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  Topic: Has the Mystery of Life's Origin Been Solved?, Current status of abiogenesis< Next Oldest | Next Newest >  
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Dec. 06 2006,16:09   

What is the status of current abiogenesis research? Have plausible mechanisms been found for each of the major steps? Are the steps thermodynamically plausible?

The best creationist critique of abiogenesis is The Mystery of Life's Origin, but most of the references are seriously out of date. Nevertheless, it outlines many of the physical hurdles that any scenario must overcome. As far as I know, no one has successfully rebutted it.

This article summarises the current evidence, but does not discuss the possible mechanisms in any detail.

So does The Mystery of life's Origin retain its sting? If not, why not?

All productive criticism is appreciated.

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Dey can't 'andle my riddim.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Dec. 06 2006,16:30   

Quote
As far as I know, no one has successfully rebutted it.

This article summarises the current evidence, but does not discuss the possible mechanisms in any detail.

What's your position on this Paley?

Do you think that life originated on Earth through natural processes or do you take our current lack of detailed explanation as evidence of the contrary (argument from ignorance, as Behe's Irreducible Complexity)?

  
Faid



Posts: 1143
Joined: Mar. 2006

(Permalink) Posted: Dec. 06 2006,17:56   

Quote
Has the Mystery of Life's Origin Been Solved?


No.

Does this mean it can't be solved? No.

Does "rebutting" a book whose basic argument is "you haven't succesfully proved anything yet, so you are wrong" serve any purpose? No.

Is this thread meaningful in any way, if we are to discuss a creationist book? No (Unless you were bored and decided to set the troll loose again).

The only reason I see in participating in this thread is if we discuss all the recent efforts in figuring out a possible mechanism for abiogenesis, and comment on whether we believe they are on the right track or not (and if other possible mechanisms exist).

Otherwise, no dice.

--------------
A look into DAVE HAWKINS' sense of honesty:

"The truth is that ALL mutations REDUCE information"

"...mutations can add information to a genome.  And remember, I have never said that this is not possible."

  
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Dec. 06 2006,18:25   

jeannot & Faid:

 
Quote
Do you think that life originated on Earth through natural processes or do you take our current lack of detailed explanation as evidence of the contrary (argument from ignorance, as Behe's Irreducible Complexity)?


 
Quote
The only reason I see in participating in this thread is if we discuss all the recent efforts in figuring out a possible mechanism for abiogenesis, and comment on whether we believe they are on the right track or not (and if other possible mechanisms exist).


First: I think that scientists will eventually discover a naturalistic mechanism for abiogenesis. However, I am skeptical that the current efforts achieve that goal --that's why I'm interested in learning from any expert in this field. If I'm wrong, I will be delighted to admit so, because I suspect that God is smart enough to create laws that permit the development of life from scratch. I would be a bit disappointed if God did not do this.

Second: I brought up the book because it lays out the problems with naturalistic scenarios. To my knowledge, the only serious rebuttal was from a talk origins contributor who didn't have the required expertise, and presented a flawed criticism that another poster (a non-creationist, by the way) had to debunk. Basically, I think serious efforts from creationists need to be addressed, because this encourages better dialogue on their part. Ignoring serious work makes us look cowardly IMHO.

I hope this helps.

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Dey can't 'andle my riddim.

  
Faid



Posts: 1143
Joined: Mar. 2006

(Permalink) Posted: Dec. 06 2006,19:11   

Quote
First: I think that scientists will eventually discover a naturalistic mechanism for abiogenesis. However, I am skeptical that the current efforts achieve that goal

And you are right. There is no debate here. They try to, however, and are optimistic. That's all there is for now.
Quote
that's why I'm interested in learning from any expert in this field. If I'm wrong, I will be delighted to admit so, because I suspect that God is smart enough to create laws that permit the development of life from scratch. I would be a bit disappointed if God did not do this.

Then you should be glad, because scientists seem optimistic that they will get it eventually.
Quote
Second: I brought up the book because it lays out the problems with naturalistic scenarios.

If by "problems" you mean the issues that have to be resolved, we don't need a creo book to learn about them- the scientists know them, they're facing them every day.
Quote
To my knowledge, the only serious rebuttal was from a talk origins contributor who didn't have the required expertise, and presented a flawed criticism that another poster (a non-creationist, by the way) had to debunk.

I don't know about this rebuttal you speak of- I simply do ont think any "rebuttal" is necessary. From what I've read, this book does not give any valid, fundamental reasons why abiogenesis  cannot possibly work: Its author presents the thermodynamic hurdles, spending quite some time in them, and concludes that a "coupling mechanism" is needed -something accepted by scientists already (see here for instance). In fact, this mechanism (mineral catalysis, authocatalysation process, photocatalysis, combinations of those) is the very thing they are looking for.
The rest of his argument is basically "since they didn't reproduce it yet in the lab, it does not exist". See the conclusion of the last chapter. Same old, same old.

Quote
Basically, I think serious efforts from creationists need to be addressed, because this encourages better dialogue on their part. Ignoring serious work makes us look cowardly IMHO.

Of course they need to be addressed, when they are presented. Do you think "No point in looking for it, you should have already found it" is a serious argument, Ghost? If that is the case, then why are you not convinced too, and disbelieve in abiogenesis, in contrast to what you said before?


As for appearing "cowardly" when we don't address their blabber... Come on. We're talking creationists here. How can anyone appear cowardly to people who are so spineless, they have to deny reality for fear that their faith will crumble?


:p

--------------
A look into DAVE HAWKINS' sense of honesty:

"The truth is that ALL mutations REDUCE information"

"...mutations can add information to a genome.  And remember, I have never said that this is not possible."

  
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Dec. 06 2006,20:56   

Faid:

 
Quote
From what I've read, this book does not give any valid, fundamental reasons why abiogenesis  cannot possibly work: Its author presents the thermodynamic hurdles, spending quite some time in them, and concludes that a "coupling mechanism" is needed -something accepted by scientists already (see here for instance). In fact, this mechanism (mineral catalysis, authocatalysation process, photocatalysis, combinations of those) is the very thing they are looking for.


Correct. To further the discussion, here are a few of the book's objections:

   
Quote
Mineral Catalysis

Mineral catalysis is often suggested as being significant in prebiotic evolution. In the experimental investigations reported in the early 1970's15 mineral catalysis in polymerization reactions was found to operate by adsorption of biomonomers on the surface or between layers of clay. Monomers were effectively concentrated and protected from rehydration so that condensation polymerization could occur. There does not appear to be any additional effect. In considering this catalytic effect of clay, Hulett has advised, "It must be remembered that the surface cannot change the free energy relationships between reactants and products, but only the speed with which equilibrium is reached."16

Is mineral catalysis capable of doing the chemical work and/or thermal entropy work? The answer is a qualified no. While it should assist in doing the thermal entropy work, it is incapable of doing the chemical work since clays do not supply energy. This is why successful mineral catalysis experiments invariably use energy-rich precursors such as aminoacyl adenylates rather than amino acids.17

Is there a real prospect that mineral catalysis may somehow accomplish the configurational entropy work, particularly the coding of polypeptides or polynucleotides? Here the answer is clearly no. In all experimental work to date, only random polymers have been condensed from solutions of selected ingredients. Furthermore, there is no theoretical basis for the notion that mineral catalysis could impart any significant degree of information content to polypeptides or polynucleotides. As has been noted by Wilder-Smith,18 there is really no reason to expect the low-grade order resident on minerals to impart any high degree of coding to polymers that condense while adsorbed on the mineral's surface. To put it another way, one cannot get a complex, aperiodic-sequenced polymer using a very periodic (or crystalline) template.

In summary, mineral catalysis must be rejected as a mechanism for doing either the chemical or configurational entropy work required to polymerize the macromolecules of life. It can only assist in polymerizing short, random chains of polymers from selected high-energy biomonomers by assisting in doing the thermal entropy work.


 
Quote
Chemical Energy (Energy-Rich Precursors)

Because the formation of even random polypeptides from amino acids is so energetically unfavorable (G = 300 kcal/mole for 100 amino acids), some investigators have attempted to begin with energy-rich precursors such as HCN and form polypeptides directly, a scheme which is "downhill" energetically, i.e., G < 0. There are advantages to such an approach; namely, there is no chemical work to be done since the bonding energy actually decreases as the energy-rich precursors react to form more complex molecules. This decrease in bonding energy will drive the reaction forward, effectively doing the thermal entropy work as well. The fly in the ointment, however, is that the configurational entropy work is enormous in going from simple molecules (e.g., HCN) directly to complex polymers in a single step (without forming intermediate biomonomers).

The stepwise scheme of experiments is to react gases such as methane, ammonia, and carbon dioxide to form amino acids and other compounds and then to react these to form polymers in a subsequent experiment. In these experiments the very considerable selecting-work component of the configurational entropy work is essentially done by the investigator who separates, purifies, and concentrates the amino acids before attempting to polymerize them. Matthews39 and co-workers, however, have undertaken experiments where this intermediate step is missing and the investigator has no opportunity to contribute even obliquely to the success of the experiment by assisting in doing the selecting part of the configurational entropy work. In such experiments-undoubtedly more plausible as true prebiotic simulations-the probability of success is, however, further reduced from the already small probabilities previously mentioned. Using HCN as an energy-rich precursor, and ammonia as a catalyst, Matthews and Moser40 have claimed direct synthesis of a large variety of chemicals under anhydrous conditions. After treating the polymer with water, even peptides are said to be among the products obtained. But as Ferris et al.,41 have shown, the HCN polymer does not release amino acids upon treatment with proteolytic (protein splitting) enzymes; nor does it give a positive biuret reaction (color test for peptides). In short, it is very hard to reconcile these results with a peptidic structure.

Ferris42 and Matthews43 have agreed that direct synthesis of polypeptides has not yet been demonstrated. While some peptide bonds may form directly, it would be quite surprising to find them in significant numbers. Since HCN gives rise to other organic compounds, and various kinds of links are possible, the formation of polypeptides with exclusively alpha-links is most unlikely. Furthermore, no sequencing would be expected from this reaction, which is driven forward and "guided" only by chemical energy.

While we do not believe Matthews or others will be successful in demonstrating a single step synthesis of polypeptides from HCN, this approach does involve the least investigator interference, and thus, represents a very plausible prebiotic simulation experiment. The approach of Fox and others, which involves reacting gases to form many organic compounds, separating out amino acids, purifying, and finally polymerizing them, is more successful because it involves a greater measure of investigator interference. The selecting portion of the configurational entropy work is being supplied by the scientist. Matthew's lack of demonstrable success in producing polypeptides is a predictable indication of the enormity of the problem of prebiotic synthesis when it is not overcome by illegitimate investigator interference.


One note of optimism as far as HCN concentration levels are concerned.

Here's Moritz's summary:

 
Quote
In any case, minerals most likely provide the clue to a lot of the answers regarding the origin of life. They have been demonstrated to allow for the prebiotic synthesis of nucleotide precursors that have so far proven elusive, for example, the synthesis of ribose in sufficient purity – borate minerals stabilize ribose (Ricardo, A et al. 2004; see also press release; however, for a possible stereoselective synthesis of D-ribose catalyzed by amino acids, see below). Minerals have also been shown to catalyze polymerization of nucleotide-like molecules (Orgel 2004). Vesicle formation is aided by them as well, and mineral particles could have wound up inside vesicles and there exhibited catalytic properties (Hanczyc et al. 2003, Hanczyc et al. 2006).

In a different putative scenario, minerals also play an interesting role. Instead of in an aqueous "prebiotic soup" on or near the surface of the earth, it has been hypothesized that life may have begun in the depths of the ocean, in the unique environment of deep-sea hydrothermal vents. In high-pressure, high-temperature water as there, organic molecules show a level of (albeit not always particularly specific) chemical reactivity that is usually observed in "normal" aqueous environments only upon speeding-up of reaction rates by enzymes. See for example the review Hazen et al. 2002. For the physico-chemical properties of high-pressure, high-temperature water, see Basset M-P 2003 and Gen-e-sis: 1. Catalysis by minerals, such as those present in deep-sea hydrothermal vents, further enhances chemical reactions in such an aqueous environment. Degradation under these high-temperature and high-pressure conditions of synthesized organic molecules may be prevented by minerals as well – at least this has been shown for amino acids (see Hazen et al. 2002). Fatty acids, as a source of membrane-forming material, might have been synthesized there too (see Orgel 2004).


The bolded & italicised part doesn't address the book's concerns with configurational entropy. This source seems to agree:

 
Quote
Initial studies using thermal energy (heat) to drive the formation of polynucleotides and polypeptides from monomers were only marginally successful even if they were carried out in the absence of water. Polymer formation in the presence of water is a more plausible prebiotic scenario since it is likely that water was prevalent on the primitive Earth. Therefore, the only way to prepare RNA or proteins in the presence of water is to supply the required energy to "active" them (to change the structure by adding a reactive group) thus making polymer bond formation more favorable. While current theories suggest that RNA or protein was involved in early life, scientists have yet to provide a feasible explanation for how the individual activated monomers would have been formed on the early Earth.


