Antievolution.org - Antievolution.org Discussion Board -Topic::Has the Mystery of Life's Origin Been Solved?

Posted: Dec. 09 2006,10:38

Louis, I don't have any problem with abiogenesis as a theory it just the specifics that I'd like to know more about. I understand that RNA, DNA, proteins etc represent endpoints. My problem (or more rightly, limitation) is that I have trouble conceiving of the primitive molecules and the transitions to get to where we are today. That is why I thanked GoP because whether he is sincere or not a discussion insues and I have an opportunity to learn from others. Case in point, the links you posted are greatly appreciated and gives me an opportunity to dig deeper.

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Posted: Dec. 09 2006,11:08

Oooh, here's a pretty good paper that discusses a lot of the issues involved. Notice the configurational component involves the Shannon information formula, although they use it quite differently from Bradley/Thaxton (and similarly to Hamilton's definition).

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Posted: Dec. 09 2006,15:12

Quote (skeptic @ Dec. 09 2006,10:38)

Louis, I don't have any problem with abiogenesis as a theory it just the specifics that I'd like to know more about.

Well heck, so would everyone else. That is why it is an area of such widespread research. (shrug) After all, there isn't much point in sinking a lot of research resources into something that we already know about in great detail, huh.

Note, though, that there are no ID/creationists involved in any of this research. None. Not a one. Zip. Zilch. Zero.

That's mostly because ID/creationists simply have nothing scientific to say. Nor anything useful to add. (shrug)

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Posted: Dec. 09 2006,15:22

Quote (skeptic @ Dec. 09 2006,10:38)

I understand that RNA, DNA, proteins etc represent endpoints. My problem (or more rightly, limitation) is that I have trouble conceiving of the primitive molecules and the transitions to get to where we are today.

Oddly enough, "I can't conceive of the transitionals" is EXACTLY what the fundie nutjobs were saying, just 20 years ago, about whales, and birds, and woodpecker tongues, and bombardier beetle chemicals.

Funny thing is, none are saying that today. Well, OK, maybe the *stupid* ones still are.

I suspect in 20 years, your "I can't conceive of any transitions to RNA" will sound just as idiotic as "I can't conceive of any transitions to whales" does today.

In science, knowledge and understanding continually advances. That's why people who say "we'll NEVER understand X, Y or Z", usually end up looking pretty stupid.

Like, ya know, creationists.

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Faid

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Posted: Dec. 09 2006,17:14

This is a 2001 paper that seems to get a lot of spotlights on the net- it's hard to miss, in fact.

http://arxiv.org/PS_cache/cond-mat/pdf/0107/0107315.pdf

Does this represent the most recent proposed pathways for OOL? It seems quite convincing to me (as well as to many others who refer to it on the web), but I lack the chemistry skills to evaluate it properly.

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Posted: Dec. 10 2006,09:47

Faid,

Thanks for that, fascinating and relevant paper. I think people (me included!! ) often forget how favourable (energetically) certain protein folding conformations are. The similarities between, for example, some elements of solution and solid state protein structures can be quite striking in some respects.

A lot of the creationist crap I see has the standard "deck of cards" problems wuth this kind of thing, i.e. they whine on about how improbable certain configurations are whilst ignoring that from the standpoint of their calculations all configurations are equally improbable. The next "unfortunate" thing for the creationists is they almost exclusively ignore the underlying physics. Not all conformations are energetically equivalent, and evolution doesn't only apply to biological systems. More stable conformations, or in the case of abiogenesis, more fecund/accurate/efficient self replicators (something that can be influence by conformation for example, e.g. Soai reaction...again! ) are going to be more favoured (i.e. hang around longer, produce more "offspring" etc etc). We have exactly the things we need for an evolutionary scenario: a gradient along which certain qualities can locate, a huge range of accessible possible locations which have different consequences (e.g. biological activity related to structure), a huge stock of raw materials, and wodges of time compared to the speed of processes involved. Fun fun fun.

