Rubisco is the most important enyzme on the planet.
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19-08-2015, 06:50 AM
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.

I have dealt with this canard . Yes

<quote-mining>
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.

...

Self-organizing biochemical cycles

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.
</quote-mining>

You have answered it in your own mind because you have not considered all possibilities.

Scientists on the other hand are always open to other possibilities because they recognise that there will always be something that they have not thought of.

What you have posted above suggests metabolism-first rather than RNA-first.

Again you are posing a leading question where the answer is most likely to be "no" and then placing your own answer of "goddidit" without considering any other possibilities.

The possibility in this case being that a self organising metabolism came first that grew and repeatedly split apart and that RNA came afterwards to produce self replication to make the system more efficient.

Many scientists are now seriously considering this. The one single feature of all life is that it has a metabolism. Metabolisms degrade usable energy to produce work. This is a fundamental feature of all self organisation.

The fact that your mined quote is actually about self-organisation yet you do not even mention metabolism-first reproduction shows that you do not understand the subject nor care about considering other possibilities.

So in answer to my question, it seems no, you don't want to address whether a simpler self replicating cell can exist.
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19-08-2015, 12:15 PM (This post was last modified: 19-08-2015 12:19 PM by Godexists.)
RE: Rubisco is the most important enyzme on the planet.
(19-08-2015 06:50 AM)Mathilda Wrote:  Again you are posing a leading question where the answer is most likely to be "no" and then placing your own answer of "goddidit" without considering any other possibilities.

Outstanding problems in science

From a recent conversation i had at Evolution and Creationism Open Debate group :

Me: science cannot explain most things through evolution. Always, when science comes to a dead end of the road, it just says : we dont know yet, we have to search further. That is, because supernatural causes are not permitted as explanation. And guess what ?? When it comes to almos ALL relevant questions of origins, that will be the last answer of main stream scientific papers. I am collecting these answers btw. The list is far from complete. It does not even scratch the surface. But it provides good examples. If you replace each of these answers, rather than with we don't know, with its designed, it fits perfectly the bill.

Carrie Griego Not yet. That's why they're hypotheses. Hypotheses come first. At least we don't make crap up. We research and figure it out rather than saying goddidit.

Me. Carrie Griego We research and figure it out rather than saying goddidit.//thats the problem. God is NEVER permitted to get into the picture. He is excluded right from the beginning, and in the end, rather than admit that design is the best explanation, the design hypothesis is ignored, and replaced with " we don't know yet ". Nice evolution of the gaps..... btw.

http://reasonandscience.heavenforum.org/...in-science

But back to Rubisco: What about the RbcX Assembly Chaperone, specifically used as assembly tool of Rubisco ? What about the barrel shaped GroEL/GroES chaperonins which perform their function with extremely impressive simplicity and elegance, namely helping over 100 different proteins to get into their correct shape and form, essential for function ? ( in our case, helping the Rubisco RbcL subunits to get their proper shape ) Or how do proponents of evolution explain how natural selection would have favoured the emergence of Hsp70 chaperones, central components of the cellular network, proteins which assist a large variety of protein folding processes in the cell by transient association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins ? That is in our case, their function of which was to prevent a still-useless rubisco small subunit from folding outside the chloroplast? They are made, used during the synthesis process, and once Rubisco assembly has finished, these enzymes are discarted. This is very much a factory-like production and assembly-line process, using fully automatized and programmed nano-robot like molecular machines, namely enzymes. Most parts, if missing, render 1. the assembly of Rubisco impossible, and 2. Rubisco useless. Many parts, if missing render it not fully functional and defective. Beside the enzymes that have use in other biological systems, there would be no reason to make them unless all other parts were there too, and the assembly insctructions of Rubisco. As a analogy, if you had to make the implementation of a car factory, why would you make the assembly chain of a piston, if you do not have all the precise instructions to make 1. the car as a whole, and 2. the instructions of the precise shape and the materials required for the piston in particular, and how to mount it in the motor ?

Further issues : Why would natural chemical reactions produce three enzymes that are uniquely used in the Calvin cycle ( they are not used in any other metabolic reaction ),
that is Rubisco, sedoheptulose bisphosphatase , and Phosphoribulokinase , if they have function only in the Calvin Cycle ?

