fact that peptide bond formation is spontaneous probably helpful for the industrial synthesis of synthetic polymers like nylon and kevlar.

Oh, but I do comprehend chemistry.*
And because I do gives me just as much right to point out spelling mistakes as if I didn't.

* I don't think you can say the same.

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Well, I believe you do and as for my comprehension of chemistry, of course, as I will admit is rudimentary (as a majority of my knowledge of chemistry is from biology textbooks but even with this considered I still know alot more than most laymen as biology textbooks demonstrate important concepts like acid base equilibra, properties of functional groups, bonding theories, and thermodynamics quite well). My questioning of your comprehension of chemistry was based on my misunderstanding. I apologize for any misunderstanding or juvinile personal attacks. Well, your previous post is didactic and there was less "personal attacks."

As for my knowledge of biochemistry, I still have alot more to learn as it much more than memorizing substrates, products, and the names of enzymes in a given biochemical pathway.

Arik Soong said:

Excellent elucidation.

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Thanks.

Arik Soong said:

It does but it is really slow for reasons like you mentioned like resonance (http://www.chemguide.co.uk/organicprops/amides/hydrolysis.html). I am sure that in the presence of a catalyst like nylonase (an enzyme which evolved in some bacteria), one would achieve appreciable hydrolysis. Of course, the properties of the polymer also determine the rate of hydrolysis, for example, kevlar is more resistant to hydrolysis compared to nylon.I did not try to say peptide bond hydrolysis was instantaneous but rather inevitable.

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Resonance is only one reason. The fact that amide anions are poor leaving groups is another. Proteases do the trick for proteins.

Arik Soong said:

BTW, chitin is a polysaccharide (so it is a bad example to demonstate the metastability of the peptide bond) but I do understand the metastability of peptide bond which was you were attempting to convey. It is correct chitin has an amide group but amide linkages do not link the monosaccharides together but rather a beta 1,4 glycosidic bond.

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You are absolutely correct about chitin. My mistake. (It was late.)

Arik Soong said:

I do not dispute dry-phase synthesis as a method to form peptide bonds nor was I attempting to in previous posts.

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But you hadn't answered the question.

Arik Soong said:

You have demonstrate that you are correct as my skeptism of your assertion was based on a personal misunderstanding but I will still assail the notion that it is favored in aqueous solution though. Although, you did not say this nonsense explicitly, I thought it was implied when you mentioned amide bond formation was spontaneous. Of course, the fact that peptide bond formation is spontaneous probably helpful for the industrial synthesis of synthetic polymers like nylon and kevlar.

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Ah-ha! You've hit the nail on the head. In dilute solution, the reverse reaction (hydrolysis) occurs by LeChatelier's Principle (keeping in mind that the reverse reaction is also kinetically challenged)! But even then, it merely displaces the equilibrium - it doesn't make the forward reaction not occur. And when it occurs enough (under these or more favourable conditions) to fold and form beta sheets and alpha-helices and a globular protein, which curls up, it's more resistant to hydrolysis. And when the hydrophobic side-chains are sufficiently numerous, the product falls out of solution or diffuses into fatty material, protected even more efficiently from hydrolysis. And when the salt content is high, the water's activity drops and hydrolysis becomes less probable. And so on. All kinds of ways to facilitate protein synthesis. It is these things that have me prefer a protein-first scenario of abiogenesis.

Arik Soong said:

I apologize for any misunderstanding or juvinile personal attacks. Well, your previous post is didactic and there was less "personal attacks."

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I never attacked you, the person. Only your behaviour.

Arik Soong said:

Well, I believe you do and as for my comprehension of chemistry, of course, as I will admit is rudimentary ...
As for my knowledge of biochemistry, I still have alot more to learn ...

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Still, I found your knowledge of abiogenesis research impressive.