I'm no chemist by any means, so any assistance is appreciated.

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Dey can't 'andle my riddim.

  
pwe



Posts: 46
Joined: Sep. 2006

(Permalink) Posted: Dec. 07 2006,07:54   

Quote (The Ghost of Paley @ Dec. 06 2006,16:09)
The best creationist critique of abiogenesis is The Mystery of Life's Origin, but most of the references are seriously out of date. Nevertheless, it outlines many of the physical hurdles that any scenario must overcome. As far as I know, no one has successfully rebutted it.

Well, I have read some chapters of the book, and for a layman like me, they appear to point at real problems. But then again, I am a layman, so what do I know?

And the book is hosted by Lambert Dolphin, who claims that the 2nd Law of Thermodynamics was part of the curse of the creation caused by Adam and Eve's eating of the forbidden fruit. And that the expansion of the universe is due to rebellious angels that abandoned their job of keeping the stars in place.

So, basically we are given the choice of still accepting prebiotic evolution or giving in to complete make-believe.


- pwe

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 07 2006,08:49   

All,

1) I am unwilling to be drawn into a troll distraction and dishonesty game, which this surely is. Since this is my field I will make this one comment.

If anyone else wants to start a seperate thread on possible abiogenesis mechanisms in which the troll is not permitted to comment then I'm more than willing to join in. I'm not playing with mindless trolls any more. I am totally unwilling to provide the education in basic chemistry that the troll lacks, not least because I cannot be bothered with endless quote mining and google trawling from someone who has neither the knowledge or ability to understand the subject. Honest enquiry is a good thing, dishonest trolling, baiting and attention whoring isn't.

2) The creationist second law of thermodynamics claims are the usual baseless creationist red herrings, bullshit and baloney. Don't believe the hype! One factor that creationists always ignore when invoking the second law of thermodynamics in chemical systems is that they are dealing with open systems. Bond forming processes normally involve the release of energy, usually (although by no means exclusively) as electromagnetic radiation in the IR region of the spectrum. In the creationist canard, as the entropy of the system decreases by bonding (which is bullshit anyway, polymers have vastly greater degrees of freedom than their component monomers for example) they omit the comensurate increase of entropy of the overall system.  There is no thermodynamic barrier to abiogenesis in general any more than there is a thermodynamic barrier to chemical bonding in general. The problem isn't that we don't know how abiogenesis COULD happen, but that we don't know how it DID happen.

The book cited by the troll has no merit and never had merit or any sting to retain. Thraxton and buddies were talking out of their arses in the 70s and still are. The objection is basically: "because we don't know the exact path taken, it's impossible", all the bloviating about polymerisation not being possible on crystal surfaces etc was bollocks disproven by decades of surface science research before the book was even written. There's little point "rebutting" lies and distortions.

3) Yes we have well known mechanisms for all possible stages of abiogenesis, what we don't know is which of a massive variety of possible routes to self replicating systems (the key intermediate needed for an evolutionary scenario) were taken. We also don't know for certain what the Ur-replicator was. It certainly wasn't anything as "advanced" as DNA, or possibly RNA, although this latter is a possible candidate for a variety of reasons. Key mechanisms for abiogenesis involve polymerisation,  encapsulation, auto-catalysis, mutually coupled replicating systems, self replicating systems and a whole host of other properties exhibited by naturally occuring molecules both on earth and even in some cases in space.

4) There are a huge variety of astrochemicals of varying degrees of complexity. Some of the most vital molecules, such as simple sugars, simple amino acids and aromatic hydrocarbons, all key monomers for known chemical systems in living systems, are found in space. There are even some dipeptides etc found in interstellar ices etc. As for the origins of homochirality, one need look no further than autocatalysis and perhaps circular dichroism. The Soai reaction, for example, whilst not even suggested as a point on the abiogenetic pathway, is a good example of a simple system in which chiral products are produced from achiral strating materials and in which the products autocatalyse not only their own formation but also which enantiomer of product is produced. This is a fascinating reaction to explore btw. The understanding of chelation, mixing effects and a whole host of chemical processes involved is not for the faint hearted. Or indeed anyone wiithout a serious amount of undergraduate and postgraduate organic chemistry in their heads I'm sad to say. Which is annoying because it's a great little reaction!

5) Some groups/work I can think of off the top of my head that those with a chemical bent might want to check out are the Rebek group at Scripps (although his work in self replication is a few years old now), Nigel Mason's group at the Open University UK, John Brown's group at Oxford, obviously Leslie Orgel's work, Donna Blackmond at Imperial (I think she's still there, amazing lady, every time I see her lecture I am in awe of how dedicated and bloody smart she is). A great but relatively obscure journal "The Origins of Life and the Evolution of Biospheres" is also an interesting read, mainly because it's surprisingly philosophical and non-technical in places.

Argh huge field, too much to even begin to encompass in anything approaching the detail required.

Louis

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Bye.

  
Russell



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(Permalink) Posted: Dec. 07 2006,09:05   

Quote
The best creationist critique of abiogenesis is The Mystery of Life's Origin
If you're interested in the topic, why start out with a creationist critique? These guys are completely discredited and unreliable. Why not start with something like Robert Shapiro's "Origins: a skeptic's guide to creation of life on earth"?

(Disclaimer: I haven't read either of these; Shapiro is "on my list", the other one isn't)

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Must... not... scratch... mosquito bite.

  
Alan Fox



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(Permalink) Posted: Dec. 07 2006,11:13   

It's a shame Professor Shapiro was so roundly insulted when he made an appearance on PT a while back. i thought he was a real nice guy. BTW I'd link to the thread but the PT arguments thingie doesn't work like it used to. What's with that?

  
The Ghost of Paley



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Joined: Oct. 2005

(Permalink) Posted: Dec. 07 2006,11:57   

Before discussing this issue further, I'd like to make a few points:

1) Mel is right when he says that I could use a few chemistry lessons. That's part of what this thread is about: (1) what is the current status of abiogenesis research (available in books, journals, and perhaps online), and (2) have the arguments in Mystery been addressed in the literature (difficult for nonspecialists to answer)? For example, do mineral substrates have organisational in addition to catalytic ability, and if they do, is it enough to code nonrandom polymers? A specialist might be able to answer this question. So I don't think this thread is pointless, because we can all learn a little bit about the subject.

2) Despite what Mel would have you believe, I really am willing to listen to good explanations. Rhetoric, insults, and "that's been answered in the literature, but I won't show you where" don't count as good explanations. This is one reason that I'm glad that Louis is not participating, because he's not going to give a straight answer to anything I ask. Please keep in mind that Charles Thaxton has a doctorate in physical chemistry, while Walter Bradley has a doctorate in materials science, so one can't dismiss their opinions and calculations with hand-waving.

3) Mel doesn't get to choose who comments in which threads.

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Dey can't 'andle my riddim.

  
Mr_Christopher



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(Permalink) Posted: Dec. 07 2006,12:54   

Here is a better question:

What is the status of God research? Have plausible mechanisms been found for each of the major steps?  Obviously God could not just appear out of thin air.  You don't get something from nothing.

So what's the latest research on rescuing deities?  How could "he" have come to exist?  And what matter is he made up of?  

Bonus question, since the universe is billions of years old, and mankind has only been around for 10s of thousands of years (and the NFL has only been around for less than 100 years) what did God do to occupy his time for all those billions of years prior to mankind.

All productive criticism is appreciated.

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Uncommon Descent is a moral cesspool, a festering intellectual ghetto that intoxicates and degrades its inhabitants - Stephen Matheson

  
Mr_Christopher



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(Permalink) Posted: Dec. 07 2006,13:02   

Think about it peeps, lifes "origin" didn't start at the first cell.  It started at the "emergence" of the first deity.  So identifying the deity (that dude who created life) is ground zero.

So like I was saying, what is the status of God research?

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Uncommon Descent is a moral cesspool, a festering intellectual ghetto that intoxicates and degrades its inhabitants - Stephen Matheson

  
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Dec. 07 2006,13:52   

Quote (Mr_Christopher @ Dec. 07 2006,13:02)
Think about it peeps, lifes "origin" didn't start at the first cell.  It started at the "emergence" of the first deity.  So identifying the deity (that dude who created life) is ground zero.

So like I was saying, what is the status of God research?

I think that might be a typo. Didn't you mean "Ditty" as in " the music of the spheres"?

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Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
The Ghost of Paley



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(Permalink) Posted: Dec. 07 2006,14:28   

I read somewhere that the difference between science and an ideology is that a science can answer a question like, "What evidence do you have for your position?" without resorting to jokes, insults and tu quoque retorts.

Does anyone have anything to offer than one of the above?

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Dey can't 'andle my riddim.

  
Ved



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(Permalink) Posted: Dec. 07 2006,14:37   

No.

  
Mr_Christopher



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(Permalink) Posted: Dec. 07 2006,14:52   

Quote (The Ghost of Paley @ Dec. 07 2006,14:28)
I read somewhere that the difference between science and an ideology is that a science can answer a question like, "What evidence do you have for your position?" without resorting to jokes, insults and tu quoque retorts.

Does anyone have anything to offer than one of the above?

Can you tell us what the status is on the God research?  
And you do see how the origin of life did not begin on planet Earth.  It began with God and then He created Earth and the little cells and stuff.  

So...Before we can answer how did Earth life begin, we must answer how did God begin.  

So...How is the God research coming along?  The bible clearly tells us what his mental state is (jealous, irritable, angry, two faced, dishonest, murderous, cruel, clearly NOT a good example for children)  But has anyone come up with a theory regarding what God might be made of.   I'm talking chemistry and biology here, peeps.  Does God have DNA or?

Paley, I believe this is your realm of expertise, no?  What is God comprised of, please.  At least what does the most recent scientific research suggest?

Thanks!

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Uncommon Descent is a moral cesspool, a festering intellectual ghetto that intoxicates and degrades its inhabitants - Stephen Matheson

  
The Ghost of Paley



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Joined: Oct. 2005

(Permalink) Posted: Dec. 07 2006,15:18   

Mr_Christopher:

 
Quote
Can you tell us what the status is on the God research?  
And you do see how the origin of life did not begin on planet Earth.  It began with God and then He created Earth and the little cells and stuff.  


How convenient. According to you, origin of life researchers don't have to answer the tough questions. All they have to say is, "Well, God isn't much of an explanation either!"

So not only does this field have the answers, it doesn't even have to sweat the questions. So when do I get a tax break?  :angry:

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Dey can't 'andle my riddim.

  
tiredofthesos



Posts: 59
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(Permalink) Posted: Dec. 07 2006,15:29   

Since he has no entertainment value, I cannot fathom why anyone responds to anything GOP says except to, out of simple courtesy, remind him once again that he's a dishonest and pretentious ass who is completely full of shit.

 GOP!  You are COMPLETELY full of shit! :)

  
Mr_Christopher



Posts: 1238
Joined: Jan. 2006

(Permalink) Posted: Dec. 07 2006,15:41   

Quote (The Ghost of Paley @ Dec. 07 2006,15:18)
Mr_Christopher:

   
Quote
Can you tell us what the status is on the God research?  
And you do see how the origin of life did not begin on planet Earth.  It began with God and then He created Earth and the little cells and stuff.  


How convenient. According to you, origin of life researchers don't have to answer the tough questions. All they have to say is, "Well, God isn't much of an explanation either!"

So not only does this field have the answers, it doesn't even have to sweat the questions. So when do I get a tax break?  :angry:

What?

You still have not answered my questions.

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Uncommon Descent is a moral cesspool, a festering intellectual ghetto that intoxicates and degrades its inhabitants - Stephen Matheson

  
Dr.GH



Posts: 2113
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(Permalink) Posted: Dec. 07 2006,15:57   

The best book for general readers currently available is still;

Iris Fry,
2000 "The Emergence of Life on Earth: A Historical and Scientific Overview" Rutgers University Press

It really needs to be updated because the last 7 years have been more productive for OOL than the prior 20.

Old earth creationists Rana and Ross have a book out on OOL.  I have a critical review in the stack which should be published by NCSE in a month or two.  R&R set as one of their goals to update "The Mystery of Life’s Origin" (1984).  They needn't have bothered.

Edited by Dr.GH on Dec. 07 2006,15:58

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Faid



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(Permalink) Posted: Dec. 07 2006,16:30   

Quote (The Ghost of Paley @ Dec. 07 2006,14:28)
I read somewhere that the difference between science and an ideology is that a science can answer a question like, "What evidence do you have for your position?" without resorting to jokes, insults and tu quoque retorts.

Does anyone have anything to offer than one of the above?