Furthermore : Would not only a designer know why it would be necessary to produce a special sequence of chain reactions and the right order and sequence of the enzymes provoking the reactions, handing over each of the products to the next processing step ? and to get the end products, required for further metabolic reactions ?

Following enzymes are required in the Light-independent reactions of the Calvin Cycle :

in the first stage:

1.Rubisco
2.phosphoglycerate kinase
3.glyceraldehyde 3-phosphate dehydrogenase

in the second stage:

1.Triose phosphate isomerase Fructose 1,6-bisphosphatase
2.Aldolase
3.Transketolase
4.Sedoheptulose-bisphosphatase
5.Sedoheptulose-1,7-bisphosphatase
6.Ribose-5-phosphate isomerase
7.phosphopentose epimerase


and in the last stage:

1.phosphoribulokinase

So the whole pathway requires 11 enzymes, of which 3 are unique to the pathway.

But lets assume we would have all enzymes required for the Calvin cycle. These reactions take the products (ATP and NADPH) of light-dependent reactions and perform further chemical processes on them. So unless the light dependent reactions of photosynthesis are in place, the Calvin cycle will not work.

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.

So this is one more irreducible and interdependent complex nanomolecular factory, which requires the planning and programming of a designer, and all parts functioning right from the start in a intelocked complex manner.

We must observe that Darwin's proposed test, on at least one major interpretation, is less generous than it first appears: "If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." For, as Shapiro acidly but aptly noted, on the defects in such an appeal to bare possibility in defense of the RNA world hypothesis -- making a remark that, we observe, inadvertently also applies to his preferred metabolism first scenario -- that:

On the one side you have a intelligent agency based system of irreducible complexity of tight integrated , information rich functional systems which have ready on hand energy directed for such, that routinely generate the sort of phenomenon being observed. And on the other side imagine a golfer, who has played a golf ball through an 12 hole course. Can you imagine that the ball could also play itself around the course in his absence ? Of course, we could not discard, that natural forces, like wind , tornadoes or rains or storms could produce the same result, given enough time. the chances against it however are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12 hole course.

Quote:So in answer to my question, it seems no, you don't want to address whether a simpler self replicating cell can exist.

First of all, i have already shown the sheer impossibility of life arising without intelligence involved:

http://reasonandscience.heavenforum.org/...iving-cell

and secondly. even if lets say a first self replicating RNA enzyme would arise on earth, so what ? You still have a loooooooong way to go from that to a first self replicating living cell.

To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis

http://reasonandscience.heavenforum.org/...impossible
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19-08-2015, 12:38 PM
RE: Rubisco is the most important enyzme on the planet.
(19-08-2015 12:15 PM)Godexists Wrote:  Me: science cannot explain most things through evolution. Always, when science comes to a dead end of the road, it just says : we dont know yet, we have to search further. That is, because supernatural causes are not permitted as explanation.

Argument from ignorance fallacy.

(19-08-2015 12:15 PM)Godexists Wrote:  And guess what ?? When it comes to almos ALL relevant questions of origins, that will be the last answer of main stream scientific papers.

Bare assertion fallacy, with hints of the argument from personal incredulity.

(19-08-2015 12:15 PM)Godexists Wrote:  If you replace each of these answers, rather than with we don't know, with its designed, it fits perfectly the bill.

Argument from ignorance and personal incredulity, leading into a bare assertion and begging the question. Also leads into special pleading when the inevitable question of where the wizard in question came from is asked.

(19-08-2015 12:15 PM)Godexists Wrote:  thats the problem. God is NEVER permitted to get into the picture. He is excluded right from the beginning, and in the end, rather than admit that design is the best explanation, the design hypothesis is ignored, and replaced with " we don't know yet ".

Begging the question, subtly disguised by means of deliberate misunderstanding of the burden of proof.

(19-08-2015 12:15 PM)Godexists Wrote:  Or how do proponents of evolution explain how natural selection would have favoured the emergence of Hsp70 chaperones, central components of the cellular network, proteins which assist a large variety of protein folding processes in the cell by transient association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins ?

Argument from personal incredulity and ignorance.

