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Author Topic:   Thermodynamics, Abiogenesis and Evolution
JonF
Member
Posts: 3483
Joined: 06-23-2003
Member Rating: 2.8


Message 46 of 128 (99907)
04-14-2004 9:14 AM
Reply to: Message 45 by DNAunion
04-14-2004 12:35 AM


Re: Let Confusion Reign
Somehow, I'm not sure how, you're setting some kind of trap for me, aren't you?

Nope, just simple logic.

Either the 2LoT poses a problem for abbiogenesis, or it doesn't (whether or not we have the informatioin required to determine which). Clear so far?

If the 2LoT poses a problem for abiogenesis, that problem can't be solved. Therefore that problem is not a "problem that has yet to be fully solved."

If the 2LoT does not pose a problem for abiogenesis, then there is no thermodynamic problem with abiogenesis. Therefore there is no thermodynamic"problem that has yet to be fully solved."

No matter what, there is no thermodynamic "problem that has yet to be fully solved" with abiognesis. There cannot be.

Of course, there are plenty of questions and problems with abiogenesis that are not fully solved, and we don't know anywhere near what we'd like to about the thermodynamics of abiogenesis, but ...

"The second law of thermodynamics poses no problem at all for evolution: abiogenesis is a different story." is an unsupported assertion, and you have made no attempt to support it. All you've done is blather.

Where are your calculations that demonstrate that the second law of thermodynamics is a problem for abiogenesis?


This message is a reply to:
 Message 45 by DNAunion, posted 04-14-2004 12:35 AM DNAunion has responded

Replies to this message:
 Message 48 by DNAunion, posted 04-14-2004 9:52 AM JonF has responded

  
Percy
Member
Posts: 15491
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 47 of 128 (99913)
04-14-2004 9:42 AM
Reply to: Message 42 by berberry
04-13-2004 11:43 PM


Re: Let Confusion Reign
berberry replying to DNAunion writes:

My only argument with you, DNA, is that I don't see it necessary that one should explain a mechanism by which abiogenesis could occur before one can consider the thermodynamic implications of abiogenesis.

Life is just complicated chemistry. Abiogenesis was also complicated chemistry. Chemistry obeys all laws of physics, including 2LOT (which began life as a chemical law, anyway). There are no "themodynamic implications of abiogenesis" that uniquely distinguish it from all other chemical reactions.

The entropy of chemicals is decreased when externally provided energy, such as from the sun or from geothermal sources or from a Bunsen burner, is stored in the form of chemical bonds. This is true for all chemical reactions, though it can often be hard to tell if overall entropy has increased or decreased, since most chemical reactions involve both the breaking and forming of bonds.

We're still learning what goes on in a modern cell, and studies of those chemical reactions do not attempt to track cellular chemistry on an entropic basis because they are very complicated with many unknowns.

While poking around on the Internet I found an interesting paper studying self-organizing and self-reproducing chemistry: Cellular Evolution in a 3D Lattice Artificial Chemistry.

--Percy


This message is a reply to:
 Message 42 by berberry, posted 04-13-2004 11:43 PM berberry has responded

Replies to this message:
 Message 67 by berberry, posted 04-15-2004 3:48 PM Percy has responded

    
DNAunion
Inactive Member


Message 48 of 128 (99915)
04-14-2004 9:52 AM
Reply to: Message 46 by JonF
04-14-2004 9:14 AM


Re: Let Confusion Reign
quote:
DNAunion: Somehow, I'm not sure how, you're setting some kind of trap for me, aren't you?

quote:
JohnF: Nope, just simple logic.

Either the 2LoT poses a problem for abbiogenesis, or it doesn't (whether or not we have the informatioin required to determine which). Clear so far?


Good enough...it's the next stuff where you run off track.

quote:
JohnF: If the 2LoT poses a problem for abiogenesis, that problem can't be solved.

That's a flawed premise. None of your other "simple logic" matters since this premise of yours is wrong.

quote:
JohnF: Where are your calculations that demonstrate that the second law of thermodynamics is a problem for abiogenesis?

I told you before, I don't need calculations. I have logic that shows, for example, that polymerization is an uphill process from free monomers. There's the problem. How was it solved prebiotically?

