Calilasseia: 78 Papers on Abiogenesis

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Re: Calilasseia: 78 Papers on Abiogenesis

#41  Postby byofrcs » Mar 31, 2010 11:02 am

.....


What clues?
Was it RNA, DNA, polypeptides, a vesicle based on fatty acids?
A metabolic cycle perhaps?
Pray tell.

We are not looking for one magic reaction, but a simple replicator. Something that can evolve into something more complex.


Well it's the "evolve into something more complex" that is the gotcha isn't it ?.

Rather.
If we measure complexity as simply a molecular weight then clearly polymers get more "complex".

...which would be wrong.
If we measure complex as the steps in a chain then is something like Glycolysis is more complex than each step.

I'm not sure what you're saying here.



It is suggesting that complexity is the number of steps in metabolic pathway. More steps means more complex, less steps is less complex.

It's only a suggestion - you said "complex".



How do you measure complex ?

Admittedly a difficult one, complexity is difficult to define, and understand.
There is an example that invokes design, but I'll avoid that as it will most likely invoke mass hysteria.
...so I won't.


Mass hilarity more like - The ID claim is that the presence of a designer is implied by the existence of some step that was irreducibly complexity. Not unsurprising the offered processes fall apart into reducibly un-complex steps.
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Re: Calilasseia: 78 Papers on Abiogenesis

#42  Postby rainbow » Mar 31, 2010 11:21 am

byofrcs wrote:.....


What clues?
Was it RNA, DNA, polypeptides, a vesicle based on fatty acids?
A metabolic cycle perhaps?
Pray tell.

We are not looking for one magic reaction, but a simple replicator. Something that can evolve into something more complex.


Well it's the "evolve into something more complex" that is the gotcha isn't it ?.

Rather.
If we measure complexity as simply a molecular weight then clearly polymers get more "complex".

...which would be wrong.
If we measure complex as the steps in a chain then is something like Glycolysis is more complex than each step.

I'm not sure what you're saying here.



It is suggesting that complexity is the number of steps in metabolic pathway. More steps means more complex, less steps is less complex.

It's only a suggestion - you said "complex".



How do you measure complex ?

Admittedly a difficult one, complexity is difficult to define, and understand.
There is an example that invokes design, but I'll avoid that as it will most likely invoke mass hysteria.
...so I won't.


Mass hilarity more like - The ID claim is that the presence of a designer is implied by the existence of some step that was irreducibly complexity. Not unsurprising the offered processes fall apart into reducibly un-complex steps.


Actually I was thinking more in terms of what was said by He-whose-name-may-not-be-spake in The Blind Watchmaker - complexity arises if its parts are "arranged in a way that is unlikely to have arisen by chance alone."
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Re: Calilasseia: 78 Papers on Abiogenesis

#43  Postby byofrcs » Mar 31, 2010 11:55 am

Yeah, well I don't like that definition of complexity (The Blind Watchmaker and then argued in TGD and then possibly, necessarily, criticised by Plantinga).

It just feels like something is missing because I think chance is a two-edged sword that can both cause and erase (un-cause ?) and I think that what is left after this annealing is what exists (else it would be like those isotopes that last for a split second and fission to something else).

It's like when you use Monte-Carlo to discover a problem landscape - a nice example is using Buffon's needle to estimate pi. I think we shouldn't avoid the word "chance" as I think the memoryless nature of stochastic processes are the driving forces in reality but the trick to existing is not getting erased by these same processes.
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Re: Calilasseia: 78 Papers on Abiogenesis

#44  Postby Rumraket » Mar 31, 2010 12:27 pm

rainbow wrote:
Better replicators, like RNA would have totally replaced any simpler precursors, and since we are talking about events that happened over 3.8 billion years ago, much, if not all information could be lost.

Invisible Pink Unicorns might also exist, but we have no way of knowing either, do we?


It's a bad equivocation. By inference from evolutionary principles we would have reason to believe in increasingly reliable and complex replicators. Obviously we can't just assert it, but there is a basis for researching the possiblity.

In contrast, we don't have any empirical evidence on which to assert the existence of pink Unicorns. On that basis, I think it would also be a waste of time and research money to start looking for them.
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Re: Calilasseia: 78 Papers on Abiogenesis

#45  Postby rainbow » Mar 31, 2010 3:03 pm

Rumraket wrote:
rainbow wrote:
Better replicators, like RNA would have totally replaced any simpler precursors, and since we are talking about events that happened over 3.8 billion years ago, much, if not all information could be lost.

Invisible Pink Unicorns might also exist, but we have no way of knowing either, do we?


It's a bad equivocation. By inference from evolutionary principles we would have reason to believe in increasingly reliable and complex replicators. Obviously we can't just assert it, but there is a basis for researching the possiblity.

In contrast, we don't have any empirical evidence on which to assert the existence of pink Unicorns. On that basis, I think it would also be a waste of time and research money to start looking for them.


