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Reciprocating Bill



Posts: 4244
Joined: Oct. 2006

(Permalink) Posted: Oct. 15 2008,18:00   

Quote (Daniel Smith @ Oct. 15 2008,17:26)
The beauty of my prediction is that it doesn't depend on my knowledge of science, it depends on yours - all of you.  I'm predicting, not only that you don't know how any of life's systems came about, but that you never will!

To make this clear, imagine for a moment that there are no scientists, including "all of us," in the discussion.

What we are left with is you, and your ilk, holding to your position without regard to your knowledge of science - a stance that includes holding fast to your position with no knowledge of the relevant science whatsoever. Not just with regard to origins of life - but regarding origins of anything in nature.

This probably can't be improved upon as an embrace of abject and intentional ignorance. Thank you.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
Reed



Posts: 274
Joined: Feb. 2008

(Permalink) Posted: Oct. 15 2008,20:34   

Quote (Daniel Smith @ Oct. 15 2008,14:26)
I've read through all your comments and I must say that none of you have tried to answer my question save Louis,

If you read them more carefully, you might have figured out why your question is irrelevant to your so called prediction.
Quote

The beauty of my prediction is that it doesn't depend on my knowledge of science, it depends on yours - all of you.  I'm predicting, not only that you don't know how any of life's systems came about, but that you never will!

The ugly side of your "prediction" is that it is purely negative and pulled out of thin air without any particular rational basis. Despite your protestations, it still boils down to the argument from ignorance. Acknowledging that you don't have any actual expertise in the relevant field, and without reading the literature Louis suggested, you don't think science will ever figure it out. We should care because ... ?

How is it different from any other unknown in science ? Better yet, how is it different from things that were completely mysterious at one time, but now are well understood ?

Compared to many of these, we actually have a pretty good idea of what is required for abiogenesis. Do we have the whole picture ? Hell no. We do however have a large set of puzzle pieces dumped out on the table, and putting it together looks like it's going to be a lot more fun that just saying "goddidit" and giving up.
     
Quote (Louis @ bathroom,wall)

Wow you read all those books and papers and the associated references in one night? Impressive. Truly amazing research Danny.

Now now, he clearly stated that he didn't need to read them to know what they would or wouldn't say ;) Truly Astonishing Reasoning Display!

  
Henry J



Posts: 4112
Joined: Mar. 2005

(Permalink) Posted: Oct. 15 2008,22:29   

Quote
Do you think that none of the best chemists have found possible natural pathways for the origin of homochiral biologically significant monomers?


T.O. had a post of the month on that subject a year or two ago.

Henry

Oops, it was only a few months ago, not years.

http://www.talkorigins.org/origins/postmonth/2008_07.html

Basic conclusion was that modern organisms are adapted to what's available now, and simply lost the ability to deal with the forms that ceased to be around, because the ability to deal with them had ceased to matter.

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 16 2008,02:53   

Quote (Henry J @ Oct. 16 2008,04:29)
Quote
Do you think that none of the best chemists have found possible natural pathways for the origin of homochiral biologically significant monomers?


T.O. had a post of the month on that subject a year or two ago.

Henry

Oops, it was only a few months ago, not years.

http://www.talkorigins.org/origins/postmonth/2008_07.html

Basic conclusion was that modern organisms are adapted to what's available now, and simply lost the ability to deal with the forms that ceased to be around, because the ability to deal with them had ceased to matter.

Thanks for that Henry, that saved me a lot of typing!

I'll bet that Danny knows what it says before he's read it though.

The "life first" possibility for biological homochirality is certainly one option, a good one even, but there are several chemical (i.e. non-biological) processes that can result in  homochiral populations of molecules. I want to know if any of the methods we chemists (not even the best chemists) have at our disposal are good enough for Danny. And as we know from previous references and books mentioned to Danny, he clearly is a terrific analyser of research data.

Louis

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

  
Stephen Elliott



Posts: 1754
Joined: Oct. 2005

(Permalink) Posted: Oct. 16 2008,07:22   

Quote (Daniel Smith @ Oct. 15 2008,16:26)
I've read through all your comments and I must say that none of you have tried to answer my question save Louis, who provided numerous links to abiogenesis papers which, I'm sure, amount to a bunch of head scratching by the best and brightest.  (Note to Louis:  Don't bother telling me when they're close (they're not now).  Let me know when they've figured it out.)

Now, let me say this, although you all have turned this into an abiogenesis argument, it doesn't have to be.  You see, I'm predicting that man will never be able to chart a detailed course for the origin of any of life's systems.  It's not just OOL, it's OOA (origin of anything).

The beauty of my prediction is that it doesn't depend on my knowledge of science, it depends on yours - all of you.  I'm predicting, not only that you don't know how any of life's systems came about, but that you never will!

It seems you'd all be chomping at the bit to prove me wrong by citing one of the trillions of life's systems for which a detailed evolutionary pathway has been found, but for some reason all I get are supposedly smart people denigrating me for my lack of knowledge.

Evotards?  Maybe.

PS.  JohnW, I'm not conceding a possible chemical pathway: I'm saying there is none.  The mere fact that the best chemists among us cannot find any possible chemical pathways for OOL, nor any possible biochemical pathways for OOA, speaks volumes about the "impossibility" of natural origins.

Even though we are made of chemicals?

What is your point?

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 16 2008,07:36   

Quote (Stephen Elliott @ Oct. 16 2008,07:22)
Quote (Daniel Smith @ Oct. 15 2008,16:26)
I've read through all your comments and I must say that none of you have tried to answer my question save Louis, who provided numerous links to abiogenesis papers which, I'm sure, amount to a bunch of head scratching by the best and brightest.  (Note to Louis:  Don't bother telling me when they're close (they're not now).  Let me know when they've figured it out.)