As opposed to what, Ghost?

Like I explained (and you agreed) there is no conflict here. Everyone agrees that the origins of life have not been discovered yet, and that research is underway. The creationist arguments of "since you haven't found it, you will never find it", are ridiculous, as I'm sure you agree... So, what's the point of this? The only meaningful debate we can have on this issue is on which method seems more promising, and on the latest research on the field (I would be interested to know about that myself, if anyone has the info).
Oh... And laugh at creationists, of course. :)

--------------
A look into DAVE HAWKINS' sense of honesty:

"The truth is that ALL mutations REDUCE information"

"...mutations can add information to a genome.  And remember, I have never said that this is not possible."

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 07 2006,16:37   

Quote
Does anyone have anything to offer than one of the above?


Yes. But those of us who do are tired of casting pearls before swine

Louis

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Bye.

  
The Ghost of Paley



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Joined: Oct. 2005

(Permalink) Posted: Dec. 07 2006,16:57   

Louis:

Quote
Quote
 
Does anyone have anything to offer than one of the above?



Yes. But those of us who do are tired of casting pearls before swine


I doubt you have anything to offer. I'm looking for straight answers, and you've always been short of those. Perhaps someone like this guy can shed some light.

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Dey can't 'andle my riddim.

  
ericmurphy



Posts: 2460
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(Permalink) Posted: Dec. 07 2006,17:56   

Quote (The Ghost of Paley @ Dec. 07 2006,15:18)
How convenient. According to you, origin of life researchers don't have to answer the tough questions. All they have to say is, "Well, God isn't much of an explanation either!"

I think you're missing the point, Bill, and I think Mr. C does make a good point here.

Creationists often take abiogenesis researchers to take because they haven't resolved all the riddles of how life could have arisen from non-life in an environment vastly different form anything on earth today, at a time billions of years in the past. It's almost as if creationists think any question science cannot at present answer is a win for their side.

Meanwhile, creationists not only don't have a single answer (other than the ever-popular "goddidt"), or even reasonable guess, for how life came to exist on earth; they don't have a single answer for how God (or any variety of "intelligent designer") could have caused life to spring into being, to say nothing of all the unanswered questions about the nature of God (or said "intelligent designers") itself. Or themselves.

One of my biggest problems with creationism and intelligent design is that they don't provide any answers that the conventional theories don't already provide. Intelligent design, as far as I can determine from its own proponents, is a claim that life is too complex to have arisen by unintelligent means. Okay, fine. Let's say, arguendo, that we grant that claim. Now, where does that leave us? Does it get any closer to an understanding of how life arose? No. I think it gets us further from an understanding, because now we not only have to try to figure out whatever methods God (or unnamed "intelligent designer") used; we also have to make some determinations as to the nature of that God (or "intelligent designer"). No naturally curious person is going to be satisfied with no knowledge whatsoever about that first cause, are they? I know I'm not.

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Mr_Christopher



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(Permalink) Posted: Dec. 07 2006,18:12   

No more Mr Nice Guy from me!  

Quit acting like a snotty nosed, bratty, spoiled  little girl, Paley and tell us about the state of the current God research. Have they discovered him yet?  What is he comrised of?

How can ANYONE suggest God created the heavens and man when we haven't even discovered God?  I thought this was the subject you knew something about.  God?

I mean even you will admit to say God did ANYTHING without first having discovered God or at least having a solid scientific theory on God would be absolutely stupid beyond belief.  You're a smart guy so I know we can agree on that, Paley.

So, where are we in our quest to discover God?  This is important stuff!  Has science found him yet?  Do we even have a coherant and scientific God theory?  What the #### do you think he must be made of?  Carbon based or?

Good God man, answer my questions and stop playing opposum!

Chris

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skeptic



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(Permalink) Posted: Dec. 07 2006,18:42   

GoP, I heard a valid question even though the others missed it their hurry to be the first with a witty insult.

What is the status of abiogenesis?

The truth is it's no where at this point.  Louis is right in the sense that there are multitudes of possible mechanisms that can not be proven to have been involved but sure look interesting.

For me the big question still and always will remain how did the transition occur?

RNA -> protein -> DNA,
protein -> RNA -> DNA,
primitive molecule -> RNA, Protein -> DNA,
etc and so forth

The ability to produce precursors and amino acids or simple sugars in controled experiments get us no closer to understanding what really happened.  Maybe the best we can hope for is some potential scenarios that may give a comprehensive picture and to accept it and move on.  Certainly not very satisfing but it might be the only realistic solution.

  
The Ghost of Paley



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(Permalink) Posted: Dec. 07 2006,18:44   

eric:

     
Quote
One of my biggest problems with creationism and intelligent design is that they don't provide any answers that the conventional theories don't already provide. Intelligent design, as far as I can determine from its own proponents, is a claim that life is too complex to have arisen by unintelligent means. Okay, fine. Let's say, arguendo, that we grant that claim. Now, where does that leave us? Does it get any closer to an understanding of how life arose? No. I think it gets us further from an understanding, because now we not only have to try to figure out whatever methods God (or unnamed "intelligent designer") used; we also have to make some determinations as to the nature of that God (or "intelligent designer"). No naturally curious person is going to be satisfied with no knowledge whatsoever about that first cause, are they? I know I'm not.


OK, your point explains why theistic explanations bore scientists. I understand that. Heck, I even understand why people question my motives. I'm just surprised that no one's interested in exploring how close science is to a theory of life's origins. Personally, I don't care what the ID "explanation" is, and have no interested in God talk on this issue. Nevertheless, Thaxton and Bradley (despite their extensive biases) bring up some interesting points that are worth discussing IMHO. Why can't you guys look past your dislike for creationists for a second and use their criticisms as a springboard for a fruitful discussion? I'll admit that these guys could be full of crap -- perhaps they're using their expertise to snow laymen like myself. Heck, even if the book was honest and relevant for its time, modern research might very well have rendered their core objections obsolete. If so, great -- we all learn a little bit about the current evidence. If not -- well, the theistic explanation will still be vapid. Sounds like a win-win to me.

Christopher:

 
Quote
No more Mr Nice Guy from me!  

Quit acting like a snotty nosed, bratty, spoiled  little girl, Paley and tell us about the state of the current God research. Have they discovered him yet?  What is he comrised of?


I think that the latest discoveries in physics argue for a God who fine-tuned the universe. Beyond that, I have no idea.

See. The sky didn't fall in, now did it? Now quit being a pussy and discuss the actual topic of this thread. I promise your dink won't curl up and die.  ;)

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The Ghost of Paley



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(Permalink) Posted: Dec. 07 2006,19:16   

Skeptic:

 
Quote
For me the big question still and always will remain how did the transition occur?

RNA -> protein -> DNA,
protein -> RNA -> DNA,
primitive molecule -> RNA, Protein -> DNA,
etc and so forth

The ability to produce precursors and amino acids or simple sugars in controled experiments get us no closer to understanding what really happened.  Maybe the best we can hope for is some potential scenarios that may give a comprehensive picture and to accept it and move on.  Certainly not very satisfing but it might be the only realistic solution.


I agree. I think there's a big piece missing from the puzzle. What do you think about the PNA "world"? This model might bridge a few gaps.

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Russell



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(Permalink) Posted: Dec. 07 2006,19:39   

Quote
OK, your point explains why theistic explanations bore scientists. I understand that. Heck, I even understand why people question my motives. I'm just surprised that no one's interested in exploring how close science is to a theory of life's origins.
I'm very interested. Fascinating topic. I love to ponder it in my spare time. And I'm grateful that the world has seen fit to fund this question to the extent that it has, given the fact that progress in the field, such as it is, is not going to cure baldness or make anyone rich. But I'm afraid that I'm just going to have to accept the likelihood that no one's going to have anything better than a vague, plausible-if-we're-lucky guess before my life is through.

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ericmurphy



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(Permalink) Posted: Dec. 07 2006,21:52   

Quote (The Ghost of Paley @ Dec. 07 2006,18:44)
I'm just surprised that no one's interested in exploring how close science is to a theory of life's origins. Personally, I don't care what the ID "explanation" is, and have no interested in God talk on this issue. Nevertheless, Thaxton and Bradley (despite their extensive biases) bring up some interesting points that are worth discussing IMHO. Why can't you guys look past your dislike for creationists for a second and use their criticisms as a springboard for a fruitful discussion? I'll admit that these guys could be full of crap -- perhaps they're using their expertise to snow laymen like myself. Heck, even if the book was honest and relevant for its time, modern research might very well have rendered their core objections obsolete. If so, great -- we all learn a little bit about the current evidence. If not -- well, the theistic explanation will still be vapid. Sounds like a win-win to me.

I'm no expert on abiogenetic theories (to put it mildly), but I would say those theories are probably more advanced than, e.g., superstring theories or loop quantum gravity. I.e., as Louis pointed out, there are several methods that seem adequate to at least get self-catalyzing reactions going, and there are several candidates for self-replicators. Meanwhile, superstring theories cannot even seem to make any predictions as to things like particle masses.

Again, given that we're discussing events over a billion years in the past, it seems doubtful that anyone will ever be able to determine exactly which mechanisms initially got life started started on earth, but there are plenty of potential candidates. There doesn't seem to be any obstacle to life having arisen on earth without the need to invoke supernatural agency.

Seems like a decent-enough start to me.

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"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 08 2006,06:28   

Quote (The Ghost of Paley @ Dec. 07 2006,18:44)
Why can't you guys look past your dislike for creationists for a second and use their criticisms

"Their" criticisms?  **"THEIR"** criticisms??????  

ID/creationists don't HAVE any "criticisms".  Indeed, they have nothing at all whatsoever original to say on the subject.  The best they can do is parrot OTHER PEOPLE'S CRITICISMS, and add "therefore godiddit".

All of the arguments and questions regarding abiogenesis come from scientists who are working in the field.

None of them come from creationists or IDers (who, by the way, are NOT working in the field).

It is also scientists who are working in the field that are carrying out the research towards answering those questions.

ID/creationists, on the other hand, aren't doing dick.

Therefore there simply is no reason to listen to ID/creationists.  They add nothing.  Nothing at all whatsoever.

(shrug)

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Louis



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(Permalink) Posted: Dec. 08 2006,09:48   

Lenny,

I've been debating whether to comment or not for a variety of reasons, not least of which is that I'm fecking busy and cannot be arsed with (as I said) casting pearls before swine like the troll. The whole reason that pursuing this thread with the troll is worthless is because it is, yet again, an attempt to play silly buggers. Even when pretending to be reasonable the troll shows his true colours and thus fails.

What's the reason we've been given by the troll for taking the comments of Thraxton and chums seriously? Because they have PhDs in chemistry? So what? I have a PhD in chemistry and you'll note the troll's lack of keenness to accept my (or indeed any non creationist's) work or word in any fashion, especially in anything remotely like the way they accept the faux critique of people who agree with them. You'll note btw they often project this illogic onto others, as if the whole world thinks like they do. It's fascinating psychologically.

The whole argument from the creationists and the troll is the usual non sequitur: "I personally find something significant/insiginificant (dependant on the situation) and thus any comments that may reinforce my pre-existing conclusions are worth consideration". Look at the poncing about with regards to fine tuning as a great example. The argument amounts to no more than "LOOOK LOOOOOK!!!! It's SO significant!" covered up with phoney probability calculations and obfuscatory use of jargon they rarely understand. The Thraxton book is a joke, was a joke when it was published, and will remain a joke. Amusingly in complaining that scientists use techinical terms and owe them explanations the trolls and creobots of this world demonstrate a laudible skepticism. Unfortunately this skepticism seems only directed against those with whom they are precommitted to disagree, which is laess laudible. This of course is projected as well. Ah sweet irony.

Further evidence that this is yet another pointless gambit in the troll's game of being an annoying tit is the responses we're getting. When any reluctance to discuss any topic is expressed, based on the demonstrated and well recorded trolling behaviour exhibited, we get fake umbrage and insinuation (I'm shocked no one wants to  discuss this,implying that there must be some hidden problem), ridiculous bravado (you are incapable of answering the comments of creationists), and the usual obfuscation (this is about your dislike for creationists).

Another point to note is that it is assumed by the troll that the creationists have some genuine criticisms which need answering when they don't (as any tiny quantity of knowledge of the subjects in hand demonstrates). Also of note is the fact that, despite calling the troll's behaviour as it is (which is a distraction from any scientific topic other than aberrant psychology), there have been examples of key mechanisms and pointers to the lit and groups working in the area from both myself  and Dr GH and these have been ignored. Yet another data point in evidence that this is another troll bullshit saga.

Oh and whilst I think of it, if anyone has access (I do but no point posting a link because it requires payment of about $170 for non subscribers) there's a recent special issue of Phil Trans R Soc B on OOL research. There's also a technical conference in Florence next year (I think might be 2008, I've signed up but don't have the details to hand) for those interested. Check the ISSOL website (www.issol.org) for details.

