Rubisco is the most important enyzme on the planet.
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18-08-2015, 11:17 AM
RE: Rubisco is the most important enyzme on the planet.
(18-08-2015 07:44 AM)Godexists Wrote:  Argument from incredulity

http://reasonandscience.heavenforum.org/...ulity#2738

Incredulity is based on human experience and on what we actually know.

No, it isn't. It is based on what the person making the fallacious argument believes.

(18-08-2015 07:44 AM)Godexists Wrote:  For example, the belief in abiogenesis can be strongly doubted, one can be skeptical of it, because it has never been observed and all proposals have lead to a dead end so far.

False. In fact, all predictions made by abiogenesis - such as inefficient, imperfect biological systems existing due to replication and mutation being an inefficient process - have been proven right. The fact that it has not yet been observed in a laboratory is entirely irrelevant, since it's an indication of practical limitations rather than theoretical ones, and creationists can hardly claim to have observed creation either. All the evidence that it can and did happen still exists.

(18-08-2015 07:44 AM)Godexists Wrote:  You might implie that incredulity is an unreasonable position, but it is in fact a foundation for all critical thought. Sensible people do not believe things without evidence.

That is not what "argument from incredulity" means. Attempting to strawman away a fallacy does not make your argument any stronger. It just adds another problem to the list.

(18-08-2015 07:44 AM)Godexists Wrote:  When i say that something is unbelievable or inconceivable, i give good reasons. If my whole argument were simply an unsupported statement of unbelief, you would have a good point; to say something is unbelievable without giving a reason is not a good argument. But the problem is that you oversimplify; you do not address the reasons for incredulity.

Because there are no reasons given. You simply dump a wall of text onto the site and say "it's complicated, therefore I can't imagine it happening naturally".

That isn't an argument.

(18-08-2015 08:46 AM)Godexists Wrote:  In case of the first living self replicator however, much more would be needed

<snip>

Argument from personal incredulity fallacy.

Again.

(18-08-2015 09:24 AM)Godexists Wrote:  thats precisely the problem of evolution. there is no forsight. So why would evolution produce a assembly chaperone enzyme to make rubisco ?

Why wouldn't it?

You seem to be operating under the misapprehension that evolution is some sort of external force. It's really just shorthand for the consequences of a fairly simple list of facts regarding chemistry:

1) Chemical reactions happen.
2) Chemical reactions can cause themselves to happen again.
3) Chemical reactions that cause themselves to happen again may cause themselves to happen again slightly differently.
4) Some chemical reactions are better at making themselves happen again than others.
5) If a difference between two chemical reactions causes one to happen again more frequently than the other, the altered version will become more numerous.

It's really not complicated.

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18-08-2015, 11:20 AM
RE: Rubisco is the most important enyzme on the planet.
(18-08-2015 07:44 AM)Godexists Wrote:  Argument from incredulity
.... but it is in fact a foundation for all critical thought. Sensible people do not believe things without evidence.

So you don't believe in a god then.

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18-08-2015, 04:52 PM
RE: Rubisco is the most important enyzme on the planet.
(18-08-2015 09:56 AM)Mathilda Wrote:  
(18-08-2015 09:22 AM)Godexists Wrote:  i have already posted, what it would require to make the first self replicating living cell.

In my view, impossible only through natural mechanisms.

But you don't address whether a simpler self replicating cell can exist. And you can't argue along the lines of every component of a modern cell is necessary because that's like looking at a modern car and saying the minimum number of wheels required for a vehicle is 4 because if you took one wheel away then it would not work. A modern car is balanced for 4 wheels, a chariot is balanced for 2 wheels.

I have dealt with this canard . Yes

http://reasonandscience.heavenforum.org/...ns-of-life

"Unless the molecule can literally copy itself," Joyce and Orgel note, "that is, act simultaneously as both template and catalyst, it must encounter another copy of itself that it can use as a template." Copying any given RNA in its vicinity will lead to an error catastrophe, as the population of RNAs will decay into a collection of random sequences. But to find another copy of itself, the self-replicating RNA would need (Joyce and Orgel calculate) a library of RNA that "far exceeds the mass of the earth."18

In the face of these difficulties, they advise, one must reject

the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNA's catalytic potential. If you doubt this, ask yourself whether you believe that a replicase ribozyme would arise in a solution containing nucleoside 5'-diphosphates and polynucleotide phosphorylase!