Now, let me say this, although you all have turned this into an abiogenesis argument, it doesn't have to be.  You see, I'm predicting that man will never be able to chart a detailed course for the origin of any of life's systems.  It's not just OOL, it's OOA (origin of anything).

The beauty of my prediction is that it doesn't depend on my knowledge of science, it depends on yours - all of you.  I'm predicting, not only that you don't know how any of life's systems came about, but that you never will!

It seems you'd all be chomping at the bit to prove me wrong by citing one of the trillions of life's systems for which a detailed evolutionary pathway has been found, but for some reason all I get are supposedly smart people denigrating me for my lack of knowledge.

Evotards?  Maybe.

PS.  JohnW, I'm not conceding a possible chemical pathway: I'm saying there is none.  The mere fact that the best chemists among us cannot find any possible chemical pathways for OOL, nor any possible biochemical pathways for OOA, speaks volumes about the "impossibility" of natural origins.

Even though we are made of chemicals?

What is your point?

I suspect Daniel was not 100% sure that everybody thought he was an idiot, so he's just making sure.

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Albatrossity2



Posts: 2779
Joined: Mar. 2007

(Permalink) Posted: Oct. 16 2008,07:59   

Quote (oldmanintheskydidntdoit @ Oct. 16 2008,07:36)
I suspect Daniel was not 100% sure that everybody thought he was an idiot, so he's just making sure.

It worked...

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 16 2008,08:06   

Quote (Albatrossity2 @ Oct. 16 2008,13:59)
Quote (oldmanintheskydidntdoit @ Oct. 16 2008,07:36)
I suspect Daniel was not 100% sure that everybody thought he was an idiot, so he's just making sure.

It worked...

That's what I like about you Albatrossity, you're always on hand to praise good work done well. After all, Danny is trying very very hard, it's only right he should get the recognition he deserves.

I'm still impressed he read tens of thousands of pages of fairly complex chemistry in one night, and absorbed the information sufficiently well to discount all of it. We are truly in the presence of a tremendously astute reasoning dude!

;-)

Louis

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

  
J-Dog



Posts: 4369
Joined: Dec. 2006

(Permalink) Posted: Oct. 16 2008,08:35   

Um... I'll take the Enchidna instead...



--------------
Come on Tough Guy, do the little dance of ID impotence you do so well. - Louis to Joe G 2/10

Gullibility is not a virtue - Quidam on Dembski's belief in the Bible Code Faith Healers & ID 7/08

UD is an Unnatural Douchemagnet. - richardthughes 7/11

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 16 2008,13:38   

Quote (didymos @ Oct. 15 2008,15:06)
       
Quote (Daniel Smith @ Oct. 15 2008,14:26)

Now, let me say this, although you all have turned this into an abiogenesis argument, it doesn't have to be.

WTF?  Chucky, did you not kick this whole thing off by linking to your "Argument From Impossibility"?  Do you recall what the first sentence of that was?  Apparently not:

               
Quote
I propose that the ultimate origins of life on this planet will forever be impossible to fully explain.


Now, that bolded part?  You know that there's another way to say that right?  It's fucking (that one's for Louis) abiogenesis.  So, there's no "you all" turning this into anything. It's exactly the discussion you wanted, and it's what you've gotten.  Your memory is either severely impaired or you're just dishonest.

Did you notice I said "origins" (plural)?  Did you also notice that the specific question I posed in my argument was about amino acid synthesis in E. coli?  
From my "Argument From Impossibility":    
Quote
In E. coli, (one of the simplest unicellular lifeforms on the planet), the amino acids lysine, threonine, isoleucine, and methionine are synthesized from the compound oxaloacetate via a series of biochemical steps - each of which requires its own specific enzyme, (remember?). To get from oxaloacetate to lysine requires nine such steps, (and nine specific enzymes). Oxaloacetate to threonine requires five such steps and specific enzymes. Isoleucine requires ten steps, and methionine seven. Some of these steps are shared though: the first three steps are shared by all four amino acids, then three of the four share the next step, and two of the four the next. Therefore, all that needs explaining are a total of nineteen steps and enzymes - not thirty-one.

So the challenge is to explain how the current amino acid synthesis system in E. coli originated via natural mechanisms. How did each of the nineteen specific enzymes come to be? How did each of the nineteen steps in the biochemical pathway come together in the correct order to form these essential amino acids? What was the immediate precursor to the current system? What were all the intermediate steps? Remember that this explanation must account for each enzyme and each step.

I predict though that no one will be able to answer this challenge with any detail. This, and countless other origins, will forever remain an "Impossibility".
(notice that bolded part?)  It's clear, if you read the entire argument, that I'm not just talking about abiogenesis.

I was trying to make it easier on you!  Instead of saying merely that abiogenesis research was a dead end, I'm saying that all research into random undirected origins - for any of life's systems - is a dead end.  Now, instead of having to explain OOA to prove me wrong, all you have to do is explain the origin of one biosystem in any organism via a natural, undirected pathway.

Either way, you're all still avoiding the issue.  None of you has any answers as to how life or any of its subsequent systems originated.
             
Quote
     
Quote

PS.  JohnW, I'm not conceding a possible chemical pathway: I'm saying there is none.  The mere fact that the best chemists among us cannot find any possible chemical pathways for OOL, nor any possible biochemical pathways for OOA, speaks volumes about the "impossibility" of natural origins.


Ah yes: very trenchant indeed.  Just like generations of the best mathematicians among us failing to devise any proof of Fermat's Last Theorem spoke volumes about the impossibility of said proof.  Oh, wait, that's right: 357 years later a couple guys ended up proving it using completely novel techniques unknown to pre-20th century mathematics

Well then, good luck!  Let me know when you have an answer.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 16 2008,13:50   

Quote (Louis @ Oct. 15 2008,15:36)
Rather than get stuck in an endless loop of generalities, let's take one simple chemical issue: the origin of homochirality. Do you think that none of the best chemists have found possible natural pathways for the origin of homochiral biologically significant monomers?