Louis

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Posted: Dec. 13 2006,13:04

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A lot of the creationist crap I see has the standard "deck of cards" problems wuth this kind of thing, i.e. they whine on about how improbable certain configurations are whilst ignoring that from the standpoint of their calculations all configurations are equally improbable.

No, their argument is that useful configurations are much rarer (and consequently harder to find in a blind search in configuration space) than useless ones. But, as you subsequently point out:

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The next "unfortunate" thing for the creationists is they almost exclusively ignore the underlying physics. Not all conformations are energetically equivalent, and evolution doesn't only apply to biological systems. More stable conformations, or in the case of abiogenesis, more fecund/accurate/efficient self replicators (something that can be influence by conformation for example, e.g. Soai reaction...again! ) are going to be more favoured (i.e. hang around longer, produce more "offspring" etc etc). We have exactly the things we need for an evolutionary scenario: a gradient along which certain qualities can locate, a huge range of accessible possible locations which have different consequences (e.g. biological activity related to structure), a huge stock of raw materials, and wodges of time compared to the speed of processes involved. Fun fun fun.

This paper outlines some possible ways to calculate distances within conformation space:

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In this article we focus on construction of a numerical form for this distribution function for models of protein chains. We can use the distribution function to assess the probability of a conformer lying within a given distance of another conformer and the number of �effective� degrees of freedom that operate at that distance. With some standard assumptions, we can estimate the change in conformational entropy upon protein folding.

My second paper tries to accomodate energy considerations into conformational entropy:

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A more sophisticated approach is to take into account that the rotamers in the unfolded state are not equally populated. Figure 1 shows three conformations accessible in the unfolded state with different energies. A state with higher energy will be populated less often. Nkmethy et al. (1966) and Finkelstein and Janin (1989) used Equation 1, with Was 2-3 for each rotatable bond. A more accurate approach is to use Equation 2, where pI is the fractional population of each rotamer state i in the unfolded state.
[...]
The populations of each rotamer in the unfolded state cannot yet be observed directly. Instead, Pickett and Sternberg (1993) assumed that the conformations adopted by side chains in protein crystal structures are representative of unfolded conformations. The distribution ofs ide-chain rotamers at interior positions of a-helices is unusual, however, so they were excluded.
The results of their survey were used to determine AS,,,,, using Equation 2. It was necessary to correct some residues for symmetry (discussed above) and they added a term for groups that showed essentially free rotation in the unfolded state, restricted by hydrogen bonding when buried.

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Koehl and Delarue (1994) found pI for each rotatable bond in the folded state by calculating the energy of each rotamer. The energies were calculated for different conformations of nearby rotamers and weighted by how often each neighboring conformation was adopted. The entropy of the unfolded state was found using Equation 1, where W is the number of possible rotamers for each side chain in the rotamer library of Tuffery et al. (1991). The difference between these quantities gives AS,.,, (Table 1).

etc, etc.

So obviously Mystery's attempts at defining entropy as targeting a certain sequence of amino acids comprising the polymer were off the mark, because the correct calculations also consider the changes in bond energies as well as the loss of conformational degrees of freedom when the polymer folds. At least that's my take.

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Posted: Dec. 14 2006,10:35

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My second paper......

And here we have yet another issue. How is this paper in any way "yours"? Rampant ego YET again from the troll I note.

Not only is it manifestly irrelevant, just like the creationist ramblings of Thraxton et al., it's the same google trawled irrelevance as before. Just because they use similar words does not mean they have similar meanings.

Again, for the hard of thinking (troll, I'm looking at you), the whole "target" metaphor is horribly misleading.

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No, their argument is that useful configurations are much rarer (and consequently harder to find in a blind search in configuration space) than useless ones

Define "useful". Useful in what context, in what system, under what conditions? This is the whole tawdry and mistaken point. There was no "useful", no "purpose", no "target". I know you creationists don't get this, but life is a possible consequence of the way this universe works, perhaps even a probable one. "Useful" is a pretty meaningless term in the sense you are using it. Pissing about with callculations is merely mental masturbation when the whole reason you are doing those calculations is irrelevant or erroneous. May as well calculate the number of angels dancing on the head of a pin.