(19-08-2015 12:15 PM)Godexists Wrote:  Furthermore : Would not only a designer know why it would be necessary to produce a special sequence of chain reactions and the right order and sequence of the enzymes provoking the reactions, handing over each of the products to the next processing step ? and to get the end products, required for further metabolic reactions ?

Begging the question again, assuming that something had to "know".

(19-08-2015 12:15 PM)Godexists Wrote:  So this is one more irreducible and interdependent complex nanomolecular factory, which requires the planning and programming of a designer, and all parts functioning right from the start in a intelocked complex manner.

Straw man argument by means of ignoring the part of the theory of evolution which clearly states that these parts did not necessarily come into being in their current forms.

(19-08-2015 12:15 PM)Godexists Wrote:  On the one side you have a intelligent agency based system of irreducible complexity of tight integrated , information rich functional systems which have ready on hand energy directed for such, that routinely generate the sort of phenomenon being observed. And on the other side imagine a golfer, who has played a golf ball through an 12 hole course. Can you imagine that the ball could also play itself around the course in his absence ? Of course, we could not discard, that natural forces, like wind , tornadoes or rains or storms could produce the same result, given enough time. the chances against it however are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12 hole course.

False dilemma, straw man, Texas sharpshooter fallacy.

(19-08-2015 12:15 PM)Godexists Wrote:  First of all, i have already shown the sheer impossibility of life arising without intelligence involved

Simply wrong.

(19-08-2015 12:15 PM)Godexists Wrote:  and secondly. even if lets say a first self replicating RNA enzyme would arise on earth, so what ? You still have a loooooooong way to go from that to a first self replicating living cell.

To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis

And finishing off with another dash of argument from personal incredulity.

"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."
- A. A. Milne, The House at Pooh Corner
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19-08-2015, 12:42 PM
RE: Rubisco is the most important enyzme on the planet.
(19-08-2015 12:38 PM)Unbeliever Wrote:  
(19-08-2015 12:15 PM)Godexists Wrote:  And guess what ?? When it comes to almos ALL relevant questions of origins, that will be the last answer of main stream scientific papers.

Oh look, drawing only one conclusion while ignoring every other answer. How shocking. Drinking Beverage

On the plus side, since he's obviously intent on placing every bit of the content of this bullshit website on this forum, there will be a response to his bullshit if someone does a Google search.

Gods derive their power from post-hoc rationalizations. -The Inquisition

Using the supernatural to explain events in your life is a failure of the intellect to comprehend the world around you. -The Inquisition
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19-08-2015, 12:49 PM
RE: Rubisco is the most important enyzme on the planet.
And all the while still ignoring the very strong possibility that the first cell was likely to be metabolism-first rather than RNA-first.

This is because it makes GE's entire argument based on the difficulty of explaining how an RNA-first cell came into being completely and utterly irrelevant if shown to be true.
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19-08-2015, 01:31 PM
RE: Rubisco is the most important enyzme on the planet.
And to again illustrate just how broken his reasoning process is, he thinks humans lived at the same time as trilobites, unwilling to consider the obvious scientific explanation:

[Image: ye3c_d10.jpg]

He sees god in everything, to the point he discredits himself.

Gods derive their power from post-hoc rationalizations. -The Inquisition

Using the supernatural to explain events in your life is a failure of the intellect to comprehend the world around you. -The Inquisition
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19-08-2015, 01:44 PM
RE: Rubisco is the most important enyzme on the planet.
(19-08-2015 12:15 PM)Godexists Wrote:  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.

Is meaningless. Be more careful when you copy-paste your nonsense.

Quote:First of all, i have already shown the sheer impossibility of life arising without intelligence involved:

You are obviously incompetent to discuss this subject. Far more intelligent people with Nobel prizes agree with none of this crap, and you have no such prize, or even advanced degree.

Quote:To go from a bacterium to people is less of a step than to go from a mixture of amino acids to a bacterium. — Lynn Margulis

And yet it happened. Actually it's not. Once a process is begun, the next step is far more probable. You have establised none of the probabilities associated with any of the steps.

You have wasted your time here. Not one person is convinced by one thing you have said.