This is why I've said that the best forum to discuss this interesting topic in is one troll free, which means the troll that started this thread is not able to join in. The troll seems ignorant of the fact that, as you pinted out, it isn't the creationists that have valid questions and critiques regarding any scientific field let alone this one, it's the people working in it.

For example, one criticism of OOL research I have is there's too many biologists! The OOL is a chemical problem, as indeed is the origin and operation of the cell. But I'm not greedy I'll let the bacteria bashers have a go! Ok so that's slightly tongue in cheek, but there is a serious point. We have all the mechanisms necessary for self replicating, replicator/effector and cellular chemical systems to evolve very well understood. That's not the problem. The problem is, in a sense a synthetic chemistry problem. We know reactions that have worked on similar chemical substrates to give products like those desired but we haven't done the synthesis on the system we really want, only on these models. We even know that some of the substrates we want are available to us in nature. With abiogenesis we have this slightly backwards, we still know all the reactions and where the substrates are, but we don't yet know what we're trying to make. To a synthetic chemist this is a bit of an interesting one because the one thing we usually do know is what we're trying to make! But I digress.

When discussing PNA world vs RNA world etc what's the point when people don't know the structures or chemistry of the molecules? Or how common the monomeric elements are in space/nature? Or even what the structural aspects mean? The problem is that this type of chemistry doesn't easily lend itself to colloquial discussion at a non technical level. At a technical level it's great. The answers to the troll's original questions are, as I've already said, "excellent", "yes", and "of course they are. That question is a non sequitur and exposes both the ignorance of the questioner and the dishonesty of those who try to obfuscate the issue". As mentioned before the entropy angle is a standard creationist red herring. Just like the "information" challenge. It's the sort of question which annoys rather than interests or informs because it's based either on ignorance or dishonesty. Of course when this is mentioned we get the revealing comments from the troll/creobot. Ignorance is not a problem, in fact of anyone had a problem with ignorance we'd be shooting undergrads at the start of term. Willful ignorance is a different bag.

Lenny, you ask an excellent question. On what basis does the troll think that the comments of creationists like Thraxton have any merit at all? Why does the troll think that scientists owe him an answer or Thraxton's nonsense anything other than the annoyed contempt it deserves? Why do creationist lies seem to get a "by" when it comes to these discussions with the troll?

I imagine the answers, or indeed the evasion of them I expect, will be illuminating.

Louis

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BWE



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(Permalink) Posted: Dec. 08 2006,11:39   

Quote (Louis @ Dec. 08 2006,09:48)
Lenny,

The whole argument from the creationists and the troll is the usual non sequitur: "I personally find something significant/insiginificant (dependant on the situation) and thus any comments that may reinforce my pre-existing conclusions are worth consideration".
[snip]
The Thraxton book is a joke, was a joke when it was published, and will remain a joke. Amusingly in complaining that scientists use techinical terms and owe them explanations the trolls and creobots of this world demonstrate a laudible skepticism. Unfortunately this skepticism seems only directed against those with whom they are precommitted to disagree, which is laess laudible. This of course is projected as well. Ah sweet irony.

...we get fake umbrage and insinuation (I'm shocked no one wants to  discuss this,implying that there must be some hidden problem), ridiculous bravado (you are incapable of answering the comments of creationists), and the usual obfuscation (this is about your dislike for creationists).

Another point to note is that it is assumed by the troll that the creationists have some genuine criticisms which need answering when they don't (as any tiny quantity of knowledge of the subjects in hand demonstrates)...

...as you pinted out, it isn't the creationists that have valid questions and critiques regarding any scientific field let alone this one, it's the people working in it.

For example, one criticism of OOL research I have is there's too many biologists! ***screeeeech! no no, keep moving, there's nothing to see here*** The OOL is a chemical problem, as indeed is the origin and operation of the cell. But I'm not greedy I'll let the bacteria bashers have a go! Ok so that's slightly tongue in cheek, but there is a serious point. We have all the mechanisms necessary for self replicating, replicator/effector and cellular chemical systems to evolve very well understood. That's not the problem. The problem is, in a sense a synthetic chemistry problem. We know reactions that have worked on similar chemical substrates to give products like those desired but we haven't done the synthesis on the system we really want, only on these models. We even know that some of the substrates we want are available to us in nature. With abiogenesis we have this slightly backwards, we still know all the reactions and where the substrates are, but we don't yet know what we're trying to make. To a synthetic chemist this is a bit of an interesting one because the one thing we usually do know is what we're trying to make! But I digress.

When discussing PNA world vs RNA world etc what's the point when people don't know the structures or chemistry of the molecules? Or how common the monomeric elements are in space/nature? Or even what the structural aspects mean? The problem is that this type of chemistry doesn't easily lend itself to colloquial discussion at a non technical level. At a technical level it's great. The answers to the troll's original questions are, as I've already said, "excellent", "yes", and "of course they are. That question is a non sequitur and exposes both the ignorance of the questioner and the dishonesty of those who try to obfuscate the issue". As mentioned before the entropy angle is a standard creationist red herring. Just like the "information" challenge. It's the sort of question which annoys rather than interests or informs because it's based either on ignorance or dishonesty. Of course when this is mentioned we get the revealing comments from the troll/creobot. Ignorance is not a problem, in fact of anyone had a problem with ignorance we'd be shooting undergrads at the start of term. Willful ignorance is a different bag.

Lenny, you ask an excellent question. On what basis does the troll think that the comments of creationists like Thraxton have any merit at all? Why does the troll think that scientists owe him an answer or Thraxton's nonsense anything other than the annoyed contempt it deserves? Why do creationist lies seem to get a "by" when it comes to these discussions with the troll?

I imagine the answers, or indeed the evasion of them I expect, will be illuminating.

Louis

Louis,

That was a beautiful post.

Until I got to this part:    
Quote
too many biologists!
Yaaahhhggghhhh! Then I figured out that you didn't mean it globally as in "too many kittens" and I went back to reading.

Is there then, some differentiation of substrates at this point? Is there research that is creating some form of peptide based replicating compound? I mean, you don't know which compounds you are shooting for, wouldn't it make a difference? Are you looking at non enzymatic ligation systems and guessing at interesting ways to produce covalent bonds? That seems kind of random. How do you know which ones you want? Are you modeling these using software then I assume? I understand we are talking about the chemistry but you are assuming that you are going to try to create what? full-on RNA? A cell? Something that has been described biologically already? I think I am missing your point. Are you talking about engineering from a schematic which you can't read or needing to engineer one small part for a larger machine and you have no schematic for that part? Maybe more specifically, what are biologists doing that you would critisize as hindering or obfuscating?

Also, what is the current state of the art for PNA ligation? (I have never studied this in depth, although one of the labs we use does more normal DNA cloning and I am familiar with the methodology)

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The Ghost of Paley



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(Permalink) Posted: Dec. 08 2006,12:19   

BWE:

Quote
Louis,

That was a beautiful post.



Excellent! So now you're in a position to answer this question:

Is there experimental evidence or thermodynamic calculations in the literature that demonstrate that mineral catalysis can overcome the configurational entropy hurdles that Thaxton and Bradley mention? Or is there something wrong with their formulae? If there is, could you point out where they go wrong? Thanks.

Because I didn't see an answer in Louis's post.

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The Ghost of Paley



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(Permalink) Posted: Dec. 08 2006,12:45   

By the way, I keep hearing about how Mystery, a joke, etc. Well, if this is true, can someone give a specific example?

Here's where they discuss configurational entropy:

 
Quote
3. Configurational Entropy Work
Finally, we need to quantify the configurational entropy change (Sc) that accompanies the formation of DNA and protein. Here we will not get much help from standard experiments in which the equilibrium constants are determined for a polymerization reaction at various temperatures. Such experiments do not consider whether a specific sequence is achieved in the resultant polymers, but only the concentrations of randomly sequenced polymers (i.e., polypeptides) formed. Consequently, they do not measure the configurational entropy (Sc) contribution to the total entropy change (S). However, the magnitude of the configurational entropy change associated with sequencing the polymers can be calculated.

Using the definition for configurational "coding" entropy given in eq. 8-2c, it is quite straightforward to calculate the configurational entropy change for a given polymer. The number of ways the mass of the linear system may be arranged © can be calculated using statistics. Brillouin20 has shown that the number of distinct sequences one can make using N different symbols and Fermi-Dirac statistics is given by


= N!  (8-6)
If some of these symbols are redundant (or identical), then the number of unique or distinguishable sequences that can be made is reduced to



c = N! / n1!n2!n2!...ni!  (8-7)
where n1 + n2 + ... + ni = N and i defines the number of distinct symbols. For a protein, it is i =20, since a subset of twenty distinctive types of amino acids is found in living things, while in DNA it is i = 4 for the subset of four distinctive nucleotides.
A typical protein would have 100 to 300 amino acids in a specific sequence, or N = 100 to 300. For DNA of the bacterium E. coli, N = 4,000,000. In Appendix 1, alternative approaches to calculating c are considered and eq. 8-7 is shown to be a lower bound to the actual value.

For a random polypeptide of 100 amino acids, the configurational entropy, Scr, may be calculated using eq. 8-2c and eq. 8-7 as follows:



Scr = k lncr

since cr = N! / n1!n2!...n20! = 100! / 5!5!....5! = 100! / (5!;)20

= 1.28 x 10115  (8-8)
The calculation of equation 8-8 assumes that an equal number of each type of amino acid, namely 5, are contained in the polypeptide.
Since k, or Boltzmann's constant, equals 1.38 x 10-16 erg/deg, and ln [1.28 x 10115] = 265,



Scr = 1.38 x 10-16 x 265 = 3.66 x 10-14 erg/deg-polypeptide
If only one specific sequence of amino acids could give the proper function, then the configurational entropy for the protein or specified, aperiodic polypeptide would be given by



Scm = k lncm
= k ln 1
= 0
(8-9)
Determining scin Going from a Random Polymer to an Informed Polymer

The change in configurational entropy, Sc, as one goes from a random polypeptide of 100 amino acids with an equal number of each amino acid type to a polypeptide with a specific message or sequence is:



Sc = Scm - Scr

= 0 - 3.66 x 10-14 erg/deg-polypeptide
= -3.66 x 10-14 erg/deg-polypeptide  (8-10)
The configurational entropy work (-T Sc) at ambient temperatures is given by



-T Sc = - (298oK) x (-3.66 x 10-14) erg/deg-polypeptide
= 1.1 x 10-11 erg/polypeptide
= 1.1 x 10-11 erg/polypeptide x [6.023 x 1023 molecules/mole] / [10,000 gms/mole] x [1 cal] / 4.184 x 107 ergs

= 15.8 cal/gm  (8-11)
where the protein mass of 10,000 amu was estimated by assuming an average amino acid weight of 100 amu after the removal of the water molecule. Determination of the configurational entropy work for a protein containing 300 amino acids equally divided among the twenty types gives a similar result of 16.8 cal/gm.


In like manner the configurational entropy work for a DNA molecule such as for E. coli bacterium may be calculated assuming 4 x 106 nucleotides in the chain with 1 x 106 each of the four distinctive nucleotides, each distinguished by the type of base attached, and each nucleotide assumed to have an average mass of 339 amu. At 298oK:



-T Sc = -T (Scm - Scr)

= T ( Scr - Scm)

= kT ln (cr - lncm)

= kT ln [(4 x 106)! / (106)!(106)!(106)!(106)!] - kT ln 1

= 2.26 x 10-7 erg/polynucleotide

= 2.39 cal/gm  8-12
It is interesting to note that, while the work to code the DNA molecule with 4 million nucleotides is much greater than the work required to code a protein of 100 amino acids (2.26 x 10-7 erg/DNA vs. 1.10 x 10-11 erg/protein), the work per gram to code such molecules is actually less in DNA. There are two reasons for this perhaps unexpected result: first, the nucleotide is more massive than the amino acid (339 amu vs. 100 amu); and second, the alphabet is more limited, with only four useful nucleotide "letters" as compared to twenty useful amino acid letters. Nevertheless, it is the total work that is important, which means that synthesizing DNA is much more difficult than synthesizing protein.