Absolutely no doubt, I'd like to see research on making a simpler replicator. A little collection of molecules that can make copies of itself, and sometimes making mistakes in that copying - leading to an improved, evolved version.
It would not even need to be based on the exact same chemistry of known life.
The applications in medicine and industry could be enormous.
Money well spent, I would say.
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Re: Calilasseia: 78 Papers on Abiogenesis

#46  Postby byofrcs » Mar 31, 2010 3:50 pm

rainbow wrote:
Rumraket wrote:
rainbow wrote:
Better replicators, like RNA would have totally replaced any simpler precursors, and since we are talking about events that happened over 3.8 billion years ago, much, if not all information could be lost.

Invisible Pink Unicorns might also exist, but we have no way of knowing either, do we?


It's a bad equivocation. By inference from evolutionary principles we would have reason to believe in increasingly reliable and complex replicators. Obviously we can't just assert it, but there is a basis for researching the possiblity.

In contrast, we don't have any empirical evidence on which to assert the existence of pink Unicorns. On that basis, I think it would also be a waste of time and research money to start looking for them.


Absolutely no doubt, I'd like to see research on making a simpler replicator. A little collection of molecules that can make copies of itself, and sometimes making mistakes in that copying - leading to an improved, evolved version.

It would not even need to be based on the exact same chemistry of known life.
The applications in medicine and industry could be enormous.
Money well spent, I would say.


That's the idea here. There probably are novel applications but for replication today we can just hijack bacteria.
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Re: Calilasseia: 78 Papers on Abiogenesis

#47  Postby Rumraket » Mar 31, 2010 4:52 pm

byofrcs wrote:
rainbow wrote:
Rumraket wrote:
rainbow wrote:
Better replicators, like RNA would have totally replaced any simpler precursors, and since we are talking about events that happened over 3.8 billion years ago, much, if not all information could be lost.

Invisible Pink Unicorns might also exist, but we have no way of knowing either, do we?


It's a bad equivocation. By inference from evolutionary principles we would have reason to believe in increasingly reliable and complex replicators. Obviously we can't just assert it, but there is a basis for researching the possiblity.

In contrast, we don't have any empirical evidence on which to assert the existence of pink Unicorns. On that basis, I think it would also be a waste of time and research money to start looking for them.


Absolutely no doubt, I'd like to see research on making a simpler replicator. A little collection of molecules that can make copies of itself, and sometimes making mistakes in that copying - leading to an improved, evolved version.

It would not even need to be based on the exact same chemistry of known life.
The applications in medicine and industry could be enormous.
Money well spent, I would say.


That's the idea here. There probably are novel applications but for replication today we can just hijack bacteria.


That's awesome, but i'm confused. Myers states :
PZ Myers wrote:Another cool thing about this experiment is that the enzymes proved to be efficient and robust. Below, you can see that they acheived exponential growth, only leveling out when the substrates were exhausted.


And goes on further:
PZ Myers wrote:These enzymes worked well. If they were producing deleterious byproducts that were interfering with the reaction, you'd expect to see a gradual decline in the rate that was independent of the reduction in concentration of the substrates; no such effect was observed in the experiment below, where substrates were regularly replenished. These paired chemical replicators were just cruising, reliably making lots of copies of themselves, and they could keep going for ages…like, 4 billion years.


And this is where I get confused. In the latest Szostak paper on attempting to find reliable replicators it is stated:
Efficient and Rapid Template-Directed Nucleic Acid Copying Using 2′-Amino-2′,3′-dideoxyribonucleoside-5′-hosphorimidazolide Monomers
(http://genetics.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Schrum_et_al_JACS_2009.pdf)
We have also demonstrated repeated cycles of growth and division for fatty acid vesicles without loss of encapsulated aterial.4 However, no general nucleic acid copying mechanism has been demonstrated with the capacity to function as a self-replicating protocellular genome, even though many ribozyme-mediated and nonenzymatic genetic polymer replication schemes have been investigated.5-10 Ribozymes such as the naturally occurring sunY and Tetrahymena self-splicing introns or the in Vitro evolved class I and R3C ligases and polymerases are able to assemble short oligonucleotides or ononucleotides in a template-directed manner. All, however, lack the high reaction efficiency and sequence-general copying ability required for the replication of a protocell genome.11-16

The Szostak-lab paper is specifically citing the Joyce et al paper in citations 11-16(paper # 15).

So, uhh... I guess the confusion may lie in my lack of understanding of how "reaction efficiency" and "sequence-general copying ability" in the [E catalyzes A+B => E']-selfreplicator failed to live up to "requirements" for protocell genomes.

Sum1 enlighten me pleaze :)
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Re: Calilasseia: 78 Papers on Abiogenesis

#48  Postby rainbow » Apr 02, 2010 10:24 am

byofrcs wrote:
That's the idea here. There probably are novel applications but for replication today we can just hijack bacteria.

Yes that is the idea, but the case you refer to involves substrates that are very complex to start with. It is a different matter to have a Replicator that can use simple molecules as its substrates. I'm thinking of such as what can be produced by Miller-Urey, or Volcanic Vents, or maybe even carbonaceous chondrites.
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Re: Calilasseia: 78 Papers on Abiogenesis

#49  Postby Darwinsbulldog » Apr 03, 2010 10:04 am

rainbow wrote:
Better replicators, like RNA would have totally replaced any simpler precursors, and since we are talking about events that happened over 3.8 billion years ago, much, if not all information could be lost.