Self-organizing biochemical cycles

How were ribonucleotides first formed on the primitive earth? This is a very difficult problem. Stanley Miller's synthesis of the amino acids by sparking a reducing atmosphere (2) was the paradigm for prebiotic synthesis for many years, so at first, it was natural to suppose that similar methods would meet with equal success in the nucleotide field. However, nucleotides are intrinsically more complicated than amino acids, and it is by no means obvious that they can be obtained in a few simple steps under prebiotic conditions. A remarkable synthesis of adenine (3) and more or less plausible syntheses of the pyrimidine nucleoside bases (4) have been reported, but the synthesis of ribose and the regiospecific combination of the bases, ribose, and phosphate to give β-nucleotides remain problematical.

The novel, potentially replicating polymers that have been described up to now, like the nucleic acids, are formed by joining together relatively complex monomeric units. It is hard to see how any could have accumulated on the early earth. A plausible scenario for the origin of life must, therefore, await the discovery of a genetic polymer simpler than RNA and an efficient, potentially prebiotic, synthetic route to the component monomers. The suggestion that relatively pure, complex organic molecules might be made available in large amounts via a self-organizing, autocatalytic cycle might, in principle, help to explain the origin of the component monomers. I have emphasized the implausibility of the suggestion that complicated cycles could self-organize, and the importance of learning more about the potential of surfaces to help organize simpler cycles.


1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18793/
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18-08-2015, 04:59 PM
RE: Rubisco is the most important enyzme on the planet.
(18-08-2015 11:17 AM)Unbeliever Wrote:  chaperone enzyme to make rubisco ?

Why wouldn't it?

because there would be no reason to make it unless all other parts were there too, and the insctruction how to make Rubisco. Why would you make a piston, if there is no motor to mount it in to get function ??

But i go further. Why would evolution make Rubisco without the other enzymes to get the Calvin Cycle ?

But lets say, these other enzymes where there.

Why would the Calvin Cycle arise without the light reactions of photosynthesis ? It would not have any function either.

But what, if we had the whole mechanism of photosynthesis ??

Unless you have the cell to host the organelles , and the stroma, and the chloroplast, and all the parts to synthesize the molecular machines, nothing done either.

But even if you have a fully operational cell, lets say, cyanobacterias, you need all the fine tuning of the earth, the right atmosphere etc....

Drinking Beverage
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18-08-2015, 04:59 PM
RE: Rubisco is the most important enyzme on the planet.
(18-08-2015 04:52 PM)Godexists Wrote:  
(18-08-2015 09:56 AM)Mathilda Wrote:  But you don't address whether a simpler self replicating cell can exist. And you can't argue along the lines of every component of a modern cell is necessary because that's like looking at a modern car and saying the minimum number of wheels required for a vehicle is 4 because if you took one wheel away then it would not work. A modern car is balanced for 4 wheels, a chariot is balanced for 2 wheels.

I have dealt with this canard . Yes

http://reasonandscience.heavenforum.org/...ns-of-life

"Unless the molecule can literally copy itself," Joyce and Orgel note, "that is, act simultaneously as both template and catalyst, it must encounter another copy of itself that it can use as a template." Copying any given RNA in its vicinity will lead to an error catastrophe, as the population of RNAs will decay into a collection of random sequences. But to find another copy of itself, the self-replicating RNA would need (Joyce and Orgel calculate) a library of RNA that "far exceeds the mass of the earth."18

In the face of these difficulties, they advise, one must reject

the myth of a self-replicating RNA molecule that arose de novo from a soup of random polynucleotides. Not only is such a notion unrealistic in light of our current understanding of prebiotic chemistry, but it should strain the credulity of even an optimist's view of RNA's catalytic potential. If you doubt this, ask yourself whether you believe that a replicase ribozyme would arise in a solution containing nucleoside 5'-diphosphates and polynucleotide phosphorylase!

Self-organizing biochemical cycles

How were ribonucleotides first formed on the primitive earth? This is a very difficult problem. Stanley Miller's synthesis of the amino acids by sparking a reducing atmosphere (2) was the paradigm for prebiotic synthesis for many years, so at first, it was natural to suppose that similar methods would meet with equal success in the nucleotide field. However, nucleotides are intrinsically more complicated than amino acids, and it is by no means obvious that they can be obtained in a few simple steps under prebiotic conditions. A remarkable synthesis of adenine (3) and more or less plausible syntheses of the pyrimidine nucleoside bases (4) have been reported, but the synthesis of ribose and the regiospecific combination of the bases, ribose, and phosphate to give β-nucleotides remain problematical.