There wasn't a little picture of a bloke carved into the first atom that coalesced out of the big bang, the future of said atom was neither determined nor deterministic. The papers you cite refer to a human "reverse engineering" activity of exploring conformation space and protein thermodynamics to better understand why:

a) certain molecules are biologically active and how we can better design molecules that are biologically active.

b) why proteins take the confirmations they do and are as stable as they are.

c). The review by Doig and Sternberg is to do with incorporating data to do with amino acid side chain conformations into the understanding of how and why proteins adopt certain conformations. Not only are they dealing with modern, complex, highly evolved proteins that are derived from modern biological systems, but the topic is barely relevant to abiogenesis at all in any sense other than thermodynamics is relevant to all chemistry. It's talking about how, when proteins fold, the conformations of the amino acid side chains are restricted and how this restriction plays a part in the overall stability of the folded protein.

d) The paper by Sullivan and Kuntz is a different thing again. What these guys are doing is trying to show how calculating the "information content" of a macromolecule can run into certain issues and what those issues are. Again, this is massively irrelevant to abiogenesis in all but the most trivial "thermodynamics has something to do with it" way. Please don't start reproducing the standard creationist "information" errors that even I can see as someone very unfamiliar with information theory.

You're wasting your time and ours by pissing about with concepts you don't understand. Stop it and you might actually learn something useful. We know YOU think these things are relevant. Shit, you even think that the vomittings of Thraxton are vaguely relevant. The fact that they are not seems to have passed you by. Your personal opinion that something is important, fascinating or relevant to a specific topic is not evidence. Turn your pigshit ignorant, arrogant, fundamentalist, bigotted ego to off for a second and maybe, just maybe you'll have the remotest chance of understanding that. The fact that you don't know the first thing about the topic you are discussing is massively obvious. Attempting to baffle with bullshit and blind with science will not serve you one jot. You are attempting to discuss a topic about which you clearly know nothing. If you genuinely have an interest in this topic (which I severely doubt) then abandon your current course of irrelevancy and take up a new tack. I doubt you will do this for a variety of reasons, not least of which: a) you are clearly trolling, why else start from a creationist irrelevance?, b) still playing your silly game of "win at tah intanetz", and c) in my (and everyone else's) evidence based opinion a deluded fruitcake with the intellectual gifts of dry wall and far too much time attached to google.

Louis

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Posted: Dec. 14 2006,12:25

After all the posturing, we finally see what Mel's got.....and it ain't much. Even in his own specialty.

Wow.

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Again, for the hard of thinking (troll, I'm looking at you), the whole "target" metaphor is horribly misleading.

Yes. And I expressed reservations about this earlier:

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So obviously Mystery's attempts at defining entropy as targeting a certain sequence of amino acids comprising the polymer were off the mark, because the correct calculations also consider the changes in bond energies as well as the loss of conformational degrees of freedom when the polymer folds. At least that's my take.

I can see why you missed it, because I said this just before your post, right where you wouldn't find it. What a clever lad am I.

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No, their argument is that useful configurations are much rarer (and consequently harder to find in a blind search in configuration space) than useless ones

Define "useful". Useful in what context, in what system, under what conditions?

Oh, that's right, I keep forgetting that you don't read what you criticise. Here's some spoon feeding:

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The requirements for a biologically functional protein molecule are: (1) all L-amino acids, (2) all alpha-links, and (3) a specified sequence. This being so, the calculation of the configurational entropy of the protein molecule using equation 8-8 is unchanged except that the number of ways the system can be arranged, (cr), is increased from 1.28 x 10115 to 1.0 x 10175 as shown in equations 9-3 and 9-4. We may use the relationships of equations 8-7 and 8-8 but with the number of permutations modified as shown here to find a total configurational entropy work. When we do, we get a total configurational entropy work of 195 kcal/mole, of which 159 kcal/mole is for sequencing and 36 kcal/mole to attain all L-amino acids and all alpha-links.