They've tried triphosphates and gave them up, they've tried imidazolides - but their prebiotic plausibility is questionable, they've tried other activating agents but they are either not very effective or their prebiotic plausibility is in doubt too. There is a problem that has yet to be fully solved.

Again, I don't need calculations - go back and look at post #30.


This message is a reply to:
 Message 46 by JonF, posted 04-14-2004 9:14 AM JonF has responded

Replies to this message:
 Message 49 by JonF, posted 04-14-2004 11:36 AM DNAunion has responded
 Message 50 by Loudmouth, posted 04-14-2004 1:15 PM DNAunion has responded

  
JonF
Member
Posts: 3483
Joined: 06-23-2003
Member Rating: 2.8


Message 49 of 128 (99932)
04-14-2004 11:36 AM
Reply to: Message 48 by DNAunion
04-14-2004 9:52 AM


Re: Let Confusion Reign
ohnF: If the 2LoT poses a problem for abiogenesis, that problem can't be solved.

That's a flawed premise. None of your other "simple logic" matters since this premise of yours is wrong.

Indeed? You think that, if the 2LoT forbids abiogenesis, then abiogenesis can still take place?

I told you before, I don't need calculations. I have logic that shows, for example, that polymerization is an uphill process from free monomers. There's the problem. How was it solved prebiotically?

It is not necessary to know the process to evaluate the thermodnamics (although it often helps). The fact that polymerization is an uphill process does not lead to your conclusion that there's a thermodynamic problem; "uphill" processes happen spntaneously all the time. I'll tentatively accept your claim that tests have been unsuccessful; that still doen't mean that there's a thermodynamic problem.

It's a problem for abiogenesis researchers ... but it is not necessarily a thermodynamic problem, as you have claimed. The only thing that will demonstrate a thermodynamic problem is calculations.

Your logic is flawed; try writing it out as a syllogism and laugh at it.


This message is a reply to:
 Message 48 by DNAunion, posted 04-14-2004 9:52 AM DNAunion has responded

Replies to this message:
 Message 51 by DNAunion, posted 04-14-2004 1:30 PM JonF has not yet responded
 Message 52 by DNAunion, posted 04-14-2004 1:43 PM JonF has responded

  
Loudmouth
Inactive Member


Message 50 of 128 (99955)
04-14-2004 1:15 PM
Reply to: Message 48 by DNAunion
04-14-2004 9:52 AM


Re: Let Confusion Reign
quote:
They've tried triphosphates and gave them up, they've tried imidazolides - but their prebiotic plausibility is questionable, they've tried other activating agents but they are either not very effective or their prebiotic plausibility is in doubt too. There is a problem that has yet to be fully solved.

So maybe this is why abiogenesis research is still ongoing? I think you are mistaking dead ends in research with impossible goals. The very fact that scientists are very frank about plausible pathways and prebiotic activators should tell you that they fully realize the thermodynamic and free energy problems that face abiogenesis. I think we can all agree that science has not found a reliable pathway, and I think that we can all agree that entropy factors into pathways hypothesized by abiogenesis scientists.

You seem to understand what you are talking about. What I can't understand is what you are all in a huff about. None of us are arguing that the most plausible pathways violate the 2LoT. I think we can all agree that any pathway in abiogenesis must adhere to known physical and chemical laws, such as thermodynamics. I think we can also agree that there may be a viable pathway, using available energy in a prebiotic environment, that leads to nucleotide polymerization. Just to go back to one of my previous examples, it seems at times that you are arguing against mountain formation (which goes against gravity, ie uphill) while claiming that plate tectonics is not enough to explain an uphill "reaction". Maybe you could clarify things by answering one question. Do you think that a pathway exists within the confines of a prebiotic environment that would result in nucleotide polymerization? Only that one may exist, not if one has been found.

My opinion is that scientists are answering a bigger question first, could nucleotide polymers, either DNA or RNA, result in an imperfect replicator. If they are able to show this, then they will start searching for a viable polymerization pathway. There are already hints that simple organic compounds could pre-activate nucleotides and could lead to simpler organic compounds once the reactions and conditions are optimized.