It should be emphasized that these estimates of the magnitude of the configurational entropy work required are conservatively small. As a practical matter, our calculations have ignored the configurational entropy work involved in the selection of monomers. Thus, we have assumed that only the proper subset of 20 biologically significant amino acids was available in a prebiotic oceanic soup to form a biofunctional protein. The same is true of DNA. We have assumed that in the soup only the proper subset of 4 nucleotides was present and that these nucleotides do not interact with amino acids or other soup ingredients. As we discussed in Chapter 4, many varieties of amino acids and nucleotides would have been present in a real ocean---varieties which have been ignored in our calculations of configurational entropy work. In addition, the soup would have contained many other kinds of molecules which could have reacted with amino acids and nucleotides. The problem of using only the appropriate optical isomer has also been ignored. A random chemical soup would have contained a 50-50 mixture of D- and L-amino acids, from which a true protein could incorporate only the Lenantiomer. Similarly, DNA uses exclusively the optically active sugar D-deoxyribose. Finally, we have ignored the problem of forming unnatural links, assuming for the calculations that only CL-links occurred between amino acids in making polypeptides, and that only correct linking at the 3', 5'-position of sugar occurred in forming polynucleotides. A quantification of these problems of specificity has recently been made by Yockey.21


Now, the assumption of an 100 amino acid polypeptide might be too restrictive, because I believe that there is some evidence that a smaller polypeptide might have been able to kick things off. If so, the Scr component of the configurational entropy would be decreased, thus reducing the work involved. But to what extent? Or is this calculation relevant? If not, why not?

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Mr_Christopher



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(Permalink) Posted: Dec. 08 2006,12:57   

"I think that the latest discoveries in physics argue for a God who fine-tuned the universe."

How dense can you be?  And what a dumb, stupid cop out.  You cannot argue that godditit until you prove god exists.  You might as well say "I think that the latest discoveries in physics argue for a santa claue who fine-tuned the universe."  or "I think that the latest discoveries in physics argue for Elvis who fine-tuned the universe."

And I thought you knew something about science.  That's why these threads of yours are so patently useless and stupid I might add.  Paley says goddidit, well where is your evidence that god even exists?  Prove god exists and we can theorize how he might have done it but until you prove god exists you're just another creationist troll.

Where is the latest god research?  And what are scientists proposing he might be made of?

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The Ghost of Paley



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(Permalink) Posted: Dec. 08 2006,13:12   

Mr_Christopher:

 
Quote
"I think that the latest discoveries in physics argue for a God who fine-tuned the universe."

How dense can you be?  And what a dumb, stupid cop out.  You cannot argue that godditit until you prove god exists.  


Really, Christopher. This stuff belongs in the LUCA thread. Since the existence (or nonexistence) of God plays no part in origins of life research, why are you bringing this issue up here? Why not try to demonstrate that the latest OOL hypotheses are plausible, or link to a source that answers my questions? That would be more effective, I think. Because it sounds to me like you wish to paper over the difficulties in scientific models by ridiculing theism. The problem with your approach is that science doesn't progress on the failures of its competitors (so called), but on its inherent strengths.

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Dey can't 'andle my riddim.

  
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Dec. 08 2006,13:30   

Quote (The Ghost of Paley @ Dec. 08 2006,12:19)
BWE:

 
Quote
Louis,

That was a beautiful post.



Excellent! So now you're in a position to answer this question:

Is there experimental evidence or thermodynamic calculations in the literature that demonstrate that mineral catalysis can overcome the configurational entropy hurdles that Thaxton and Bradley mention? Or is there something wrong with their formulae? If there is, could you point out where they go wrong? Thanks.

Because I didn't see an answer in Louis's post.

**EDIT** This is Louis' answer to your question:
Quote
Another point to note is that it is assumed by the troll that the creationists have some genuine criticisms which need answering when they don't (as any tiny quantity of knowledge of the subjects in hand demonstrates). Also of note is the fact that, despite calling the troll's behaviour as it is (which is a distraction from any scientific topic other than aberrant psychology), there have been examples of key mechanisms and pointers to the lit and groups working in the area from both myself  and Dr GH and these have been ignored. Yet another data point in evidence that this is another troll bullshit saga.


--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Dec. 08 2006,14:25   

BWE:

       
Quote
     
Quote
     
Quote
(The Ghost of Paley @ Dec. 08 2006,12:19)
BWE:

Louis,

That was a beautiful post.




Excellent! So now you're in a position to answer this question:

Is there experimental evidence or thermodynamic calculations in the literature that demonstrate that mineral catalysis can overcome the configurational entropy hurdles that Thaxton and Bradley mention? Or is there something wrong with their formulae? If there is, could you point out where they go wrong? Thanks.

Because I didn't see an answer in Louis's post.


**EDIT** This is Louis' answer to your question:
   
Quote
Another point to note is that it is assumed by the troll that the creationists have some genuine criticisms which need answering when they don't (as any tiny quantity of knowledge of the subjects in hand demonstrates). Also of note is the fact that, despite calling the troll's behaviour as it is (which is a distraction from any scientific topic other than aberrant psychology), there have been examples of key mechanisms and pointers to the lit and groups working in the area from both myself  and Dr GH and these have been ignored. Yet another data point in evidence that this is another troll bullshit saga. 



In other words:

1) "We've got the answers";

2) "Here are a few links";

3) "You're a troll for even asking these questions. The evidence is there. We won't show you where, but it's out there. Trust us."

Sorry, that won't cut it. Can't you answer the questions in your own words, or at least quote from one one of those sources that the good doctors link too? Because if the answers are in their sources, it shouldn't be hard to find, should it?

Because Louis would never literature bluff, correct?

Here are the questions again:

 
Quote
Is there experimental evidence or thermodynamic calculations in the literature that demonstrate that mineral catalysis can overcome the configurational entropy hurdles that Thaxton and Bradley mention? Or is there something wrong with their formulae? If there is, could you point out where they go wrong? Thanks.


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Dey can't 'andle my riddim.

  
Ogee



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(Permalink) Posted: Dec. 08 2006,14:37   

Some better questions:

Is there any evidence that the there is such a thing as a "configurational entropy hurdle"?  Is this an accepted concept in chemistry or physics?  Is there peer-reviewed support of this sort of work?

Good luck!

  
Ogee



Posts: 89
Joined: Mar. 2006

(Permalink) Posted: Dec. 08 2006,14:56   

To put this in perspective, using this sort of energy calculation, a 300-page novel contains about 1,000,000 characters, from a set of about 65 (including spaces, punctuation, capital and small letters).

The "configurational entropy" of one specific arrangment of those 1M characters is 0 (ln1=0).

The "configurational entropy" of a random distribution of 1M letters from a population of 65 is:

k * (1e6)!/ 65 / 15385!

Which is a number somewhere around 10 ^ 3,000,000 ergs/letter.

OMFG!!! WHERE WILL THIS ENERGY COME FROM!??!?!! NOVELS ARE IMPOSSIBLE!!!! GODDIDDIT!!!!

  
phonon



Posts: 396
Joined: Nov. 2006

(Permalink) Posted: Dec. 08 2006,16:02   

That really great Ogee.

This is something from here.

Quote
Chance

Before the specified complexity of living systems began to be appreciated, it was thought that, given enough time, "chance" would explain the origin of living systems. In fact, most textbooks state that chance is the basic explanation for the origin of life. For example, Lehninger in his classic textbook Biochemistry states,

   We now come to the critical moment in evolution in which the first semblance of "life" appeared, through the chance association of a number of abiotically formed macromolecular components, to yield a unique system of greatly enhanced survival value.1

More recently the viability of "chance" as a mechanism for the origin of life has been severely challenged.2

We are now ready to analyze the "chance" origin of life using the approach developed in the last chapter. This view usually assumes that energy flow through the system is capable of doing the chemical and the thermal entropy work, while the configurational entropy work of both selecting and coding is the fortuitous product of chance.

To illustrate, assume that we are trying to synthesize a protein containing 101 amino acids. In eq. 8-14 we estimated that the total free energy increase (G) or work required to make a random polypeptide from previously selected amino acids was 300 kcal/mole. An additional 159 kcal/mole is needed to code the polypeptide into a protein. Since the "chance" model assumes no coupling between energy flow and sequencing, the fraction of the polypeptide that has the correct sequence may be calculated (eq. 8-16) using equilibrium thermodynamics, i.e.,

[protein concentration] / [polypeptide concentration] = exp ( - G / RT), eq. (9-1)

= exp (-159,000) / 1.9872 x 298)

or approximately 1 x 10^-117

This ratio gives the fraction of polypeptides that have the right sequence to be a protein.

   [NOTE: This is essentially the inverse of the estimate for the number of ways one can arrange 101 amino acids in a sequence (i.e., I / c in eq. 8-7)].

Eigen3 has estimated the number of polypeptides of molecular weight 10^4 (the same weight used in our earlier calculations) that would be found in a layer 1 meter thick covering the surface of the entire earth. He found it to be 10^41. If these polypeptides reformed with new sequences at the maximum rate at which chemical reactions may occur, namely 10^14/s, for 5 x 10^9 years [1.6 x 10^17 s], the total number of polypeptides that would be formed during the assumed history of the earth would be

10^41 x 10^14/s x 1.6 x 10^17s = 10^72 (9-2)

Combining the results of eq. 9-1 and 9-2, we find the probability of producing one protein of 101 amino acids in five billion years is only 1/ 10^45. Using somewhat different illustrations, Steinman4 and Cairns-Smith5 also come to the conclusion that chance is insufficient.

It is apparent that "chance" should be abandoned as an acceptable model for coding of the macromolecules essential in living systems. In fact, it has been, except in introductory texts and popularizations.


This is really terrible stuff.

Quote
This ratio gives the fraction of polypeptides that have the right sequence to be a protein.

They left out the word 'particular' here. As in, this ratio gives the fraction of polypeptides that have the right sequence to be a particular protein. Of course, any polypeptide of sufficient length (arbitrarily anything over ~20 or so residues) is by definition a protein.

If you have a whole lot of random peptide sequences all over the place, some of them are going to do something. They will have some sort of chemical reactivity toward other substances in their enviroment.

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With most men, unbelief in one thing springs from blind belief in another. - Georg Christoph Lichtenberg

To do just the opposite is also a form of imitation. - Georg Christoph Lichtenberg

  
Tracy P. Hamilton



Posts: 1239
Joined: May 2006

(Permalink) Posted: Dec. 08 2006,16:41   

Quote (Ogee @ Dec. 08 2006,14:37)
Some better questions:

Is there any evidence that the there is such a thing as a "configurational entropy hurdle"?  Is this an accepted concept in chemistry or physics?  Is there peer-reviewed support of this sort of work?

Good luck!



No.  There is an entropy from the number of ways a single material can have configurations, all of which have the same energy (such as solid CO, which is oriented one of two ways, i.e two distinct microstates).  In other words, entropy is the number of ways to distribute energy.  

An ensemble of many molecules made of a single peptide sequence has a "configurational" (conformational) entropy, but that is due to thermal effects (energy spread among discrete quantum vibration, rotation and translation energy levels, and hence nothing more special than the vibrations in water molecules), and its entropy would be zero at absolute zero (as any other perfectly ordered crystal would be).  A random mix of peptides with the same number of molecules would have the same entropy.

http://www.entropysite.com/cracked_crutch.html  Yes, it is a peer reviewed article.

--------------
"Following what I just wrote about fitness, you’re taking refuge in what we see in the world."  PaV

"The simple equation F = MA leads to the concept of four-dimensional space." GilDodgen

"We have no brain, I don't, for thinking." Robert Byers

  
Faid



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Joined: Mar. 2006

(Permalink) Posted: Dec. 08 2006,16:42   

Quote (The Ghost of Paley @ Dec. 08 2006,12:19)
Excellent! So now you're in a position to answer this question:

Is there experimental evidence or thermodynamic calculations in the literature that demonstrate that mineral catalysis can overcome the configurational entropy hurdles that Thaxton and Bradley mention? Or is there something wrong with their formulae? If there is, could you point out where they go wrong? Thanks.

Because I didn't see an answer in Louis's post.

Seriously, Ghost, give it a rest.

You have defined yourself as a "theistic evolutionist", who believes abiogenesis took place.

We have both agreed that definite, indisputable "experimental evidence" for a mechanism for the OOL does NOT exist at the moment. There are only indications, that point to certain pathways for further research.

We have also agreed that the creationists simply resort to arguments from incredulty, and provide nothing of worth in this issue.

So, what is the point of asking this meaningless question?

If you want us to debate the thermodynamic hurdles, or all the other obstacles in OOL research, the best place to get them is in the scientific papers that identify them, examine them and try to overcome them- that's where creos copy them from in the first place!
How many of those experiments were done by creationists, Ghost?

All creationists do, is copy/paste the known, described and accounted for, undoubtedly existing problems in the research, and then gloat and say "Nyah nyah you haven't found a way, that means there IS no way, we win nyah nyah".

And that is as useless for research as it is ridiculous.

You have already agreed with this- so let me ask you again, and I hope you won't ignore me this time:

How do creationists contribute anything meaningful in the search for OOL? What do they offer that has not been already identified by biologists, who strive to figure things out?

If you are genuinely interested in learning about the latest on the OOL, why not discuss the actual data and research made in it (the same one creos copycat to use for their blithering nonsense)?

...