Now granted, this definition should have been given from the start, and not simply as a sidenote to a criticism of Sidney Fox's work, but it was there. How ever did you miss it?

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There wasn't a little picture of a bloke carved into the first atom that coalesced out of the big bang, the future of said atom was neither determined nor deterministic. The papers you cite refer to a human "reverse engineering" activity of exploring conformation space and protein thermodynamics to better understand why:

a) certain molecules are biologically active and how we can better design molecules that are biologically active.

b) why proteins take the confirmations they do and are as stable as they are.

I think you meant "conformations" here; nevertheless, I see your point. But don't scientists have to know more about part b in order to calculate entropy changes in (admittedly far simpler) prebiotic molecules? I would think an OOL researcher would need to have an empirical footing before rushing off with a lot of equations.

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c). The review by Doig and Sternberg is to do with incorporating data to do with amino acid side chain conformations into the understanding of how and why proteins adopt certain conformations. Not only are they dealing with modern, complex, highly evolved proteins that are derived from modern biological systems, but the topic is barely relevant to abiogenesis at all in any sense other than thermodynamics is relevant to all chemistry. It's talking about how, when proteins fold, the conformations of the amino acid side chains are restricted and how this restriction plays a part in the overall stability of the folded protein.

But wouldn't an OOL researcher want to know how hydrophobic side chains contribute to the protein folding? Even if you're talking about the simpler peptide precursors, the electronic properties of amino acids contribute to the protein's secondary, and ultimately tertiary, structure, so small peptides might be able to organise themselves contra to Thaxton/Bradley's dictum that a long, specified primary structure is the only way to get things started. As I understand it, that was the gist of their objection to Steinman/Cole's work. I could be wrong.

More later.

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Posted: Dec. 14 2006,14:08

What's funny about Louis's carping is that I never claimed to have more than a layman's understanding (if that) of the issue. Once Tracy Hamilton pointed out the discrepancy between the book's use of informational entropy and the literature's use of the concept, I admitted that the creationists were off base. I was only trying to probe how the real calculations were done. I figured that studying modern proteins could give some parameters that OOL researchers could use for their work. Apparently, Louis feels that the work is largely irrelevant to abiogenesis. Fine, but please note the equations that the authors use in my second reference -- Boltzmann's formula in particular. Also check out how they calculate conformational energy.....the formula should be familiar to everyone who's read Dave's thread. But hey, only an idiot would assume that two papers using the same words and formulas have any sort of relevance to each other.....right? Notice that Louis doesn't discuss the math involved. In fact, most of his post doesn't make any particular objection to my ideas other than noting that modern proteins are more complex than the simple polymer that the creationists analyse.

Stick to gay-bashing, Louis, because as someone once said:

A man's got to know his limitations!

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Posted: Dec. 14 2006,14:39

BWWWWWWAAAAAAAAAAAAAAAAAHAHAHAHAHAHAHA

Quotemining and silly piccies. Is that really the best you can do?

Looks like I was both right and wrong. Right that you couldn't understand why the creationist calculations and googletrawling �are irrelevant. Wrong for even thinking there was a vague possibility you were doing anything other than trolling. Again.

Go back to sleep troll. You've had your arse handed to you yet again and you're manifestly too dumb to notice.

Louis

P.S. Gaybashing? Sorry but point out just one instance of me bashing gays and I'll happily confess. Oh and mocking you for posting sweaty wrestler pics isn't gay bashing you do know that don't you you dumb fuck?

P.P.S.