Invisible Pink Unicorns might also exist, but we have no way of knowing either, do we?

No, that is true, we do not. But extrapolating back in time to a theoretical precursor of RNA, while a little speculative, is rather different from speculating a character out of a children's story book into reality. :) Perhaps if you find this discussion a little too difficult, then you should visit a children's library, fiction section.

No humans have seen the life-cycle of a single star. We see stars in all 'stages" of development, from gas clouds to brown dwarfs, neutron stars, etc. While such theories can be questioned, as all scientific theories can, you are welcome to present your own theory, and be attacked in turn. In science however, we look at the evidence for and against, and the reasoning involved. Erecting straw man arguments is not the general custom.
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Re: Calilasseia: 78 Papers on Abiogenesis

#50  Postby chairman bill » Apr 03, 2010 10:18 am

Ah, but who created the cosmic rays? Eh? I don't know, therefore goddidit. Hallelujah. Proof. Darwin never thought of that, did he?
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Re: Calilasseia: 78 Papers on Abiogenesis

#51  Postby rainbow » Apr 03, 2010 11:00 am

chairman bill wrote:Eh? I don't know, therefore goddidit. Hallelujah. Proof. Darwin never thought of that, did he?

A strawman, a very old and feeble strawman.
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Re: Calilasseia: 78 Papers on Abiogenesis

#52  Postby hackenslash » Apr 12, 2010 3:05 pm

Have you anything?
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Re: Calilasseia: 78 Papers on Abiogenesis

#53  Postby rainbow » Apr 12, 2010 3:06 pm

hackenslash wrote:Have you anything?

Evidence that shows Abiogenesis actually occurred?
Nope, not a thing.

Have you?
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Re: Calilasseia: 78 Papers on Abiogenesis

#54  Postby hackenslash » Apr 12, 2010 3:08 pm

Well, do you want the true answer, which is that abiogenesis definitely did occur, or are you still fucking equivocating and insisting that the word abiogenesis only refers to the theory? In which case the answer is, no.
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Re: Calilasseia: 78 Papers on Abiogenesis

#55  Postby rainbow » Apr 12, 2010 3:12 pm

hackenslash wrote:Well, do you want the true answer, which is that abiogenesis definitely did occur, or are you still fucking equivocating and insisting that the word abiogenesis only refers to the theory? In which case the answer is, no.

There is no equivocation.
I've no evidence that Abiogenesis occurred according to any one of the hypotheses presented in the 78 Papers.
Hard fact.
...so what is the true answer, hack.
Do you have any evidence?
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Re: Calilasseia: 78 Papers on Abiogenesis

#56  Postby hackenslash » Apr 12, 2010 3:22 pm

The true answer is that abiogenesis did occur, whether by intervention of a cosmic curtain twitcher or by other means. First no life, then life, ergo abiogenesis.

Would you like all the literature on the early universe?
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Re: Calilasseia: 78 Papers on Abiogenesis

#57  Postby Rumraket » Apr 12, 2010 3:23 pm

rainbow wrote:
hackenslash wrote:Well, do you want the true answer, which is that abiogenesis definitely did occur, or are you still fucking equivocating and insisting that the word abiogenesis only refers to the theory? In which case the answer is, no.

There is no equivocation.
I've no evidence that Abiogenesis occurred according to any one of the hypotheses presented in the 78 Papers.
Hard fact.
...so what is the true answer, hack.
Do you have any evidence?


Those 78 papers themselves constitute evidence. They don't present the whole picture, but they are evidence nonetheless. To say that you have no evidence is simply bullshit.
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Re: Calilasseia: 78 Papers on Abiogenesis

#58  Postby rainbow » Apr 12, 2010 3:25 pm

Rumraket wrote:
rainbow wrote:
hackenslash wrote:Well, do you want the true answer, which is that abiogenesis definitely did occur, or are you still fucking equivocating and insisting that the word abiogenesis only refers to the theory? In which case the answer is, no.

There is no equivocation.
I've no evidence that Abiogenesis occurred according to any one of the hypotheses presented in the 78 Papers.
Hard fact.
...so what is the true answer, hack.
Do you have any evidence?


Those 78 papers themselves constitute evidence. They don't present the whole picture, but they are evidence nonetheless. To say that you have no evidence is simply bullshit.

They present no evidence that Abiogenesis did occurr. They present evidence that it could've occurred.
There is a very big difference.
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Re: Calilasseia: 78 Papers on Abiogenesis

#59  Postby Rumraket » Apr 12, 2010 3:26 pm

If you claim those papers do not constitute evidence, you may aswell say that there is "no evidence for macroevolution" since, noone has ever seen a fish turn in to a mammal. Its false on the same level.
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Re: Calilasseia: 78 Papers on Abiogenesis

#60  Postby Rumraket » Apr 12, 2010 3:27 pm

All you will ever get is evidence for how it COULD have occured, by the nature of time and history. Plain and simple.
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