This message is a reply to:
 Message 48 by DNAunion, posted 04-14-2004 9:52 AM DNAunion has responded

Replies to this message:
 Message 53 by DNAunion, posted 04-14-2004 2:06 PM Loudmouth has responded

  
DNAunion
Inactive Member


Message 51 of 128 (99958)
04-14-2004 1:30 PM
Reply to: Message 49 by JonF
04-14-2004 11:36 AM


Re: Let Confusion Reign
quote:
JohnF: If the 2LoT poses a problem for abiogenesis, that problem can't be solved.

quote:
DNAunion: That's a flawed premise. None of your other "simple logic" matters since this premise of yours is wrong.

quote:
JohnF: Indeed?

Indeed.

quote:
JohnF: You think that, if the 2LoT forbids abiogenesis, then abiogenesis can still take place?

No, I don't think that, I haven't said that, I haven't implied that, and I've stated that I am not climaing that the second law of thermodynamics forbids abiogenesis.

Your distorting things: problems are solvable, impossibilities aren't. What's I've stated is that the second law of themodynamics poses a PROBLEM for abiogenesis, NOT that it forbids it. Problems are solvable; impossibilities are not. Two very different things.

And I will point out that by this time you know damned well what I am NOT saying. Your ignoring that is an act of disingenuousness on your part.

[This message has been edited by DNAunion, 04-14-2004]


This message is a reply to:
 Message 49 by JonF, posted 04-14-2004 11:36 AM JonF has not yet responded

  
DNAunion
Inactive Member


Message 52 of 128 (99964)
04-14-2004 1:43 PM
Reply to: Message 49 by JonF
04-14-2004 11:36 AM


Re: Let Confusion Reign
quote:
DNAunion: I told you before, I don't need calculations. I have logic that shows, for example, that polymerization is an uphill process from free monomers. There's the problem. How was it solved prebiotically?

quote:
JohnF: It is not necessary to know the process to evaluate the thermodnamics (although it often helps).

Yeah, so what?

quote:
JohnF: The fact that polymerization is an uphill process does not lead to your conclusion that there's a thermodynamic problem; "uphill" processes happen spntaneously all the time.

Uhm, uphill processes never happen spontaneously: in fact, uphill indicates nonspontaneous.

Uphill process can happen only if some mechanism coupling them to downhill processes is involved (or energy is provided by some other means). But then, the process that is spontaneous - downhill - is the OVERALL process, not the single one that was originally being considered.

Since polymerization is uphill - which you accept - then it will not happen spontaneously. There's the problem. How is it solved? We know how it occurs in today's cells: not yet fully worked out is a plausible method of how it would have occurred prebiotically as part of kickstarting life.

quote:
JohnF: I'll tentatively accept your claim that tests have been unsuccessful; that still doen't mean that there's a thermodynamic problem.

It's a problem for abiogenesis researchers ... but it is not necessarily a thermodynamic problem, as you have claimed.


It is a problem OOL researchers and nature face/faced because of thermodynamics: the problem is imposed on them by the second law. If the second law didn't exist, there would be no problem getting monomers to polymerize prebiotically: (1) there would not be any restriction based on the process reducing entropy: no second law, no restrictions on changes in entropy; (2) nor would there be a restriction based on the process being energetically uphill: no second law, no restrictions on the energetics of processes. But the second law does exist.

Let me make another point, which should have been clear all along. I am not saying there is a problem with thermodynamics, as in thermodynamics is flawed somehow: nope, haven't said that.

[This message has been edited by DNAunion, 04-14-2004]


This message is a reply to:
 Message 49 by JonF, posted 04-14-2004 11:36 AM JonF has responded

Replies to this message:
 Message 54 by JonF, posted 04-14-2004 2:06 PM DNAunion has responded
 Message 55 by Percy, posted 04-14-2004 2:06 PM DNAunion has responded

  
DNAunion
Inactive Member


Message 53 of 128 (99971)
04-14-2004 2:06 PM
Reply to: Message 50 by Loudmouth
04-14-2004 1:15 PM


Re: Let Confusion Reign
quote:
DNAunion: They've tried triphosphates and gave them up, they've tried imidazolides - but their prebiotic plausibility is questionable, they've tried other activating agents but they are either not very effective or their prebiotic plausibility is in doubt too. There is a problem that has yet to be fully solved.

quote:
LoudMouth: So maybe this is why abiogenesis research is still ongoing? I think you are mistaking dead ends in research with impossible goals.