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The requirements for a biologically functional protein molecule are: (1) all L-amino acids, (2) all alpha-links, and (3) a specified sequence. This being so, the calculation of the configurational entropy of the protein molecule using equation 8-8 is unchanged except that the number of ways the system can be arranged, (cr), is increased from 1.28 x 10115 to 1.0 x 10175 as shown in equations 9-3 and 9-4. We may use the relationships of equations 8-7 and 8-8 but with the number of permutations modified as shown here to find a total configurational entropy work. When we do, we get a total configurational entropy work of 195 kcal/mole, of which 159 kcal/mole is for sequencing and 36 kcal/mole to attain all L-amino acids and all alpha-links.

WRONG. This is a very narrow requirement for a very modern, highly evolved protein. As I said waaaaay back at the start, this is supremely irrelevant because nobody is proposing (apart from creationist loons) that modern proteins or modern nucleic acids are necessarily anything like those things that got going way back at the start of abiogenesis. Lordy troll you are a moron. Not only is the quote wrong in terms of what it applies to, it isn't even right in what it is claiming. Just a for instance all L-amino acids are not a requirement for biological activity, nor indeed is alpha linkage. Of course I suppose bacteria don't count. Bwaaahahahahaha Oh deary me troll, you have surpassed even my incredibly low expectations of you this time.

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Posted: Dec. 14 2006,15:38

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BWWWWWWAAAAAAAAAAAAAAAAAHAHAHAHAHAHAHA

Oh, so that's the sound of a beaten cur.

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Quotemining and silly piccies.

Notice that Mel just thinks his assertion of quote-mining equals proof of same. Sorry, Mel, my quotes were on target, which is why didn't have a proper response. Please notice, Lurkers, that I quoted the text surrounding the bolded bits I responded to, so Louis has no complaints about his statements....as for my quotes of Mystery....is Louis asserting that I'm misquoting Thaxton/Bradley? If so, he should be able to demonstrate where I misrepresented their position. The fact he doesn't says something, I think. Or is he saying I misrepresented myself? Who knows in Mel-land.....

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Looks like I was both right and wrong. Right that you couldn't understand why the creationist calculations and googletrawling �are irrelevant. Wrong for even thinking there was a vague possibility you were doing anything other than trolling. Again.

Ummm Louis, one of your major complaints echoed mine. So I can't be wrong unless you are as well.

As far as trolling is concerned, I only do it for those who deserve it. I am respectful towards those who behave in a civilised manner.

I'll italicise Chairman Mel's quotations for the rest of this post:
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P.P.S. � � � �

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The requirements for a biologically functional protein molecule are: (1) all L-amino acids, (2) all alpha-links, and (3) a specified sequence. This being so, the calculation of the configurational entropy of the protein molecule using equation 8-8 is unchanged except that the number of ways the system can be arranged, (cr), is increased from 1.28 x 10115 to 1.0 x 10175 as shown in equations 9-3 and 9-4. We may use the relationships of equations 8-7 and 8-8 but with the number of permutations modified as shown here to find a total configurational entropy work. When we do, we get a total configurational entropy work of 195 kcal/mole, of which 159 kcal/mole is for sequencing and 36 kcal/mole to attain all L-amino acids and all alpha-links.

WRONG. This is a very narrow requirement for a very modern, highly evolved protein. As I said waaaaay back at the start, this is supremely irrelevant because nobody is proposing (apart from creationist loons) that modern proteins or modern nucleic acids are necessarily anything like those things that got going way back at the start of abiogenesis. Lordy troll you are a moron. Not only is the quote wrong in terms of what it applies to, it isn't even right in what it is claiming. Just a for instance all L-amino acids are not a requirement for biological activity, nor indeed is alpha linkage. Of course I suppose bacteria don't count.

Let's contrast this with the actual context of the citation:

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No, their argument is that useful configurations are much rarer (and consequently harder to find in a blind search in configuration space) than useless ones

Define "useful". Useful in what context, in what system, under what conditions?