Stick with this one simple issue, then we can move on to others.

I don't see homochirality as the big issue.  It's a small part of the overall problem though.  Even if all amino acids were left-handed, that still does not explain the way they are utilized in life.  There has to be some form of amino acid synthesis that will work within the mild conditions of the aqueous solution required for life (Miller's synthesis method will not work inside a living cell).  There must also be some form of polynucleotide synthesis, some form of polypeptide synthesis, some method of tying these two things together and some form of self-replication.  These are far bigger hurdles that chiralty.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 16 2008,14:15   

Since I am not allowed to edit my own posts I must repost just to correct this one letter!  "OOA" should have been "OOL"  
Quote (Daniel Smith @ Oct. 16 2008,11:38)
Now, instead of having to explain OOL to prove me wrong, all you have to do is explain the origin of one biosystem in any organism via a natural, undirected pathway.


--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
didymos



Posts: 1826
Joined: Mar. 2008

(Permalink) Posted: Oct. 16 2008,14:25   

Quote (Daniel Smith @ Oct. 16 2008,11:38)
 It's clear, if you read the entire argument, that I'm not just talking about abiogenesis.


Implication:  but I am talking about it.

 
Quote (Daniel Smith @ Oct. 16 2008,11:38)

 Instead of saying merely that abiogenesis research was a dead end,  I'm saying that all research into random undirected origins - for any of life's systems - is a dead end.


Translation:  I'm nitpicking and complaining that the hyper-pathetic level of detail I demand has not been met when it comes to various sub-problems involved in OOL research, so therefore, abiogenesis cannot and did not happen.  

 
Quote (Daniel Smith @ Oct. 16 2008,11:38)
I'm saying that all research into random undirected origins - for any of life's systems - is a dead end.  


Implication: not just life's systems, but life itself: you know, that abiogenesis stuff again.

 
Quote (Daniel Smith @ Oct. 16 2008,11:38)
 Now, instead of having to explain OOA to prove me wrong, all you have to do is explain the origin of one biosystem in any organism via a natural, undirected pathway.


No one has to prove you wrong, guy. That's just done for entertainment value.  You have to prove, or at least provide some evidence that:

a. You have any sort of clue as to what the fuck you're talking about, and
b. Your claims can be scientifically substantiated

 
Quote (Daniel Smith @ Oct. 16 2008,11:38)

Either way, you're all still avoiding the issue.  None of you has any answers as to how life or any of its subsequent systems originated.
 

Translation: but I'm not talking about abiogenesis or anything.  What gave you that idea? Why are you people trying to make this all about that?

 
Quote (Daniel Smith @ Oct. 16 2008,11:38)

 
Quote (didymos @ Oct. 15 2008,15:06)

Ah yes: very trenchant indeed.  Just like generations of the best mathematicians among us failing to devise any proof of Fermat's Last Theorem spoke volumes about the impossibility of said proof.  Oh, wait, that's right: 357 years later a couple guys ended up proving it using completely novel techniques unknown to pre-20th century mathematics

Well then, good luck!  Let me know when you have an answer.


You mean me personally?  Did you not get my point there?  Wait: never mind. Don't answer that.

(edited: verb tense)

--------------
I wouldn't be bothered reading about the selfish gene because it has never been identified. -- Denyse O'Leary, professional moron
Again "how much". I don't think that's a good way to be quantitative.-- gpuccio

  
Albatrossity2



Posts: 2779
Joined: Mar. 2007

(Permalink) Posted: Oct. 16 2008,14:53   

Quote (Daniel Smith @ Oct. 16 2008,13:38)
Either way, you're all still avoiding the issue.  None of you has any answers as to how life or any of its subsequent systems originated.

Daniel

I've asked this before but it has been ignored. So I'll try again.

What level of detail can you give us regarding the think-poof explanation for the origin of life that you apparently favor?

or, more specifically

If you demand such detail from science, but cannot provide it for your explanation, isn't that just a tad hypocritical?

thanks in advance

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 16 2008,16:16   

Quote (Daniel Smith @ Oct. 16 2008,19:50)
Quote (Louis @ Oct. 15 2008,15:36)
Rather than get stuck in an endless loop of generalities, let's take one simple chemical issue: the origin of homochirality. Do you think that none of the best chemists have found possible natural pathways for the origin of homochiral biologically significant monomers?

Stick with this one simple issue, then we can move on to others.

I don't see homochirality as the big issue.  It's a small part of the overall problem though.  Even if all amino acids were left-handed, that still does not explain the way they are utilized in life.  There has to be some form of amino acid synthesis that will work within the mild conditions of the aqueous solution required for life (Miller's synthesis method will not work inside a living cell).  There must also be some form of polynucleotide synthesis, some form of polypeptide synthesis, some method of tying these two things together and some form of self-replication.  These are far bigger hurdles that chiralty.

Homochirality is not a big issue eh? Wow!

Miller-Urey conditions won't work in a cell? Double wow!

Did it ever occur to you that the origin of homochirality is an enormous problem in abiogenesis? Explaining such a massively distinct use of one (energetically identical) enantiomer over another is a big deal....well it is to real scientists. No one claims that because amino acids are (predominantly) homochiral in living systems that this explains "the way they are used in life". I think you're a bit confused. You can hand wave it away, but it is a real success story.