...Or did you get bored, and started trolling again? Because if you have, I wonder if you have any idea how unbelievably lame and immature that makes you look, and what it does to your recently aquired cred.

--------------
A look into DAVE HAWKINS' sense of honesty:

"The truth is that ALL mutations REDUCE information"

"...mutations can add information to a genome.  And remember, I have never said that this is not possible."

  
Louis



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(Permalink) Posted: Dec. 08 2006,16:44   

Ogee,

I was joking about the too many biologists in field part. I married a biologist you can never have too many of them in my book. My point was that the problem of abiogenesis is essentially a chemical one. I'm all for interdisciplinary collaboration. The trips are better! And, more importantly, as one progresses from the physics end of the scientific spectrum towards the biological end of the scientific spectrum you get more and better looking women. Whilst TAing an undergrad lab many moons ago we had three groups in: one from BSc chemistry with biochem, one from straight unadulterated BSc chemistry, and one from BSc chemistry with material science and solid state physics. It was remarked upon that human female pulchritude varied considerably between the groups. It was noted that those students of a more biological bent were generally capable of having a shower, looking halfway decent, and were generally quite sexy. However those of a more physical persuasion looked like a day out from the serious youth sex offenders institute. {shrug} Eh, go figure!

Anyway back to the tawdry reality of discussing anything near the troll. The troll is playing his game of duelling authorities again, and has avoided the question (surprise surprise). Why should we expect Thraxton et al to have raised a valid problem? The fact that Thraxton has a PhD seems to have been the only reason given thus far, except of course that the troll find certain things "personally compelling".

My answers to the troll's original questions were not precisely as you stated btw.

Quote
The answers to the troll's original questions are, as I've already said, "excellent", "yes", and "of course they are. That question is a non sequitur and exposes both the ignorance of the questioner and the dishonesty of those who try to obfuscate the issue". As mentioned before the entropy angle is a standard creationist red herring. Just like the "information" challenge. It's the sort of question which annoys rather than interests or informs because it's based either on ignorance or dishonesty.


We find naturally occuring polymers in non-biological sources, we know that life is not in anyway a necessary condition for polymerisation. We know that naturally occuring amphiphilic molecules form bilayers, or even at certain critical concentrations "cell like" micelles. We know that near racemic autocatalytic systems can "run away" to produce highly enantiopure products. We know about microscopic reversibility and Hammet's postulate and a wide variety of kinetic and thermodynamic properties that influence the course of reactions. NONE of these things, not a single one, provides one tiny problem for the perfectly natural origins of self replicating or cellular chemical systems. As for configurational entropy hurdles, these indeed exist....perhaps not in that configuration of words (or as Thraxton and buddies use it), but entropy does provide  a hinderance in certain circumstances. Simply put if you are trying to perform a cyclisation reaction there is an entropic factor involved in the competing cyclisation and  polymerisation processes. This becomes very important when one is trying to make large (i.e. macro) cyclic molecules. The long floppy molecule has so many degrees of freedom that it is entropically unfavourable for the two ends to meet, so the competing polymerisation reaction gets alook in. Concentration plays a big part in this, in more dilute reactions two molecules are less likely to come together so the macrocyclisation process becomes more favoured. Ah the joys of chemistry!

Anyway, all this is meaningless fun because the troll hasn't justified why anyone should take his non sequitur questions or the blindingly dull lies of Thraxton and chums seriously at all. This justification interests me for a key reason: why should we expect the comments of creationists with abominable track records and openly admitted agendae to be of any relevance at all?

After all abiogenesis research is fascinating and technical, why should we waste our time explaining the fringes of chemical research to someone with a demonstrated inability to comprehend school science, basic logic or even show evidence of the most basic amoount of intellectual honesty? My answer would be that we shouldn't, especially as the troll has yet again demonstrated on this thread that he can't think for shit and isn't interested in the information, just point scoring and all round wankery.

The point is not about demonstrating the incorrectness of the calculations, the point is that the calculations are irrelevant. Pointless window dressing designed purely to obfuscate and hide the fact that these guys have no actual argument. Same shit, different day.

Louis

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Bye.

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Dec. 08 2006,17:25   

Ogee Part 2:

Quote
Is there then, some differentiation of substrates at this point?


Not a relevant one I can think of.

Quote
Is there research that is creating some form of peptide based replicating compound? I mean, you don't know which compounds you are shooting for, wouldn't it make a difference?


I'm sure I read some recently, I'll see what I can dig out next week when I'm back in work and have access to the online lit. I seem to remember (possibly incorrectly) that the Rebek group's work used peptides.

Quote
Are you looking at non enzymatic ligation systems and guessing at interesting ways to produce covalent bonds?


Not me personally at the moment, but the answer to this is definitely yes. The "chemzyme", organocatalyst and organometallic filed are filled with this stuff. It's enoough material for a degree in chemistry, we might need to narrow ot down somewhat! For example, iron sulfide nodules catalyse certain chemistries, as do zeolites (clays etc). They do this via a huge number of different mechanisms. Some involve adsorption (a classic eg is Pd/C catalysed hydrogenation), some involve acid or base promotion of reaction in both a Lewis and Bronsted sense, some involve a templation, some just bring reagents into close proximity and some involve a reduction of the degrees of freedom a reagent has by encapsulating it.

Quote
That seems kind of random. How do you know which ones you want? Are you modeling these using software then I assume?


Believe me it's not being done randomnly at all! We know what sorts of systems to look at from all fields. Seriously the PNA/RNA stuff is fascinating, but it's the "higher" end kind of system. I would be very very very surprised if anything as "high tech" as polymeric RNA were the Ur-replicator. I wouldn't be at all surprised if simple nucleic acids were involved (they aren't exactly complex molecules from a chem standpoint) early on, and simple peptides and dipeptides also occur without biological intervention. Things like glycine are found in space for example. These again are exceedingly simple multifunctional molecules by comparison to anything large and biological.

Quote
I understand we are talking about the chemistry but you are assuming that you are going to try to create what? full-on RNA? A cell? Something that has been described biologically already?


Synthesising DNA/RNA etc is a simple matter and a really common research field today esp in antisense/antigene therapeutics, or trying to change DNA structure by putting in "unnatural" segments  for example. Again MASSIVE field, difficult to condense to a paragraph. Same goes for peptide chem, these things are relatively easy to make (Barry Sharpless, a recent org chem Novel laureate has started this field call "click chemistry" which involves using highly enthalpically favoured reactions like peptide bond formations using molcules predisposed to form these bonds (sprung loaded molecules) to rapidly build molecular complexity and probe structure/biological activity relationships. Ok so there's more to it than that, but that's the basics.

Quote
I think I am missing your point. Are you talking about engineering from a schematic which you can't read or needing to engineer one small part for a larger machine and you have no schematic for that part?


In terms of developing systems which do the things we want to explore like self replication, that's standard chemistry type research. Pinpointing the specific path taken from molecules to man as it were, apart from being nigh in impossible, is precisely trying to engineer without a schematic, or indeed any idea of which things happened in which order. But hey, it keeps me in a job!

Quote
Maybe more specifically, what are biologists doing that you would critisize as hindering or obfuscating?


Nothing at all, I was being humourous and unintentionally a complete arse apparently! OOL research is massively multidisciplinary. AT the moment it's gone beyond the "three blind men describing the elephant" stage, we're all on the same page talking about the same thing. We just don't know if it's a pygmy, Indian, African, Mamoth, or pink floating hangover elephant yet though! The bio guys tend to look top down, which is really useful, sort of like reverse engineering the problem from the advanced systems like DNA we have now. Tough bunnies. Mainly because the "fossil" chemical systems the preceded it are very good food for millions of microbes the planet over. These are fossils we aren't going to "dig up" with any ease!

Quote
Also, what is the current state of the art for PNA ligation? (I have never studied this in depth, although one of the labs we use does more normal DNA cloning and I am familiar with the methodology)


No clue! Not a field I've done any research in and sonly something I know the basics about. I can also try to dig something out next week. Remind me! Don't let me forget because I've finished the report with the patent boys that has kept me chained to a PC (YUCK BLECH) for weeks and I can now be back in lab playing with carcinogens and chemical weapons (one of the precursors in some chemistry I was doing a few months back was something used by the Germans in WW1 to gas punters. It's actually really innocuous compared to the other stuff I use, but it's always amusing to have to explain to your boss why you are ordering a chemical weapon: "Erm well, my neighbours have this fucking dog....")

Hope some of that helps.

Louis

--------------
Bye.

  
"Rev Dr" Lenny Flank



Posts: 2560
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(Permalink) Posted: Dec. 08 2006,17:41   

I will simply point out, once again, that Thaxton (or indeed, ANY creationist or IDer) has put forth NO arguments against abiogenesis.  None.  Zip.  Zero.  Zilch.  Nada.  Not a single one.

All they have done is parrot arguments that SCIENTISTS have made.

That, after all, is how science is done.

Sorry, Paley, that science doesn't have all the answers with absolutre certainty.  After all, that's why scientists still have jobs.

But, ignoring Paley's trolling (once again), I will simply point out that ID/creationists have contributed nothing at all whatsoever to describing the current problems in abiogenesis models, or in any sort of research to answer those questions.  Nothing.  At all.  Zip.  Zero.  Zilch.  Not a goddamn thing.

Not surprising, since ID/creationists (and Paley, too) don't give a rat's ass about science.  (shrug)

--------------
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www.RedandBlackPublishers.com

  
Steviepinhead



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(Permalink) Posted: Dec. 08 2006,17:56   

I agree the topic is interesting--in the extreme!--and I certainly wouldn't mind if Louis and others wanted to elucidate the latest efforts by actual scientists.

But I have zero interest in proceeding from a basis of the "hurdles" alleged by a couple of flaccid CreaIDiots.

Or of listening to Paley drone on and on.

  
BWE



Posts: 1898
Joined: Jan. 2006

(Permalink) Posted: Dec. 08 2006,18:58   

Quote (The Ghost of Paley @ Dec. 08 2006,14:25)
 
Quote
**EDIT** This is Louis' answer to your question:
       
Quote
Another point to note is that it is assumed by the troll that the creationists have some genuine criticisms which need answering when they don't (as any tiny quantity of knowledge of the subjects in hand demonstrates). Also of note is the fact that, despite calling the troll's behaviour as it is (which is a distraction from any scientific topic other than aberrant psychology), there have been examples of key mechanisms and pointers to the lit and groups working in the area from both myself  and Dr GH and these have been ignored. Yet another data point in evidence that this is another troll bullshit saga.



In other words:

1) "We've got the answers";

2) "Here are a few links";

3) "You're a troll for even asking these questions. The evidence is there. We won't show you where, but it's out there. Trust us."

Sorry, that won't cut it. Can't you answer the questions in your own words, or at least quote from one one of those sources that the good doctors link too? Because if the answers are in their sources, it shouldn't be hard to find, should it?

Because Louis would never literature bluff, correct?

Here are the questions again:

     
Quote
Is there experimental evidence or thermodynamic calculations in the literature that demonstrate that mineral catalysis can overcome the configurational entropy hurdles that Thaxton and Bradley mention? Or is there something wrong with their formulae? If there is, could you point out where they go wrong? Thanks.

No. I did point out Louis's answer. The answer would be that creationist crap needs to enter science the same way science crap enters science.

No need to answer the questions (Although Louis did in his last post) because they fail the first test: Is it a ligitimate question.

Had you asked simply your last question, someone could have answered you. But dragging it out of you is painful.

Anyway, fascinating topic.

Louis,

That was me rather than ogee you were responding to but thank you. I suppose I might have sounded a little defensive about the biologist bit. You'd be surprised how many folks come around here saying things like that with a, how shouold I say, less than fun attitude. I just smile and thank them for their input. If I remember correctly, even davescot once said that biologists were list makers or some such thing. Secretaries maybe. I didn't place you in that company and I do understand your point. The research really is fascinating.
 
Quote
In terms of developing systems which do the things we want to explore like self replication, that's standard chemistry type research. Pinpointing the specific path taken from molecules to man as it were, apart from being nigh in impossible,  is precisely trying to engineer without a schematic, or indeed any idea of which things happened in which order. But hey, it keeps me in a job!

I assume you mean "molecules to blue green algae"?  :) (to keep the biologists happy)

--------------
Who said that ev'ry wish would be heard and answered
When wished on the morning star
Somebody thought of that, and someone believed it
Look what it's done so far

The Daily Wingnut

   
skeptic



Posts: 1163
Joined: May 2006

(Permalink) Posted: Dec. 08 2006,20:05   

Louis, I love seeing you in your element.  Here's something I ran across today that raises (I think) more questions than it answers.  Personally I love that!

RNA-Heredity Molecule?