Oh, that's right, I keep forgetting that you don't read what you criticise. Here's some spoon feeding:

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The requirements for a biologically functional protein molecule are: (1) all L-amino acids, (2) all alpha-links, and (3) a specified sequence. This being so, the calculation of the configurational entropy of the protein molecule using equation 8-8 is unchanged except that the number of ways the system can be arranged, (cr), is increased from 1.28 x 10115 to 1.0 x 10175 as shown in equations 9-3 and 9-4. We may use the relationships of equations 8-7 and 8-8 but with the number of permutations modified as shown here to find a total configurational entropy work. When we do, we get a total configurational entropy work of 195 kcal/mole, of which 159 kcal/mole is for sequencing and 36 kcal/mole to attain all L-amino acids and all alpha-links.

Now granted, this definition should have been given from the start, and not simply as a sidenote to a criticism of Sidney Fox's work, but it was there. How ever did you miss it?

Note the part I just bolded. He was asking for a definition of "useful" based on this exchange:

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A lot of the creationist crap I see has the standard "deck of cards" problems wuth this kind of thing, i.e. they whine on about how improbable certain configurations are whilst ignoring that from the standpoint of their calculations all configurations are equally improbable.

No, their argument is that useful configurations are much rarer (and consequently harder to find in a blind search in configuration space) than useless ones. But, as you subsequently point out:

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�
The next "unfortunate" thing for the creationists is they almost exclusively ignore the underlying physics. Not all conformations are energetically equivalent, and evolution doesn't only apply to biological systems. More stable conformations, or in the case of abiogenesis, more fecund/accurate/efficient self replicators (something that can be influence by conformation for example, e.g. Soai reaction...again! ) are going to be more favoured (i.e. hang around longer, produce more "offspring" etc etc). We have exactly the things we need for an evolutionary scenario: a gradient along which certain qualities can locate, a huge range of accessible possible locations which have different consequences (e.g. biological activity related to structure), a huge stock of raw materials, and wodges of time compared to the speed of processes involved. Fun fun fun.

So he started off by mischaracterising their argument. I tried to explain their real argument to him (one I clearly didn't share, by the way, please notice above when I cited Mel's statement to refute theirs), and when he asked for a clarification of their ideas I provided it. Now he confuses their notions with mine. Wow, Mel, you really can't keep more than one idea in your head, can you?

Notice, Lurkers, that I'm providing the proof of context. Mel has just been caught with his pants down.

More later.

[p.s. - Notice that Mel refuses to acknowledge that I have repudiated the book's arguments. He still treats me as if I was trying to defend them! Which I never have, but let's not confuse Mel with subtle distinctions for now.]

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Posted: Dec. 14 2006,16:04

LOL Oh you are too funny! An AFDavesque declaration of victory in both absence and contradiction of the evidence.

Go on then troll, let's take a survey, take a vote. �Who thinks you have "beaten this cur" or that I have "been caught with my pants down". Come ye lurkers, come ye regulars. I'm MORE than happy to stand by their comments/opinions.

Come one come all let's put this to the test.

Louis

P.S. Oh and this

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As far as trolling is concerned, I only do it for those who deserve it. I am respectful towards those who behave in a civilised manner.

Is so distant from reality to be bordering on the insane. This from the same person who has confessed to trolling this board for over a year. Bwaaaaaaaaahahahahahahahaha. Sorry troll, you truly are pathetic.

P.P.S. Added in edit: Troll I haven't said that you are defending the creationist drivel, I've said it's irrelevant and more than a little telling that it's your starting point for discussion. Not only that the papers you post are STILL irrelevant to the whole topic of abiogenesis in anything beyond a trivial sense (i.e. thermodynamics is relevant) and they go little or no way to refuting the calculations of Thraxton et al. because the calculations need no refutation because they are based on misconceptions and nonsense. Incidentally the fact that you deny supporting such irrelevant misconceptions and nonsense whilst at the same time treating it as if it were relevant and accurate is hilarious. I want that dollar I sent you to buy a clue back. You clearly spent it on glue, not a clue.