As for the Miller-Urey conditions not being applicable  to the cell, well, erm, how do I put this delicately: OF COURSE THEY'RE NOT! They are proposed conditions for the synthesis of biologically significant molecules from a non biological source. These are things that are meant to happen before cells arise. Oh and whilst I think of it, brush up on the molecules that are available in space why don't you. You might find it interesting.

Take the next issue, polymerisation, do you have any idea how energetically favourable formation of the amide bond is? Especially in aqueous solution, one simple activating agent for the carboxylic acid and booooom! Polymers. Polymerisation isn't a problem, controlled polymerisation is. Bear in mind however that the current biological system of DNA/RNA + proteins is a highly evolved (i.e. "advanced") one. It's by no means certain that it, or anything like it, was the "first system". In fact it's very unlikely. If you have any background in chemistry I suggest you check out the book I recommend on the other thread by Pier Luigi Luisi. It's a cracker!

Why do I suspect that whatever hurdle we mention science has crossed you'll retreat to another one? I don't think you're entering into this discussion in good faith, which is a pity, because it's potentially a very interesting one. Still, like with FTK, I'm willing to help out if you're interested. I'd suggest you start with the basics, you appear a tad confused.

Louis

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

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 17 2008,05:03   

IT'S ALL TRUE!!!!!

Louis

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

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Oct. 17 2008,05:04   

Ooops I done did double postage. Free Richard Hughes (with every bottle of brown ale returned to the depot)!

Louis

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

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 17 2008,06:18   

Quote (Daniel Smith @ Mar. 12 2008,18:54)
I think I'm done here.

I'm just getting tired of arguing.

There's really no point to it anymore.  We're starting to cover topics we've already covered - sometimes several times.

I've learned lots since coming here.  Thanks to everyone who challenged me on things.  You forced me to take a long hard look at myself and my beliefs.  I'm sorry I came across as defensive and unwilling to learn because I really was listening.

I'd like to especially thank JAM for showing me the importance of evidence, data and TESTING!  I'm going to do everything in my power to destroy my own hypotheses and beliefs from now on.  Maybe I'll come back and let you all know how it turns out.

Later.

Danny boy, as you are now back and the same as ever why don't you take it back to "your" thread?

So, since you took a "long hard look at myself and my beliefs" what conclusions have you come to? That you and you alone are right and have seen the light and that everybody else is wrong, wrong, wrong?
Quote
I'm going to do everything in my power to destroy my own hypotheses and beliefs from now on.  Maybe I'll come back and let you all know how it turns out.

How did that go then?

Do you want to argue on the BW because you are embarrassed about the above quote? Afraid to return to your thread and continue the "argument" are you?

Why are you hiding away here? What are you afraid of?

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I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
oldmanintheskydidntdoit



Posts: 4999
Joined: July 2006

(Permalink) Posted: Oct. 17 2008,06:32   

Quote (Daniel Smith @ Oct. 16 2008,13:50)
I don't see homochirality as the big issue.  

What do you see as the big issue then?
 
Quote
It's a small part of the overall problem though.

What is the "overall problem"?
 
Quote
Even if all amino acids were left-handed, that still does not explain the way they are utilized in life.

What's your explanation?
 
Quote
There has to be some form of amino acid synthesis that will work within the mild conditions of the aqueous solution required for life (Miller's synthesis method will not work inside a living cell).

What is your proposed solution?
 
Quote
 There must also be some form of polynucleotide synthesis, some form of polypeptide synthesis, some method of tying these two things together and some form of self-replication.

I see. And your explanation is? The designer did it how exactly?  
Quote
These are far bigger hurdles that chiralty.

A far bigger hurdle would appear to be your Behe style rejection of evidence without giving it a proper reading.

I tell you what, I'll rip out the pages in a bible and tape in some basic biology textbooks. That way you can read it and it can have the ring of truth that you desire. If you like you can even pretend that primitive people, with no understanding of science as we know it wrote it, thus giving it that old-style ignorant veracity we know you love.

--------------
I also mentioned that He'd have to give me a thorough explanation as to *why* I must "eat human babies".
FTK

if there are even critical flaws in Gauger’s work, the evo mat narrative cannot stand
Gordon Mullings

  
Reciprocating Bill



Posts: 4244
Joined: Oct. 2006

(Permalink) Posted: Oct. 17 2008,08:34   

Quote (Albatrossity2 @ Oct. 16 2008,15:53)
 
Quote (Daniel Smith @ Oct. 16 2008,13:38)
Either way, you're all still avoiding the issue.  None of you has any answers as to how life or any of its subsequent systems originated.

Daniel

I've asked this before but it has been ignored. So I'll try again.

What level of detail can you give us regarding the think-poof explanation for the origin of life that you apparently favor?

or, more specifically

If you demand such detail from science, but cannot provide it for your explanation, isn't that just a tad hypocritical?

thanks in advance

Daniel, there is work to build upon:

I. Biological causality reflects the operation of two basic, complimentary units: Thinks and Poofs. A Think is a mind-like, timeless-sizeless representation of a Thing. A Poof is a hand-like manipulation of matter-energy such that the appropriate Thing is physically instantiated. A Think without a Poof is incapable of interacting with matter/energy, is therefore undetectable, and hence remains a somewhat of a theoretical abstraction. Similarly, a Poof can arise IFF informed by at least one Think.

Given sufficient agentic and material resources, Thinks and Poofs give rise to Things. Balanced Think/Poof calculations give rise to testable empirical predictions arising from the combinatorial mathematics of Thing Theory.

II. Thinks and Poofs are initiated by units of pure intelligent agency known as Rodins (think "The Thinker"). At the current state of theoretical development the Rodin remains a placeholder concept that has yet to be given empirical grounding. It is unclear, for example, whether there is a single Rodin, two Rodins, or countless Rodins and, if there exist more than one Rodin, whether all Rodins give rise to equally efficacious Think/Poofs. It is also unclear whether multiple Rodins stand in cooperative, competitive, or other relationship to one another, whether Rodins borrow Thinks inferred from the Things originated by other Rodins, whether Rodins have degrees of omniscience, and so forth. However, we have every reason to believe that these questions can be given empirical formulation and resolved through an appropriate combination of laboratory and field investigation.