The novel, potentially replicating polymers that have been described up to now, like the nucleic acids, are formed by joining together relatively complex monomeric units. It is hard to see how any could have accumulated on the early earth. A plausible scenario for the origin of life must, therefore, await the discovery of a genetic polymer simpler than RNA and an efficient, potentially prebiotic, synthetic route to the component monomers. The suggestion that relatively pure, complex organic molecules might be made available in large amounts via a self-organizing, autocatalytic cycle might, in principle, help to explain the origin of the component monomers. I have emphasized the implausibility of the suggestion that complicated cycles could self-organize, and the importance of learning more about the potential of surfaces to help organize simpler cycles.


1) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC18793/

Wow. More dishonest bullshit.
"The evolution of RNA is likely to have played an important role in the very early history of life on Earth but it is doubtful that life began with RNA. Consideration of what came before RNA must take into account relevant information from geochemistry, prebiotic chemistry and nucleic acid biochemistry." Gerald F. Joyce.
Someone who accepted evolution.

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18-08-2015, 05:20 PM
RE: Rubisco is the most important enyzme on the planet.
I'm forming the Committee for the Scientific Investigation of How Many Lies Creationists Can Tell Before They Realize What They're Doing and Stop (SCIHMLCCTBTRWTDS).

(We're working on a more-wieldy acronym.)

"Theology made no provision for evolution. The biblical authors had missed the most important revelation of all! Could it be that they were not really privy to the thoughts of God?" - E. O. Wilson
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18-08-2015, 05:43 PM (This post was last modified: 18-08-2015 05:48 PM by RocketSurgeon76.)
RE: Rubisco is the most important enyzme on the planet.
That's a paper from 15 years ago. I'm putting his quote back in context, then showing more recent work that answers his paper. You can click on "This article has been cited by other articles in PMC", just under the main title of the article he quotes from. Poke around a bit, and pay attention to what years these papers are published, and whether or not other authors say things like "well this objection was raised, but we solved it by..." or, "despite objections by Orgel", etc.

I would stay out of this, but it just infuriates me beyond words when they do this kind of crap:

Proc Natl Acad Sci U S A. 2000 Nov 7; 97(23): 12503–12507.
Published online 2000 Oct 31. doi: 10.1073/pnas.220406697
PMCID: PMC18793
Biochemistry
Self-organizing biochemical cycles
Leslie E. Orgel*

Conclusion:
The novel, potentially replicating polymers that have been described up to now, like the nucleic acids, are formed by joining together relatively complex monomeric units. It is hard to see how any could have accumulated on the early earth. A plausible scenario for the origin of life must, therefore, await the discovery of a genetic polymer simpler than RNA and an efficient, potentially prebiotic, synthetic route to the component monomers. The suggestion that relatively pure, complex organic molecules might be made available in large amounts via a self-organizing, autocatalytic cycle might, in principle, help to explain the origin of the component monomers. I have emphasized the implausibility of the suggestion that complicated cycles could self-organize, and the importance of learning more about the potential of surfaces to help organize simpler cycles.


(Emphasis mine, to show quote-mined segment.)

This recent (2015) article cites to the above article as reference #12:

Despite hot debates,[12] the idea that both nucleotide and amino acid polymers might have been produced by a proto-metabolism that might have evolved naturally from autocatalytic physicochemical reactions on the hypercycle model[13–15] emerged as the most robust one.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4401237/


Mechanisms of molecular self-replication have the potential to shed light on the origins of life. In particular, self-replication through RNA-catalysed templated RNA synthesis is thought to have supported a primordial 'RNA world'. However, existing polymerase ribozymes lack the capacity to synthesize RNAs approaching their own size. Here, we report the in vitro evolution of such catalysts directly in the RNA-stabilizing medium of water ice, which yielded RNA polymerase ribozymes specifically adapted to sub-zero temperatures and able to synthesize RNA in ices at temperatures as low as -19 °C. The combination of cold-adaptive mutations with a previously described 5' extension operating at ambient temperatures enabled the design of a first polymerase ribozyme capable of catalysing the accurate synthesis of an RNA sequence longer than itself (adding up to 206 nucleotides), an important stepping stone towards RNA self-replication.