By the way, I'd personally like to thank GoP for the thread.  I'd sortof forgotten about PNAs and after he brought it up I went back and did some reading last night.  Fascinating stuff.  I have some reservations but they actually apply to both RNA and PNA, as I've stated before I'm an advocate of "the protein world" but it's still great stuff.

  
skeptic



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Joined: May 2006

(Permalink) Posted: Dec. 08 2006,20:11   

BWE, you know there always been an unconscious (or conscious) attitude from chemists about biologists.  I remember well having to carry many biologists through organic as an undergrad and there was always the light-hearted banter associated with it.  But just to make you feel a bit better I'm sure the physicists felt the same about us chemists.  :D

  
"Rev Dr" Lenny Flank



Posts: 2560
Joined: Feb. 2005

(Permalink) Posted: Dec. 08 2006,20:58   

Quote (skeptic @ Dec. 08 2006,20:05)
Louis, I love seeing you in your element.  Here's something I ran across today that raises (I think) more questions than it answers.  Personally I love that!

RNA-Heredity Molecule?

By the way, I'd personally like to thank GoP for the thread.  I'd sortof forgotten about PNAs and after he brought it up I went back and did some reading last night.  Fascinating stuff.  I have some reservations but they actually apply to both RNA and PNA, as I've stated before I'm an advocate of "the protein world" but it's still great stuff.

How about TNA's?

--------------
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skeptic



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(Permalink) Posted: Dec. 08 2006,22:04   

I'm not sure that TNAs actually reduce the complexity of the molecule to any great degree.  Maybe they provide a clue if there was incremental steps between primitive molecules and nucleic acids but I honestly don't know much about them so I can not really say.  My main sticking point is still, outside of the limited catalytic properties of RNA, the nucleic acids are still largely acted upon by enzymes.  This still makes the proteins a better candidate for the initial self-replicator, in my mind.

  
Louis



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Joined: Jan. 2006

(Permalink) Posted: Dec. 09 2006,05:05   

BWE,

ARGHHHHHH!!!

My most sincere and humble apologies. Ayee, what a maroon I am! Brain was clearly not engaged, gob opened first. My bad. Lordy, I seem to have unwittingly tapped into a personal source of inner tard! Never a good thing. I shall rush off after this post and beat myself with a copy of Stryer (ok it's biochem, gimme a break) forthwith, if not fifthwith.

For the record, I absolutely categorically have no problem with biologists/biology in any way shape or form. In fact I am seriously considering changing field and becoming a biologist (I've made enquiries with an evolutionary biologist mate of mine, what will come of it is a different matter). Anyone who says biology is stamp collecting or naming stuff or secretarial work a) has never done any biology, b) is a seriously deluded wanker without clue or ability to find clue, c) if a scientist of any stripe, is probably a physicist who has never had sex with a girl, for the reasons mentioned in previous post. After all some of those chem/physics duel majors I TAd had acne you could hear!

Personally I don't find the Ancient Greek demarkation between fields of study to be useful in any intellectual sense, merely a conversational one. I've always said I'm a scientist who happens to be focussed on chemistry rather than a chemist who is interested in broader science. I have to admit I've never understood those of my colleagues for whom this is just a job. I'm an intolerant bastard, sue me!

There was an article in Nature (I think) by George Whitesides and others a while ago about "what chemists want" and of all the "big questions" that chemists needed to answer the one that everyone would really recognise is the origin of life. It's such a massively multidisciplinary area that one narrow group of punters aren't going to be enough. Geochemists and astrochemists need to discover relevant chemicals in the universe (and have done) even discovering processes that initial organic polymerisation and other reactions(and they have done) and pick out the  well hidden fossil traces of early life (and they have done).  Astrobiologists and evolutionary biologists and cell biologists and microbiologists and biochemists need to figure out which pathways and chemistry is essential to modern life (and they have done). Synthetic chemists need to look for the clues in the chemistry and biochemistry of secondary metabolites (not really being done yet, this is my idea, shhhhhh keep it under your hat! ) and need to develop reactions that can mimic key biological processes (definitely done, A LOT. #### we can improve on some processes) and need to actually try to recreate prebiotic chemistry at every level (done in every area, but we still don't know what did happen, just what could). Oh dear I've come over all girly and excited again...

As for the TNA that Lenny and Skeptic mention, ypu fascinating area of enquiry. Still comparitively high tech to some self replicating systems, and given the preponderance of simple amino acids in prebiotic chemistry their certainly a possible candidate. Unlike Skeptic I'd guess that proteins are still far too high tech to be the Ur-replicator.

My guess would be for something far simpler. For example, look at the systems of Rebek and coworkers (sorry there's no point linking the articles they're proper lit for subscribers anyway. I might, if I get a chance, draw a few things up on chemdraw next week and post the pics.). The point is that we don't need to go as high tech as known biopolymers or their analogues to find self replicating molecules. Yet again my old favourite of the Soai reaction is a  good example of one of the necessary processes for self replication: autocatalysis (the product catalyses it's own formation. The story is a little more complicated as you can read in Donna Blackmond's paper below). A couple of PNAS articles on the Soai Reaction:

Here and here.

I just did a quick google for Rebek's work (I only know him from the lit. I forget google when it comes to real science, which can a bit of a sin. When you have Scifinder and Beilstein you forget that Google is your friend). Below are some links that people might be able to get access. This is all really off the cuff so for the real deal wait until I'm back at work next week.

Abstract 1, Abstract 2, Broad article about self replication, Wikipedia on Rebek.

Hope these whet people's appetites.

Louis

P.S. Being accused of "literature bluffing" (what the fuck is that??) by the troll nearly made me fall of my chair laughing. What a totally pointless wanker that troll is. Only turds like the troll need to bluff, some of us know what we're talking about. As has been demonstrated on every thread and every topic dammit! Aieee why is my life cluttered with wazzarks, trolls and fundamentalists?

P.P.S. Lenny I presume you meant TNA rather than T 'n' A? ;-)

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Louis



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(Permalink) Posted: Dec. 09 2006,05:34   

Skeptic,

Quote
My main sticking point is still, outside of the limited catalytic properties of RNA, the nucleic acids are still largely acted upon by enzymes.  This still makes the proteins a better candidate for the initial self-replicator, in my mind.


Stick no further, no one has ever proposed that "modern, high tech" nucleic acids found in biological systems are anything like the Ur-replicator. RNA is only a possible mid candidate because it requires less effector molecules. Your lack of ability to imagine intermediates, or the lack of current exact systems does not constitute evidence, nor does it make skepticism about abiogenesis reasoned or reasonable.

Quote
Louis, I love seeing you in your element.  Here's something I ran across today that raises (I think) more questions than it answers.  Personally I love that!

RNA-Heredity Molecule?

By the way, I'd personally like to thank GoP for the thread.  I'd sortof forgotten about PNAs and after he brought it up I went back and did some reading last night.  Fascinating stuff.  I have some reservations but they actually apply to both RNA and PNA, as I've stated before I'm an advocate of "the protein world" but it's still great stuff.


And what does that article have to do with anything other than RNA can carry heritable information (which we already knew btw). More questions than it answers is great, but this is almost supremely irrelevant to prebiotic chemistry.  RNA world, PNA world, TNA world, Protein world are possible high tech intermediates en route. The chemistry doesn't need to be even remotely that complex, and the substrates don't need to be anywhere near that complex for self replicating systems, autocatalytic systems, or polymeric systems to develop without "biology".

Louis

P.S. Don't thank the troll. Mind you I'm not surprised you do. Birds of an irrational feather.... He's playing silly buggers, never think for a second that the troll is being honest. He isn't. The troll hasn't managed honesty once yet, why should anyone expect that the troll is even capable of such a feat? The troll started this thread because he knew I lack anything remotely resembling the self control not to comment. I still think the troll needs to go. Good trolls are useful. Bad trolls are annoying. Your pose as a "scientific" skeptic regarding evolution etc is an excellent case in point. When I discuss quantum physics or evolutionary biology, subjects I don't work in but have some experience and interest in, guess what? I don't bother to discuss them with "skeptics" like you and the troll. What's the point? I discuss them with people who actually know something about them, and who actually work in them. Then and only then do I start looking for problems, new ideas, areas to explore etc. I'm rarely disappointed. Usually all the holes I can think of have been plugged before I got there, occasionally not, and those are the bits that get/got me/a friend funding! That's science baby, not pricking about with the asinine witterings of trolls, the fundamentally ignorant, or the deliberately dishonest and deluded.

Louis

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Louis



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(Permalink) Posted: Dec. 09 2006,05:59   

All,

As I think of it, the issue that really bugs me whenever this topic comes up, is what do those with a "problem" (read religious predisposition to bullshit and obfuscate and piss about) with abiogenesis. What do these people think "life" is? Are viruses "alive"? Prions? What does being "alive" mean? Why do people see the need to inject this red herring of a demarkation between a rock and a pig? Both are chemical systems, one is more complex than another, but chop them both up and you won't find one atom of "life".

Ok so I am being slightly facecious about this. "Life" is a degree of organised complexity and complex adaptivity that is destroyed by such chopping up. Why insert supernatural souls and claim an elan vitale when no such thing exists (demonstrably). Wohler did away with this crap before Darwin came along. Why do people insist on these antique vitalist notions?

This is why abiogenesis is a "sticking point" (blech) for so many, because people have decided before encountering the evidence that life is a special super dooper extra banana non naturalistic god given pressie from the great super fairy in the sky that watches you masturbate. Couple that with the "ghost in the machine" illusions we pretty much all have (me included) and the hugely culturally enshrined aspects of the belief that there is a homunculus behind your eyes working the controls, and you have a huge burden of bullshit to shift.

Louis

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Chris Hyland



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(Permalink) Posted: Dec. 09 2006,07:49   

I do find it quite ironic that creationists thin the gap between life and non-life is much larger than I do yet they think we can make inferences about evolution by equating living things with manmade contraptions.

  
lkeithlu



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(Permalink) Posted: Dec. 09 2006,08:06   

Forgive my boldness in commenting here:

When a scientist makes a statement and another scientist evaluates that statement, I find it unbelievable that non-scientists insist on taking sides based only on the issue, and get huffy when said scientists cannot dumb it down enough to make it understandable to them so that they can join in the debate. If these were questions accessible to laypeople, then laypeople would be doing the science. I have a (25 year old) BS in Chemistry and some Geology and have been teaching sciences for 25 years, and although I can get the general gist of the thermodynamic obstacles and understand some of the terms, there is NO WAY I could ever pass judgement on any of the details. I have to be able to trust consensus science to pass judgement on these issues.

This is only one example of many; it is the same for all aspects of science including paleontology, historical geology, physical anthropology, climate science, the list is endless. I think this is one of the biggest problems we face-a democratic America cannot conceive of situations where THEIR opinion does not carry equal weight. Add to that the dismal state of scientific literacy (in part because people like me, science educators, clearly aren't doing what we need to do) and you have a nation that thinks science is a "belief" system. Shoot, they think justice is also a "belief" system, after all, on CNN.com you can vote whether or not OJ "did it" and somehow that determines what is true.

Sorry to rant- please continue with your regularly scheduled thread....

  
"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 09 2006,08:59   

Quote (Louis @ Dec. 09 2006,05:05)
P.P.S. Lenny I presume you meant TNA rather than T 'n' A? ;-)

Well, I do have a high interest level in both.

:)

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The Ghost of Paley



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(Permalink) Posted: Dec. 09 2006,09:10   

I would like to thank Mr. Hamilton for defining conformational entropy. Although any thermodynamic calculation has an information-theoretical component, there's a lot more to consider here and you can't treat a long polymer as merely a concatenation of monomers searching for a target sequence (as the authors appear to do). Mr. Hamilton (or even Louis), does this paper come closer to the relevant calculations? It seems interesting and possibly germane to the OOL issue.

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skeptic



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(Permalink) 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.

  
The Ghost of Paley



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(Permalink) 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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"Rev Dr" Lenny Flank



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(Permalink) 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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"Rev Dr" Lenny Flank



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(Permalink) 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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(Permalink) 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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"...mutations can add information to a genome.  And remember, I have never said that this is not possible."

  
Louis



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(Permalink) 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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The Ghost of Paley



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(Permalink) Posted: Dec. 13 2006,13:04   

Quote
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:

   
Quote
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:

   
Quote
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:

 
Quote
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.


 
Quote
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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Louis



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(Permalink) Posted: Dec. 14 2006,10:35   

Quote
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.

Quote
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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The Ghost of Paley



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(Permalink) 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.

       
Quote
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:

     
Quote
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.

     
Quote
     
Quote
 
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:

     
Quote
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?

   
Quote
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.

   
Quote
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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The Ghost of Paley



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(Permalink) 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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Louis



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(Permalink) 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.
Quote
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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The Ghost of Paley



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(Permalink) Posted: Dec. 14 2006,15:38   

Quote
BWWWWWWAAAAAAAAAAAAAAAAAHAHAHAHAHAHAHA


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

         
Quote
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.....