With the above limitations in mind, we may begin to sketch the moving parts of a science of Intelligent Design, grounding it in a calculus of Rodins, Thinks, Poofs, and Things, and indeed begin to explore the operation of entities in any given instance of Intelligent Design.

IV. Intelligent Design may be said to have occurred when a Rodin gives rise to a Think or Thinks, which in turn invoke(s) a Poof or Poofs in order to originate a Thing.

Rodin-initiated Thinks are mind-like, agentic, timeless-sizeless representations. Poofs do the hand-like work of actually arranging matter/energy to conform to the specification of a given Think, giving rise to a Thing. A Rodin may "choose" to formulate a grand system of interlocking Thinks all apiece, yet implement such a Think-Structure imperceptibly over deep time by issuing Poofs only slowly and sequentially. Alternatively, a Think-Structure may give rise to thousands of simultaneous Poofs, yielding an (only apparently) saltational Thing Structure that instantaneously mirrors the underlying Think Structure. Biological Things that display Irreducible Complexity almost certainly issue from the latter sort of process: a single Rodin exerts its intrinsic intentionality to originates a complex biological Think Structure which is intern effected by means of multiple simultaneous, interlocking Poofs.

(The reader may find it helpful to imagine countless little hands equipped with little minds - I call them "Behes" - issuing from a Rodin or Rodins, swarming over and grasping bits of matter-energy - say, base pairs in a DNA molecule - and manipulating them with special tweezers to form Irreducibly Complex Biological Things.)

V. It should be clear from the above that a calculus of Rodins, Thinks, Poofs, Behes and a completed, empirical Thing Theory promises to dissolve some of the knottiest problems in biology today. For example, we may now confidently sketch the origins of life on earth: a Rodin or Rodins originated a complex Think-Structure that gave rise to both simultaneous and sequential Poofs that created the first biological Thing, detonating life on earth. All that remains is to supply the details.

In the future we hope to infer the properties of agentic Rodin or Rodins themselves, by tracing Think-Poof-Thing pathways much as the properties of elementary particles may be inferred from the ephemeral trails left within a cloud chamber. We anticipate that the biology of the 22nd century will be characterized by Rodin simulations (e.g. of Rodin belief-desire), the computational modeling of biological Think-Structures, the detection and deconstruction of Poof-efficacy at the Think-Thing interface, the simultaneous, coordinated operation of countless Behes, and eventually a completed Thing Theory. We may also confidently anticipate that a bankrupt Darwinism with truly be a "think" of the past.

--------------
Myth: Something that never was true, and always will be.

"The truth will set you free. But not until it is finished with you."
- David Foster Wallace

"Here’s a clue. Snarky banalities are not a substitute for saying something intelligent. Write that down."
- Barry Arrington

  
dogdidit



Posts: 315
Joined: Mar. 2008

(Permalink) Posted: Oct. 17 2008,08:48   

Pea. Owe. Tee. Double you.

--------------
"Humans carry plants and animals all over the globe, thus introducing them to places they could never have reached on their own. That certainly increases biodiversity." - D'OL

  
Wesley R. Elsberry



Posts: 4520
Joined: May 2002

(Permalink) Posted: Oct. 17 2008,09:00   

Quote

Danny boy, as you are now back and the same as ever why don't you take it back to "your" thread?


Daniel is restricted to posting on the BW. Don't expect him to be posting elsewhere.

A self-professed ignorant intrusion into a discussion of evolutionary computation got him the restriction. Continued reliance on the argument from ignorance confirms that each time he comments.

E: prepositions

Edited by Wesley R. Elsberry on Oct. 17 2008,09:01

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
didymos



Posts: 1826
Joined: Mar. 2008

(Permalink) Posted: Oct. 17 2008,09:06   

From Chuck's "argument", which is in no way about abiogenesis:

 
Quote

In 1953, Stanley L. Miller and Harold C. Urey, working at the University of Chicago, conducted an experiment that showed that amino acids could be formed by shooting electricity through a mixture of methane, ammonia, hydrogen, and water. This experiment was hailed by many to be evidence that living things can arise from non-living elements. Unfortunately that's not how amino acids are formed in real living cells.


Guess what Chuck?  There's even more to ignore than ever before about Miller-Urey's amino score:
 
Quote

Now the cool part, though: the scientists who unearthed the old samples ran them through modern analysis techniques, which are a bit more sensitive than the tools they had in the 1950s. In 1953, Miller reported the recovery of five amino acids from his experiment. The reanalysis found twenty two amino acids and five amines in the vials. He was more successful than he knew!


I'm quite sure of course that you'll just bitch and moan some more that "Oh noes! Miller-Urey CAN'T happen in teh cell!!!!111111!!!!! You can't haz teh amino acids. Is teh impossible, foolish Evotards! "

Ah, but we can haz, because as Louis and now PZ have pointed out (and really, the reminder shouldn't be necessary to one such as your bad creationist self, what with your seemingly telepathy-assisted research deeds):
 
Quote

Yes, I know that Miller's reducing atmosphere is no longer considered to be an accurate representation of the ancient earth's atmosphere. However, the experiment still supported a key idea: that the synthesis of these organic compounds did not require any kind of guiding hand, but would naturally emerge from unassisted chemical reactions. Furthermore, the authors of this paper argue that while it was not a good model of the global atmosphere, it might still model local conditions in isolated areas.