https://www.ncbi.nlm.nih.gov/pubmed/24256864

And finally and most interestingly to me, these biochemists have laid out the practical problems with finding a solution to the issue of trying to reproduce the almost-infinite pathways that it would take to find the method that millions of years of evolution struck upon in producing this catalyst. Because scientists are honest people, they enumerated both the issues of how difficult it is to narrow down the thousands of possible paths in an experiment/lab, and also how/why they think they can solve the puzzle:

Having constructed the rTCA supernetwork, we are now in the position to evaluate the hypothesis of the uniqueness and predisposed nature of the rTCA cycle within the supernetwork. Specifically, we will enumerate cycles that involve acetate and glyoxylate and compare their properties. Furthermore, one can investigate its evolution following some model, for example, mass-action kinetics, and see what subset of reactions is selected. One would have to obtain rate constants for the supernetwork reactions, specify the initial concentrations, environmental conditions, such as pressure, temperature and acidity, and make assumptions about the availability of catalysts and their activity and selectivity. Such investigations are beyond the scope of the present study. A total of 1881 cycles containing acetate, glyoxylate, or both is found in the rTCA supernetwork (see SI for details).

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306138/

(Edited to add remainder of a quote I accidentally cut short.)

"Theology made no provision for evolution. The biblical authors had missed the most important revelation of all! Could it be that they were not really privy to the thoughts of God?" - E. O. Wilson
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18-08-2015, 05:57 PM
RE: Rubisco is the most important enyzme on the planet.
Incidentally, for those who don't read science, what Orgel is trying to say is that she thinks "free floating" version of these chemicals could not have happened, and that they needed a reaction surface on which to do such organizing, which would help to catalyze the reaction (as well as pointing to a direction we need to look to find the right precursors).

Several experiments on this, called RNA catalysis, are being conducted, both with and without reaction surfaces, as the reaction has proved (as I wrote above) significantly more complex due to the number of candidate precursors and pathways the evolutionary reactions may have taken. Here is one article on the issue, though of course there are dozens on that one website alone:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2184879/

Edit to Add: Note that none, repeat NONE of the researchers here are saying anything akin to, "This reaction is too complex, therefore life did not evolve by one of these pathways... or at all... we give up."

"Theology made no provision for evolution. The biblical authors had missed the most important revelation of all! Could it be that they were not really privy to the thoughts of God?" - E. O. Wilson
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18-08-2015, 06:59 PM
RE: Rubisco is the most important enyzme on the planet.
(18-08-2015 04:59 PM)Godexists Wrote:  
(18-08-2015 11:17 AM)Unbeliever Wrote:  Why wouldn't it?

because there would be no reason to make it unless all other parts were there too <snip>

More irreducible complexity nonsense, as if I haven't thoroughly refuted it before.

For the last time: your personal ignorance of the research into the evolution of these systems does not constitute an argument.

"Owl," said Rabbit shortly, "you and I have brains. The others have fluff. If there is any thinking to be done in this Forest - and when I say thinking I mean thinking - you and I must do it."
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19-08-2015, 05:32 AM
RE: Rubisco is the most important enyzme on the planet.
(18-08-2015 05:43 PM)RocketSurgeon76 Wrote:  Conclusion:
The novel, potentially replicating polymers that have been described up to now, like the nucleic acids, are formed by joining together relatively complex monomeric units. It is hard to see how any could have accumulated on the early earth. A plausible scenario for the origin of life must, therefore, await the discovery of a genetic polymer simpler than RNA and an efficient, potentially prebiotic, synthetic route to the component monomers. The suggestion that relatively pure, complex organic molecules might be made available in large amounts via a self-organizing, autocatalytic cycle might, in principle, help to explain the origin of the component monomers. I have emphasized the implausibility of the suggestion that complicated cycles could self-organize, and the importance of learning more about the potential of surfaces to help organize simpler cycles.

(Emphasis mine, to show quote-mined segment.)

There's definitely a pattern here, GE quote mines anytime an article by a biochemist uses the word difficult or hard, then tries to shove god into it without showing the rest of the paragraph where the biochemist addresses how to get around the difficulty.

Origel's rule applies to his schtick -Evolution is cleverer than you are.

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