No, you guys are the ones making mistakes. Compare my statement - "There is a problem that has yet to be fully solved." - with yours, which involves impossibilities. They are very different. In fact, I've stated multiple times in this thread that problems are solvable; impoissilibities aren't.

You - and others - continue to read into my statements things which simply aren't there: even after I've explicitly stated, multiple times, that I am not saying what you people keep trying to state, claim, or insinuate I am supposedly saying.

quote:
LoudMouth: The very fact that scientists are very frank about plausible pathways and prebiotic activators should tell you that they fully realize the thermodynamic and free energy problems that face abiogenesis.

And your own statement should tell you, and others, that there are indeed thermodynamic/free energy problems associated with abiogenesis, which is what I said: I never said thermodynamics prohibits abiogenesis - no, that's what others have tried to stuff into my mouth: that's theirs words, not mine. Don't get confused.

quote:
Loudmouth: I think we can all agree that science has not found a reliable pathway, and I think that we can all agree that entropy factors into pathways hypothesized by abiogenesis scientists.

Good. Then what's the problem everyone has with what I stated?

quote:
LoudMouth: What I can't understand is what you are all in a huff about.

1) JohnF got all up in my face with his first reply: basically, I was ignorant and dishonest

2) Several people quickly jumped and took on a gang mentallity, making it once again, basically, a gang vs. DNAunion thing

3) Memebers of the gang - for example Percy - have tried to blame me for several things which weren't my doing, but were actually other people's fault: And of course the insinutations of me supposedly being a Creationist were once again peddled (for those gullible enough to swallow that load of marlarky)

4) JohnF continues to insinuate things about my position that simply aren't true, and that he should know by now aren't true: distortion: and he continues to try to claim that I am ignorant (I'm blathering, look at my own logic and I'll laugh, etc.)

I may have missed some.

[This message has been edited by DNAunion, 04-14-2004]


This message is a reply to:
 Message 50 by Loudmouth, posted 04-14-2004 1:15 PM Loudmouth has responded

Replies to this message:
 Message 57 by Loudmouth, posted 04-14-2004 2:27 PM DNAunion has not yet responded

  
JonF
Member
Posts: 3483
Joined: 06-23-2003
Member Rating: 2.8


Message 54 of 128 (99972)
04-14-2004 2:06 PM
Reply to: Message 52 by DNAunion
04-14-2004 1:43 PM


Re: Let Confusion Reign
Uhm, uphill processes never happen spontaneously: in fact, uphill indicates nonspontaneous

You're right; I should have said "uphill processes happen all the time in nature".

And, until you produce evidence that the uphill processes involved in abiogenesis cannot happen in nature, you have failed to support your claim that "The second law of thermodynamics poses no problem at all for evolution: abiogenesis is a different story." It doesn't matter whether or not someone has found a process which can occur in nature; you have claimed that there is reason to believe that there is no such process.


This message is a reply to:
 Message 52 by DNAunion, posted 04-14-2004 1:43 PM DNAunion has responded

Replies to this message:
 Message 60 by DNAunion, posted 04-14-2004 2:51 PM JonF has responded

  
Percy
Member
Posts: 15491
From: New Hampshire
Joined: 12-23-2000
Member Rating: 4.3


Message 55 of 128 (99973)
04-14-2004 2:06 PM
Reply to: Message 52 by DNAunion
04-14-2004 1:43 PM


Re: Let Confusion Reign
DNAunion writes:

Uphill process can happen only if some mechanism coupling them to downhill processes is involved (or energy is provided by some other means).

Solar and geothermal energy was available. What's the problem?

--Percy


This message is a reply to:
 Message 52 by DNAunion, posted 04-14-2004 1:43 PM DNAunion has responded

Replies to this message:
 Message 56 by DNAunion, posted 04-14-2004 2:20 PM Percy has responded

    
DNAunion
Inactive Member


Message 56 of 128 (99976)
04-14-2004 2:20 PM
Reply to: Message 55 by Percy
04-14-2004 2:06 PM


Re: Let Confusion Reign
quote:
Percy: Solar and geothermal energy was available. What's the problem?

Hey, I just realized that matter was also present. Putting the two together, Percy and I have just solved the origin of life mystery!