I'm curious:  in your obviously deep and profound studies of abiogenesis (which we're not talking about) and other biological systems, did you mayhap chance upon this particular exercise in best-and-brightest head-scratching?

 
Quote
Evolution of Amino Acid Frequencies in Proteins Over Deep Time: Inferred Order of Introduction of Amino Acids into the Genetic Code
Dawn J. Brooks, Jacques R. Fresco, Arthur M. Lesk and Mona Singh

To understand more fully how amino acid composition of proteins has changed over the course of evolution, a method has been developed for estimating the composition of proteins in an ancestral genome. Estimates are based upon the composition of conserved residues in descendant sequences and empirical knowledge of the relative probability of conservation of various amino acids. Simulations are used to model and correct for errors in the estimates. The method was used to infer the amino acid composition of a large protein set in the Last Universal Ancestor (LUA) of all extant species. Relative to the modern protein set, LUA proteins were found to be generally richer in those amino acids that are believed to have been most abundant in the prebiotic environment and poorer in those amino acids that are believed to have been unavailable or scarce. It is proposed that the inferred amino acid composition of proteins in the LUA probably reflects historical events in the establishment of the genetic code.


If so, isn't it ever so interesting that it provides some possible steps in the establishment of the standard amino acids in the ancient genome?  Oh, but wait.  You simply must have overlooked that paper, based on this statement:

 
Quote (Daniel Smith @ Oct. 14 2008,11:46)
 It's the ability to provide possible steps that I'm predicting will be impossible.


True enough, that was actually in reference to abiogenesis specifically, but since you're not talking about that, I figure it may just as well apply to this other stuff you mentioned:

 
Quote (Daniel Smith @ Oct. 12 2008,11:43)

If you had, you'd know that the "answers" I'm talking about are answers to questions about how life's systems originated.  And yes, when it comes to origins, science has none (and never will).  That's my point.


I mean, the standard amino acids certainly qualify as one of "life's systems", wouldn't you agree?  

And then there's this from your original "argument":

 
Quote
I predict though that no one will be able to answer this challenge with any detail. This, and countless other origins, will forever remain an "Impossibility".


Any detail, you said.  Well, I say, looks like you've been answered in at least some detail on abiogenesis (with which, of course, you're actually totally not in the least concerned and you'd really rather we all stopped trying to make it all about that) and now the establishment of amino acids in the ancestral genome.  So, basically, you're just goddamn wrong.  Oh, and this?

 
Quote (Daniel Smith @ Oct. 14 2008,12:03)

What I want is an undisputed (by the experts), verifiable (all chemical steps worked out), possible pathway from non-life to life, or (if you read my blog) from some plausible precursor to the present E. coli amino acid synthesis system for lysine, threonine, isoleucine, and methionine.  There must be sufficient detail and the scientific community must reach a consensus that, 'yes, we've figured it out'.


Yeah, sorry: that goalpost-shifting crap doesn't fly.  You set the standard in your soi-disant argument.  It's been met.  But in the spirit of things, I'll make a prediction:  you'll never fucking admit it.

(edited: to strengthen some mockery)

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I wouldn't be bothered reading about the selfish gene because it has never been identified. -- Denyse O'Leary, professional moron
Again "how much". I don't think that's a good way to be quantitative.-- gpuccio

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 17 2008,17:46   

Quote (didymos @ Oct. 16 2008,12:25)
 
Quote (Daniel Smith @ Oct. 16 2008,11:38)
 It's clear, if you read the entire argument, that I'm not just talking about abiogenesis.


Implication:  but I am talking about it.

     
Quote (Daniel Smith @ Oct. 16 2008,11:38)

 Instead of saying merely that abiogenesis research was a dead end,  I'm saying that all research into random undirected origins - for any of life's systems - is a dead end.


Translation:  I'm nitpicking and complaining that the hyper-pathetic level of detail I demand has not been met when it comes to various sub-problems involved in OOL research, so therefore, abiogenesis cannot and did not happen.  

     
Quote (Daniel Smith @ Oct. 16 2008,11:38)
I'm saying that all research into random undirected origins - for any of life's systems - is a dead end.  


Implication: not just life's systems, but life itself: you know, that abiogenesis stuff again.

     
Quote (Daniel Smith @ Oct. 16 2008,11:38)
 Now, instead of having to explain OOA to prove me wrong, all you have to do is explain the origin of one biosystem in any organism via a natural, undirected pathway.


No one has to prove you wrong, guy. That's just done for entertainment value.  You have to prove, or at least provide some evidence that:

a. You have any sort of clue as to what the fuck you're talking about, and
b. Your claims can be scientifically substantiated

     
Quote (Daniel Smith @ Oct. 16 2008,11:38)

Either way, you're all still avoiding the issue.  None of you has any answers as to how life or any of its subsequent systems originated.
 

Translation: but I'm not talking about abiogenesis or anything.  What gave you that idea? Why are you people trying to make this all about that?

     
Quote (Daniel Smith @ Oct. 16 2008,11:38)

     
Quote (didymos @ Oct. 15 2008,15:06)

Ah yes: very trenchant indeed.  Just like generations of the best mathematicians among us failing to devise any proof of Fermat's Last Theorem spoke volumes about the impossibility of said proof.  Oh, wait, that's right: 357 years later a couple guys ended up proving it using completely novel techniques unknown to pre-20th century mathematics

Well then, good luck!  Let me know when you have an answer.


You mean me personally?  Did you not get my point there?  Wait: never mind. Don't answer that.

(edited: verb tense)

Career advice:  Don't become a translator.  Your translations are way off the mark!