         
Quote
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:
 
       
Quote
P.P.S.          
Quote
 
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:

       
Quote
       
Quote
 
             
Quote
 

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:

             
Quote

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:

     
Quote
     
Quote
 
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:

         
Quote
 
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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Louis



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(Permalink) 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

Quote
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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(Permalink) 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

  
The Ghost of Paley



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(Permalink) Posted: Dec. 14 2006,16:58   

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


I think Wes disabled the "poll" icon.  :D  :D  :D

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.

 
Quote
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.

Quote
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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(Permalink) Posted: Dec. 14 2006,17:49   

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

  
"Rev Dr" Lenny Flank



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(Permalink) 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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The Ghost of Paley



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(Permalink) Posted: Dec. 14 2006,18:52   

Qetzal:

 
Quote
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:

 
Quote
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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"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 14 2006,20:36   

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

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Louis



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(Permalink) 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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The Ghost of Paley



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(Permalink) 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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Louis



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(Permalink) Posted: Dec. 15 2006,12:22   



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The Ghost of Paley



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(Permalink) 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 Schrödinger cat thing that only experts can understand?

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"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 15 2006,17:54   

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

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Louis



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(Permalink) 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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The Ghost of Paley



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(Permalink) 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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The Ghost of Paley



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(Permalink) 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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Flint



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(Permalink) 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.

  
The Ghost of Paley



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(Permalink) Posted: Dec. 18 2006,14:58   

Flint:

Quote
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."


Oh, I support OOL research, and suspect that many details will get nailed down eventually. It just seems that scientists might be pursuing blind alleys right now due to a little frustration. It's nice to see some verification of a 50-year-old model like we have in the Soai reaction, but I don't think researchers are proposing that these precise reactions are how enantioselection really happened.

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"Rev Dr" Lenny Flank



Posts: 2560
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(Permalink) Posted: Dec. 18 2006,18:08   

Quote (Louis @ Dec. 15 2006,18:35)
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.

Sorry I missed this before . . . .

The thing about tree pythons is that they are, um, not terribly friendly.  In fact, they are vicious little spawns from ####.  I recommend them to people who are thinking about keeping arboreal *vipers* and want to know if they are ready for it.

Tree pythons (1) can hang on with their tails and strike out REALLY FAR, (2) make their living by catching birds on the wing, so they're REALLY FAST, and (3) need to pierce the bird feathers and hang on tight, so they have REALLY LONG TEETH.

There may be one out there somewhere that is placid and friendly towards humans. If so, I've never met it.  Every time I've ever gotten close to one, I ended up getting poked full of holes.  Yikes.  

And yes, they are kinda delicate as far as heat and humidity requirements.  They're really susceptible to respiratory infections, and giving them shots is, uh, no fun at all.

So . . .  my recommendation is that you have lots of care experience before trying them, and that you forget about ever ever under any circumstances interacting with it in any nonhostile way.  It will undoubtedly try to nail you at every opportunity.

Now, all the ones I interacted with were wildcaughts, so maybe one raised from a captive-bred youngling would have a better attitude as it got older.  But the wildcaught juvies I've seen were all just as belligerent as the adults.

Unfortunate, since they are gorgeous snakes.

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"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 18 2006,18:12   

Quote (Flint @ Dec. 18 2006,14:01)
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.

In a nutshell, the problem isn't that we have NO idea how life could have begun, but we have LOTS --- and no way as yet of knowing which are right (or if indeed all are wrong and the right one is something we haven't even thought of yet).

So at this point in research, we've barely begun to be able to rule things OUT, much less look at details of what's ruled IN.

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"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 18 2006,18:17   

It should also be pointed out that abiogenesis is a very young science -- it didn't really begin until the Urey-Miller experiments in the 50's, then languished for several decades, and didn't get any serious funding until just a few years ago when NASA (bless their hearts) managed to convince Congress that origin-of-life research is somehow a part of space exploration.

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Louis



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(Permalink) Posted: Dec. 19 2006,03:43   

Lenny,

Thnaks for your comments on green tree pythons. Pretty much as I had read elsewhere. I agree that it's a pity that these things are so tricky as terrarium pets for all the reasons mentioned.

I love royal pythons, I had a royal as my first snake and even though he was wild caught (which I didn't know when I bought him, live and learn) and a bit troublesome at first, he was a great pet. So I guess it's back to them! Also the trade in captive bred royals is much better now, obviously meaning I can get a healthier, less stressed snake, better for all concerned.

One piece of info I have heard (and sort of found to be true....ish! ) about royals that I would love to confirm is that they get stressed if given too much space in a terrarium. It sounds like baloney to me, but my royal was happier in a medium sized terrarium than a large one. And when I say happier you know what I mean, less using Louis as a pincushion, more eating mice! Have you ever heard anything like this?

Louis

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Ved



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(Permalink) Posted: Dec. 19 2006,10:48   

While you guys are on the topic of tree snakes, I just wanted to say that ever since I discovered flying snakes I've had a whole new appreciation for evolution and what trees have enabled to happen to creatures that moved into them- including our ancestors. The trees provided stepping stones into the vertical where a creature as seemingly un-flightworthy as a snake can first take advantage of being able to parachute, and then take it to the point of actually being able to truly glide (farther than it falls). Sadly this is the kind of stuff that people like afdave have absolutely no interest in.

  
"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 19 2006,18:32   

Quote (Louis @ Dec. 19 2006,03:43)
One piece of info I have heard (and sort of found to be true....ish! ) about royals that I would love to confirm is that they get stressed if given too much space in a terrarium. It sounds like baloney to me, but my royal was happier in a medium sized terrarium than a large one. And when I say happier you know what I mean, less using Louis as a pincushion, more eating mice! Have you ever heard anything like this?

It's actually not that unusual for smaller snakes, and particularly in very young ones.  In the wild, snakes are on the menu for lots of larger predators -- indeed, one of their primary predators are birds of prey, against which they have virtually no defense.  So, many snakes get EXTREMELY stressed when they are in large open areas -- it leaves them very exposed to aerial predators, and they don't like it at all.  Snakes always feel much safer in cozy closed-in areas where predators have a hard time finding them.  Even in large open areas like deserts, you'll not often find snakes out in the open -- they're usually curled up in a rock pile or under a scrub bush or something.

So the trick is to make sure they have a secure hidey-hole or hidebox where they can feel nice and safe, and can then venture out into the open areas (usually at night) as they wish.


BTW, for the American herpers out there, "royal python" is the name that people across the Pond call _Python regius_, which is known in the US as the "ball python" because of its habit of curling itself into a tight ball when frightened.

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"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 19 2006,18:45   

Quote (Ved @ Dec. 19 2006,10:48)
While you guys are on the topic of tree snakes, I just wanted to say that ever since I discovered flying snakes I've had a whole new appreciation for evolution and what trees have enabled to happen to creatures that moved into them- including our ancestors. The trees provided stepping stones into the vertical where a creature as seemingly un-flightworthy as a snake can first take advantage of being able to parachute, and then take it to the point of actually being able to truly glide (farther than it falls). Sadly this is the kind of stuff that people like afdave have absolutely no interest in.

You would like this website:

http://www.flyingsnake.org


In the "publications" section, you may even notice this, by someone you know  :)   :

Notes on the Biology and Captive Care of the Flying Snakes (Chrysopelea). By Lenny Flank, Jr. Reptile and Amphibians Hobbyist magazine, July 1999, pages 28-32. Captive care, focusing on C. ornata.


Back in 1999, Jake Socha and I were, as far as we could tell, the only people in the US who kept captive flying snakes.  I used mine in the educational talks I was doing at the time for school classes, scout troops, etc.


As for people like AFDave, you're right.  The creationuts like to loudly and endlessly blither on and on about how wondrous God's Creation is and all that, but in actuality they are all utterly totally pig-ignorant about the natural world.  Most don't know a prokaryote from a pachyderm.  And most don't care.  (shrug)

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Ved



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(Permalink) Posted: Dec. 20 2006,11:21   

Quote
You would like this website:

Heh, very cool. That was the site I had stumbled on that actually had video of the snakes moving through the air. They say a picture is worth a thousand words... I think a video is worth a million. I remember one particular vid where a snake quickly flipped around so that it flew back towards the building it was released from, I guess to try to evade recapture. Obviously it was very nimble and very much in control of it's glide.

Hmm, if I'd have paid more attention to the references at the time I probably would have recognised you. Cool, man. Small world.

  
"Rev Dr" Lenny Flank



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(Permalink) Posted: Dec. 20 2006,18:31   

Quote (Ved @ Dec. 20 2006,11:21)
I remember one particular vid where a snake quickly flipped around so that it flew back towards the building it was released from, I guess to try to evade recapture. Obviously it was very nimble and very much in control of it's glide.

I'd guess that having a long thin body is advantageous for steering, since each body section can be moved independently to adjust the glide pattern.

There are also flying frogs, which use webbing between their toes to catch air and glide.  With four independent steering surfaces, I'd guess they are pretty good steer-ers too (I've never seen one, though).

The so-called "flying geckos" don't actually fly -- they use their flaps of skin for camouflage.

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Steviepinhead



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(Permalink) Posted: Dec. 20 2006,19:15   

Quote ("Rev Dr" Lenny Flank @ Dec. 20 2006,18:31)

Lenny:
Quote
The so-called "flying geckos" don't actually fly -- they use their flaps of skin for camouflage.


Dang!  And just when I was starting to think that that old "What good is half a wing?" argument really had something going for it...

  
ScaryFacts



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(Permalink) Posted: Dec. 26 2006,19:32   

Those videos are impressive, they just need one more bad-ass mofo:


   
The Ghost of Paley



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(Permalink) Posted: Dec. 27 2006,16:44   

Ppppplllltttt! Give me a good grizzly anytime! Even if they are known to dump fights* when the bribe is tasty enough. :angry:



*Don't worry, no one gets injured - I wouldn't link to an animal getting hurt. It's just funny to watch a cougar chase a bear three times its size......

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The Ghost of Paley



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(Permalink) Posted: Jan. 03 2007,14:48   

I checked out an organic chemistry textbook and have been looking over it when I've had the opportunity. Pretty good stuff, although it doesn't cover some issues as deeply as I'd like. Does anyone recommend any particular organic chem websites?

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Dr.GH



Posts: 2113
Joined: May 2002

(Permalink) Posted: Jan. 03 2007,17:50   

Re: Scaly Friends

The most dumb lucky snake experience I ever had was in southern Yucatan.  I was walking along and saw three men with machetes drawn surrounding a bush.  I walked up and asked if there was a snake in the bush.  (I was in the town of Bacalar, and I was expecting three gringa herpetologists to visit.  I had met them in Ticul and we had had some fun.  I was a herp turned anthro guy).  The locals said yes, there was a deadly snake in the bush.  Locals always say that all snakes are deadly, so I discounted their warning. I saw a bit of it and its head.  I took my hat and waved it in front of the snake, and when it struck at my hat I grabbed the little cutie.  

It was a ferdelance about 3 feet long (a young'n).

I kept it for 3 or 4 days, but the chicas never showed up.  Luck can only last so long.

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"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Dr.GH



Posts: 2113
Joined: May 2002

(Permalink) Posted: Jan. 03 2007,18:05   

Re: Big Kitty

I worked on a mountain lion tagging/tracking project in Orange County Ca.  We were training two puppies as lion dogs.  On their first time to run with the three adults (two dogs and their mam) the pack gave up the chase except for the puppies.  They worked another hour and treed the cat!  

We had been so ticked off that these two stupid puppies were still running until we heard them switch to a "cat in the tree" yip.  The adults picked up their ears and tore off.  We only had radio collars on the two dogs, so it really helped find the tree et al.

--------------
"Science is the horse that pulls the cart of philosophy."

L. Susskind, 2004 "SMOLIN VS. SUSSKIND: THE ANTHROPIC PRINCIPLE"

   
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Jan. 04 2007,02:25   

That's one thing I do envy you Americans and Australians etc. Decent wildlife. Oh sure we in the UK have beautiful and stunning fauna and flora, but the most dangerous thing we'll ever come across is a mildly irritated badger.

Although there was this one time that I was stalking a squirrel with a flick knife.....

Naaahhh sorry. Mountain lions' got me beat!

Louis

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Bye.

  
Steviepinhead



Posts: 532
Joined: Jan. 2006

(Permalink) Posted: Jan. 04 2007,15:02   

Talk about a pinhead!

I managed to read all of Dr GH's mountain lion post--probably twice through--and still overlook the "mountain" in mountain lion both times ("ya can bring the lion to the mountain, but ya can't...).

I definitely worked out that it was an amusing post about the precocity of the lion-dog pups-in-training, but I spent a fair amount (of what passes in pinheads for) mental effort trying to figure out if there was some major sprawling big-game park in Orange County that I had managed to never hear about...

Yeesh!

  
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