After all, matter and energy were both available, so really, what's the problem? Gee, why haven't OOL researchers figured it all out yet: it should have taken them only seconds to realize what Percy and I just worked out. In fact, why are there any OOL researchers at all? There was matter and there was energy: case closed.


This message is a reply to:
 Message 55 by Percy, posted 04-14-2004 2:06 PM Percy has responded

Replies to this message:
 Message 63 by Percy, posted 04-14-2004 2:59 PM DNAunion has not yet responded

  
Loudmouth
Inactive Member


Message 57 of 128 (99978)
04-14-2004 2:27 PM
Reply to: Message 53 by DNAunion
04-14-2004 2:06 PM


Re: Let Confusion Reign
DNAUnion,

So you would agree that any abiogenesis pathway must include an input of energy to make polymerization possible? I think we all agree on this one. What we are disagreeing with is the thermodynamics poses a problem within abiogenesis. I think this same problem is faced by many inorganic reactions, but these reactions occur nonetheless, usually through a high energy intermediate or an input of energy such as heat differential or pressure. Instead of 2LoT being a problem, it is actually a blessing in that it narrows down the list of possible reactants and reactions. What you see as a "problem" others see as a hurdle, a hurdle that to this point has not been cleared. The same could be said for HIV, cancer, ALS, and many other viable fields of study. Perhaps you meant that the 2LoT poses a problem, but not an insurmountable one? Or do you see the 2LoT as prohibiting any polymerization outside of ATP/enzyme driven elongation?


This message is a reply to:
 Message 53 by DNAunion, posted 04-14-2004 2:06 PM DNAunion has not yet responded

  
rineholdr
Inactive Member


Message 58 of 128 (99979)
04-14-2004 2:31 PM
Reply to: Message 30 by DNAunion
04-13-2004 8:58 PM


would it be safe to say that after the Big Bang there was a massive amount of entropy that occured. basic and few types of elementary particals racing away from each other at the speed of light or faster, cooling as they left the initial source, what thermodinamic mechinism came into effect that caused an entropy decrease under this senerio? I guess Im going right to the inital source of everything we know or think we know...good place to start isn't it? At the bottom of the ladder and explain up.
This message is a reply to:
 Message 30 by DNAunion, posted 04-13-2004 8:58 PM DNAunion has not yet responded

Replies to this message:
 Message 59 by Loudmouth, posted 04-14-2004 2:36 PM rineholdr has responded

  
Loudmouth
Inactive Member


Message 59 of 128 (99980)
04-14-2004 2:36 PM
Reply to: Message 58 by rineholdr
04-14-2004 2:31 PM


quote:
would it be safe to say that after the Big Bang there was a massive amount of entropy that occured. basic and few types of elementary particals racing away from each other at the speed of light or faster, cooling as they left the initial source, what thermodinamic mechinism came into effect that caused an entropy decrease under this senerio? I guess Im going right to the inital source of everything we know or think we know...good place to start isn't it? At the bottom of the ladder and explain up.

Massive amounts of energy, free high energy photons, immense pressures, etc. Any input of energy can decrease entropy. The second law of thermodynamics does not deal with order/disorder directly. It could just as easily be described as "heat will always move towards a colder object." It is a law about the movement of energy. Breaking down the word thermodynamics you get thermo=heat and dynamics=movement. Heat just increases the number of states matter can be in (more order) as compared to fewer states in a colder object (less order). It has nothing to do with complexity.


This message is a reply to:
 Message 58 by rineholdr, posted 04-14-2004 2:31 PM rineholdr has responded

Replies to this message:
 Message 61 by rineholdr, posted 04-14-2004 2:53 PM Loudmouth has responded

  
DNAunion
Inactive Member


Message 60 of 128 (99985)
04-14-2004 2:51 PM
Reply to: Message 54 by JonF
04-14-2004 2:06 PM


Re: Let Confusion Reign
quote:
JohnF: And, until you produce evidence that the uphill processes involved in abiogenesis cannot happen in nature,...

I have no such burden since I have not claimed impossibility, not at all. I mentioned problems - problems are solvable; impossibilities aren't.

You continue in your dishonesty.


This message is a reply to:
 Message 54 by JonF, posted 04-14-2004 2:06 PM JonF has responded

Replies to this message:
 Message 64 by JonF, posted 04-14-2004 4:32 PM DNAunion has not yet responded

  
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