Hint: It's not that I'm not talking about abiogenesis, it's that I'm not just talking about abiogenesis.  If you want to only discuss abiogenesis, be my guest.  Let me know when the scientific community reaches a consensus on that.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Albatrossity2



Posts: 2779
Joined: Mar. 2007

(Permalink) Posted: Oct. 17 2008,18:22   

Quote (Daniel Smith @ Oct. 17 2008,17:46)
Let me know when the scientific community reaches a consensus on that.

And you be sure to let me know when you will be providing details about the think-poof notion of how life on earth came to be.

Thanks in advance for ignoring the questions next time you post.

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 17 2008,19:01   

Quote (Louis @ Oct. 16 2008,14:16)
               
Quote (Daniel Smith @ Oct. 16 2008,19:50)
                 
Quote (Louis @ Oct. 15 2008,15:36)
Rather than get stuck in an endless loop of generalities, let's take one simple chemical issue: the origin of homochirality. Do you think that none of the best chemists have found possible natural pathways for the origin of homochiral biologically significant monomers?

Stick with this one simple issue, then we can move on to others.

I don't see homochirality as the big issue.  It's a small part of the overall problem though.  Even if all amino acids were left-handed, that still does not explain the way they are utilized in life.  There has to be some form of amino acid synthesis that will work within the mild conditions of the aqueous solution required for life (Miller's synthesis method will not work inside a living cell).  There must also be some form of polynucleotide synthesis, some form of polypeptide synthesis, some method of tying these two things together and some form of self-replication.  These are far bigger hurdles that chiralty.

Homochirality is not a big issue eh? Wow!

Miller-Urey conditions won't work in a cell? Double wow!

Did it ever occur to you that the origin of homochirality is an enormous problem in abiogenesis? Explaining such a massively distinct use of one (energetically identical) enantiomer over another is a big deal....well it is to real scientists. No one claims that because amino acids are (predominantly) homochiral in living systems that this explains "the way they are used in life". I think you're a bit confused. You can hand wave it away, but it is a real success story.

As for the Miller-Urey conditions not being applicable  to the cell, well, erm, how do I put this delicately: OF COURSE THEY'RE NOT! They are proposed conditions for the synthesis of biologically significant molecules from a non biological source. These are things that are meant to happen before cells arise. Oh and whilst I think of it, brush up on the molecules that are available in space why don't you. You might find it interesting.

Take the next issue, polymerisation, do you have any idea how energetically favourable formation of the amide bond is? Especially in aqueous solution, one simple activating agent for the carboxylic acid and booooom! Polymers. Polymerisation isn't a problem, controlled polymerisation is. Bear in mind however that the current biological system of DNA/RNA + proteins is a highly evolved (i.e. "advanced") one. It's by no means certain that it, or anything like it, was the "first system". In fact it's very unlikely. If you have any background in chemistry I suggest you check out the book I recommend on the other thread by Pier Luigi Luisi. It's a cracker!

Why do I suspect that whatever hurdle we mention science has crossed you'll retreat to another one? I don't think you're entering into this discussion in good faith, which is a pity, because it's potentially a very interesting one. Still, like with FTK, I'm willing to help out if you're interested. I'd suggest you start with the basics, you appear a tad confused.

Louis

I appreciate the lesson on homochiralty being a bigger problem that I thought.  Of course that does nothing to lessen my argument since the "explanation" given was just that it might be possible (theoretically), under the right conditions, to form all one-handed amino acids.  From the T.O. article:              
Quote
First, L- amino acids will randomly convert to D- amino acids over time, and D- forms will convert to L- forms. This is called "racimization" because eventually you will end up with equal amounts of L- and D- amino acids. The rate that this occurs at varies with the amino acid, and its surroundings. The fastest conversion happens to amino acid molecules all by themselves in hot water. Under cold, dry conditions when the amino acids are attached to one another, or better yet, if they are also attached to a mineral, racimization can be very slow. Very, very slow.

This means that if there is even a tiny advantage one way or the other, the favored form will become the dominant form.

First, I'm not sure how the second statement follows from the first.  I don't see how a "tiny advantage" will cause a "dominant form".  I can see it perhaps causing a slight imbalance, but not a dominance - especially since it's only under cold, dry conditions; while attached to a mineral; and under intense selective pressure, that amino acids will supposedly favor one-handedness.  What about the mild conditions and aqueous solution necessary for life?  According to T.O., they'll naturally revert to a 50/50 mixture (unless regulated).  
Then there's this is from the paper
"Homochiral growth through enantiomeric cross-inhibition"          
Quote
The chirality of molecules in living organisms must have been fixed
at an early stage in the development of life. All life that we know is
based on RNA and DNA molecules with dextrarotatory sugars. There
is growing evidence that the RNA world (Woese, 1967; Crick, 1968;
Orgel, 1968; see also Wattis & Coveney 1999) must have been preceded
by a simpler pre-RNA world made up of achiral constituents (Bada,
1995, Nelson et al., 2000). An alternative carrier of genetic code are
peptide nucleic acids or PNA (Nielsen, 1993). These can be rather
simple and are currently discussed in connection with the idea to build
artificial life (Rasmussen et al., 2003). Furthermore, although PNA can
still be chiral (Tedeschi et al., 2002), there are also forms of PNA that
are achiral (Pooga et al., 2001), suggesting that chirality may have
developed later when the first RNA molecules formed
.
In current proposals to build artificial life, chirality does not seem to
be crucial. The PNA molecules is proposed to act primarily as charge
carrier, i.e. a very primitive functionality compared to the genetic code
in contemporary cells (Rasmussen et al., 2003). At this stage, homochirality
may have been introduced by chance. This is also supported
by the fact that chiral polymers of the same chirality tend to have a
more stable structure (Pogodina et al., 2001) and would therefore be
genetically preferred.
Since the introduction of chiral molecules is assumed to take place
at a stage when there is already growth and self-replication
, it is also
plausible to assume that the existence of chiral molecules has an autocatalytic
effect in producing new chiral molecules of the same chirality
(Kondepudi et al., 1990).(my emphasis)
 So chiralty developed "when the first RNA molecules formed" and "at a stage when there is already growth and self-replication"?  How does this jibe with the cold dry meteorite that formed all these left-handed amino acids in the first place?  I guess you'll have to explain to me how this problem has been solved.