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Shirley Knott

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Posted: Dec. 14 2006,16:15

The only thing Paley's Stale Flatulence has ever written which has any chance of being true and correct would be his admission of multiple-personality trolling.
I don't believe I've ever seen him "best" anyone on anything, at any time, on any subject.
He brings whole new levels of meaning to the phrase "delusions of adequacy".

no hugs for thugs,
Shirley Knott

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Posted: Dec. 14 2006,16:58

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Go on then troll, let's take a survey, take a vote.

I think Wes disabled the "poll" icon. �

�

Personally, I would be happy if people simply point out the flaws in my arguments; that means more to me than a poll anyway. I still don't see why thermodynamic calculations involving modern proteins can't be applied to simpler precursors, and nothing you've said suggests that this can't be done to great profit.

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Who thinks you have "beaten this cur" or that I have "been caught with my pants down".

When you mix up my arguments with people who I don't agree with, and I prove this by citing my favorable quotation of your own argument, you don't have much to say, really.

Unless I'm stupid for agreeing with you. Hmmmm....wait a minute.....no, the book's thermodynamic arguments are still crap.

p.s.

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Not only that the papers you post are STILL irrelevant to the whole topic of abiogenesis in anything beyond a trivial sense (i.e. thermodynamics is relevant) and they go little or no way to refuting the calculations of Thraxton et al. because the calculations need no refutation because they are based on misconceptions and nonsense.

What the #### is this supposed to mean? Are the calculations relevant to the thermodynamic conditions that hold under abiogenesis (as I would think they'd have to be), or aren't they? Give a straight answer, man. If they are relevant, then you're admitting that I've been right all along. If not, well.....you'll have to elaborate.

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qetzal

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Posted: Dec. 14 2006,17:49

No question about it: GOP is full of s**t.

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Posted: Dec. 14 2006,18:12

Is Paley **STILL** bleating?

And people are ***STILL*** paying attention to his bleating?

Which leads to yet **MORE** bleating?

Geez. His entertainment value ended looonnngggg ago.

(yawn)

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Posted: Dec. 14 2006,18:52

Qetzal:

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No question about it: GOP is full of s**t.

Any particular reason? You guys accused me of being narrow-minded and of having an agenda, but then proceed to bitch when I change my mind. That's why I don't take any claim at face value: people in general are full of s**t, and have an agenda. I'm not going to assume that scientists or anyone else has a monopoly on the truth, sorry. Make a good argument and I'll listen. Make a bad one or fail to support your ideas and I'll remain unpersuaded.

Lenny Flank:

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Geez. �His entertainment value ended looonnngggg ago.

And yet you keep clicking on the thread and posting. I avoid threads that bore me -- why don't you? Besides, protestations of apathy ring hollow from people like you. How's that lynch mob goin'? �

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Posted: Dec. 14 2006,20:36

(swims up, sniffs bait, shrugs and swims away)

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Posted: Dec. 15 2006,05:39

Lenny,

You're quite right. I tried to swim away from the bait but took a nibble and now I seem to have this hook in my jaw.

Luckily I have my hook removing tool handy. When we're dealing with a troll so dishonest that it doesn't understand simple phrases like "irrelevant except in the most trivial sense (i.e. thermodynamics is relevant to chemistry)" and is only interested in playing silly buggers and declaring cartoonish WICTORY in the face of evidence, it's an easy hook to remove.

Louis

Note to self, added in edit:

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Bye.

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Posted: Dec. 15 2006,12:13

Louis:

Would you mind answering a couple of questions?

You claimed that Faid's paper was interesting and relevant to abiogenesis. Yet Faid's thermodynamics paper seemed to rely on the coupling of a nucleic acid (RNA in this case) with polymers, with the chaperone role being played by the rocky substrate. If RNA is needed for the cooling of the unfolding temperature, then is this model sufficient for pre-RNA chemistry? If not, could you point to a paper that does discuss the earlier thermodynamics? Thanks.

The paper also relies a bit on Eigen hypercycles. How likely is this cycle in your opinion?

Now, I will respect your wishes and stay off your thread if and only if you behave in a civilised manner on all threads from now on. If you continue to bait me, then all bets are off.