As for polymerization, the favorability of the amide bond is a plus for your side of the argument, but without some form of organization and some form of regulation, these polymers are essentially useless.  That is a very big minus.

As for the Miller-Urey conditions, the fact that most of the chemical reactions within a living cell would occur far too slowly to be of any value unless catalyzed by specific enzymes is a big minus for you.  Enzymes, as I'm sure you know, are specific proteins.  But, without some form of protein synthesis we can't get any proteins!  Yet the chemical reactions involved in protein synthesis require - (you guessed it) enzymes!  Kind of a Catch-22 there isn't it?  Of course the standard explanation is that early life was much simpler so perhaps no enzymes were required.  To that I can argue - if life was that simple, we should be able to re-create such a thing in the lab.  I'm predicting they'll never cross that bridge.

Also, it doesn't really matter much that they were able to form amino acids from non-living molecules because, as you said, the building blocks of life are abundantly available throughout the universe.  It's the specific organization of these molecules that separates living organisms from their constituent parts.  They must show that chemicals are able to self-organize, self-catalyze, self-regulate, and self-replicate, then they'll actually be getting somewhere.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 17 2008,19:13   

Quote (oldmanintheskydidntdoit @ Oct. 15 2008,15:22)
So Daniel, find any        
Quote
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.

yes?

Sorry oldman, didn't mean to ignore you!

The answer is Yes. I did find something interesting mathematically.
http://journals.indexcopernicus.com/fulltxt.php?ICID=11633
   
Quote
Can the genetic code be mathematically described?
Diego L. Gonzalez
St. George School Foundation and National Research Council of Italy, Isola di San Giorgio Maggiore, Venice, Italy
Summary
From a mathematical point of view, the genetic code is a surjective mapping between the set
of the 64 possible three-base codons and the set of 21 elements composed of the 20 amino
acids plus the Stop signal. Redundancy and degeneracy therefore follow. In analogy with the
genetic code, non-power integer-number representations are also surjective mappings
between sets of different cardinality and, as such, also redundant. However, none of the nonpower
arithmetics studied so far nor other alternative redundant representations are able to
match the actual degeneracy of the genetic code. In this paper we develop a slightly more
general framework that leads to the following surprising results: i) the degeneracy of the
genetic code is mathematically described, ii) a new symmetry is uncovered within this degeneracy,
iii) by assigning a binary string to each of the codons, their classification into definite
parity classes according to the corresponding sequence of bases
is made possible. This last
result is particularly appealing in connection with the fact that parity coding is the basis of the
simplest strategies devised for error correction in man-made digital data transmission systems.

Parity coding within the genetic code.  I'd say that probably qualifies as a "mathematical pattern".  Whether or not it's explainable by the current theory remains to be seen.  (Of course what isn't explainable by the current theory?)

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Daniel Smith



Posts: 970
Joined: Sep. 2007

(Permalink) Posted: Oct. 17 2008,19:22   

Quote (Albatrossity2 @ Oct. 16 2008,12:53)
     
Quote (Daniel Smith @ Oct. 16 2008,13:38)
Either way, you're all still avoiding the issue.  None of you has any answers as to how life or any of its subsequent systems originated.

Daniel

I've asked this before but it has been ignored. So I'll try again.

What level of detail can you give us regarding the think-poof explanation for the origin of life that you apparently favor?

or, more specifically

If you demand such detail from science, but cannot provide it for your explanation, isn't that just a tad hypocritical?

thanks in advance

At some point we cannot go any further with detailed explanations.  This is the crux of my argument.  
As I said in my Argument From Impossibility:    
Quote
What's more, even if we concede Intelligent Design, we will still be unable to fully explain most of these things. We will not be able to decipher all of the engineering, physics, mathematics or chemistry that went into the actual planning of such systems. It will be as far above our level of intelligence as the ends of the universe are above our heads. This "Argument from Impossibility" is a necessary consequence of the chasm between an infinite mind and our limited human understandings. In short - God's ways are unfathomable.

In order to explain these things in detail, we'd need to know what God knows.  We'll never get there.

--------------
"If we all worked on the assumption that what is accepted as true is really true, there would be little hope of advance."  Orville Wright

"The presence or absence of a creative super-intelligence is unequivocally a scientific question."  Richard Dawkins

  
Wesley R. Elsberry



Posts: 4520
Joined: May 2002

(Permalink) Posted: Oct. 17 2008,19:57   

Ignorance of available evidence is not an attractive position.

Nylonase

DNT degradation pathway Paper

Krebs cycle

Mammalian middle-ear ossicular complex

--------------
"You can't teach an old dogma new tricks." - Dorothy Parker

    
Albatrossity2



Posts: 2779
Joined: Mar. 2007

(Permalink) Posted: Oct. 17 2008,20:07   

Quote (Daniel Smith @ Oct. 17 2008,19:22)
At some point we cannot go any further with detailed explanations.  This is the crux of my argument.
---snip---
In order to explain these things in detail, we'd need to know what God knows.  We'll never get there.

Then why are you demanding detailed explanations from science? If the only thing we have is our lack of understanding of "what God knows", we have nothing useful at all. How do we make progress from there?  How do we use this ignorance to advance the state of knowledge?

--------------
Flesh of the sky, child of the sky, the mind
Has been obligated from the beginning
To create an ordered universe
As the only possible proof of its own inheritance.
                        - Pattiann Rogers

   
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