PS Faid or anyone else is free to take a stab at my questions to Louis. Sorry for the rushed tone but someone's waiting for me to finish. :angry:

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Dey can't 'andle my riddim.

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Posted: Dec. 15 2006,12:22

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Bye.

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Posted: Dec. 15 2006,13:17

Ok, if that's how you want it......

You'd think that Louis could rise to the civilisational level of a family pet. But since he can't, I'll make him my pet.

By the way, Lou....how can nucleic acids be simultaneous relevant and irrelevant to the early stages of abiogenesis? Is this a Schr�dinger cat thing that only experts can understand?

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Dey can't 'andle my riddim.

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Posted: Dec. 15 2006,17:54

(swims up, sniffs fresh bait, LAUGHS, then swims away)

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Editor, Red and Black Publishers
www.RedandBlackPublishers.com

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Posted: Dec. 15 2006,18:35

Lenny,

My thoughts exactly. I think I'm going to sit back and watch the troll work himself into ever greater heights of delusion and bullshit. Good bait though, I like dogs.

Mind you, THAT dog would make a suitable lunch for the pet I used to have. A pet you share an interest in no doubt. Do you still keep reptiles? My wife and I are currently moving house (still! ARGH) so I am not going to get a new snake until we are settled. I certainly will be the moment we're stationary! I've always wanted to keep a green tree python from juvenile. However I understand that they are a relatively difficult terrarium species, and I am a relative neophyte in the herpetological universe. I've kept pythons before, but only Royal pythons and a light Indian python that I kept for a just over a year as a favour for a friend at a serpentarium. The poor sod simply didn't have room after this snake and two others were rescued, fully grown, from some cruel idiot's house. He thought keeping snakes was cool and funky, but didn't provide them with proper housing or facilities. The other two snakes died, luckily the one I kept for a while was the strongest and sanest of the three, and is happily ensconced at the serpentarium now doing very well. She's also a mummy python (one, two three: aaaahhhhhhh). Any tips from an old hand greatly appreciated.

Louis

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Bye.

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Posted: Dec. 16 2006,15:02

Louis, since your own thread is draggin ass, would you care to take the extra time to outline some thermodynamic hurdles? Or is Faid's paper the final word? If not, could quasispecies selection handle the more primitive informational work, with more advanced hypercycles creating the adsorption-refrigeration cycle that amplifies RNA replication rates, ultimately leading to more complex molecules? Do you think hypercycles are plausible, and if so, which nucleic acid is most likely to be the progenitor?

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Dey can't 'andle my riddim.

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Posted: Dec. 16 2006,15:35

I'm interested in any expert's comments, actually.

Oh, just one more thing:

Blackmond's summary seems to admit that reactions involving dialkylzinc reagents are not very realistic in a prebiotic soup. How big of a problem is this? Symmetry-breaking autocatalysis reactions seem pretty rare. Any candidate reactions on the horizon that are more realistic?

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Dey can't 'andle my riddim.

Flint

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Posted: Dec. 18 2006,14:01

I'm starting to consider myself lucky that I'm so ignorant of the abiogenesis research and everything being looked at, that I can't possibly get bogged down in the details. A quick reading shows that there's still plenty of debate as to exactly which details matter, but that research continues. All is not lost, but little has been found either.

The way I see it, either there exist one or more natural mechanisms by which life as we might recognize it could evolve through some occurrence of chemical coincidence immediately followed by some sort of selection, or else we are obliged simply to give up and admit that not only are we ignorant (and we are), but that our ignorance cannot be overcome through research (also known as magic, or goddidit).

Personally, I don't think giving up is a useful strategy, however far we may be from any good understanding, or however tempting "goddidit" might be as a way to reword our resignation to failure. I much prefer "we not only don't know yet, but we have no idea how deep our ignorance runs. We do not know how much we do not know but need to know to decode this process."

I don't see much sense in trying to puzzle out, one by one, why things that aren't the right answer, don't work. This requires a level of expertise beyond my ambitions.

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