Insufferable know-it-all.Einstein God has a plan for us. Please stop screwing it up with your prayers.
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19-08-2015, 01:52 PM
RE: Rubisco is the most important enyzme on the planet.
Holyfuckamoley, the guy is just babbling away.

What an ignorant bore. Dodgy

A new type of thinking is essential if mankind is to survive and move to higher levels. ~ Albert Einstein
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19-08-2015, 02:14 PM
RE: Rubisco is the most important enyzme on the planet.
(19-08-2015 12:15 PM)Godexists Wrote:  Outstanding problems in science

From a recent conversation i had at Evolution and Creationism Open Debate group :

Me: science cannot explain most things through evolution. Always, when science comes to a dead end of the road, it just says : we dont know yet, we have to search further. That is, because supernatural causes are not permitted as explanation.

So, I have to ask: do you have any, you know, actual evidence of supernatural causation? Not, like, arguments from ignorance or other negative nonsense- you can't get to a positive number from zero by only subtracting- but actual positive evidence?

If the answer is no, then why would we consider supernatural causation without any reason to do so?

Quote:And guess what ?? When it comes to almos ALL relevant questions of origins, that will be the last answer of main stream scientific papers. I am collecting these answers btw. The list is far from complete. It does not even scratch the surface. But it provides good examples. If you replace each of these answers, rather than with we don't know, with its designed, it fits perfectly the bill.

This may come as a shock to you, but "this answer fits," is a necessary but not sufficient criteria for a truth statement. Yes, if you wish to pose that there was a supernatural designer that can do anything, then I suppose that every question could have that as an answer that fits, but that's just because you've added "can do anything," to the description of an entity that you've provided no evidence for. To be clear, evidence is another criteria for a truth statement to be sufficient, and if you don't have any of that, your answer might "fit," in the same way that "it's just magic," fits, but it isn't necessarily true.

It might work, but if you have no reason to believe that it did work in reality, then it has no place in a scientific paper. Now, you can sit here and whine all day about how science won't consider your supernatural explanations, but you need to ask yourself why that is, and you haven't because it's the part that rips open your entire little pity party. The scientific community won't consider your explanations because you cannot provide a single solitary shred of evidence that they even exist, and that is the context that renders your complaint utterly meaningless.

Quote:Me. Carrie Griego We research and figure it out rather than saying goddidit.//thats the problem. God is NEVER permitted to get into the picture. He is excluded right from the beginning, and in the end, rather than admit that design is the best explanation, the design hypothesis is ignored, and replaced with " we don't know yet ". Nice evolution of the gaps..... btw.

If we don't have any evidence for a thing, why would we pick any answer at all? If you don't know, isn't the only honest answer "we don't know"?

However, don't let that fool you: we do have plenty of evidence that evolution happens, up to and including seeing it happen in the lab. That's the reason why it is the framework in which all other questions are interpreted, and why your god is not; we have evidence for evolution, we know that it does happen, whereas we don't for your sky daddy. I don't see you whining about how physics always just assumes that anything that happens on earth tends to assume the presence of air, but the rationale is the same; we interpret our data through the lens of other data points that we know to be real. Simply crowing "evolution of the gaps!" is little more than an insipid gotcha that betrays your utter ignorance of the actual methodology of science.
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19-08-2015, 02:29 PM
RE: Rubisco is the most important enyzme on the planet.
(19-08-2015 12:49 PM)Mathilda Wrote:  And all the while still ignoring the very strong possibility that the first cell was likely to be metabolism-first rather than RNA-first.

This is because it makes GE's entire argument based on the difficulty of explaining how an RNA-first cell came into being completely and utterly irrelevant if shown to be true.

Only someone that does not know the implications could possibly make such a uninformed assertion.

The Implausibility of Metabolic Cycles on the Prebiotic Earth
Leslie E Orgel†

http://reasonandscience.heavenforum.org/...mal-genome

Although metabolism-first avoids the infeasibility of forming functional RNA by chance, "replication of compositional information is so inaccurate that fitter compositional genomes cannot be maintained by selection and, therefore, the system lacks evolvability (i.e., it cannot substantially depart from the asymptotic steady-state solution already built-in in the dynamical equations). We conclude that this fundamental limitation of ensemble replicators cautions against metabolism-first theories of the origin of life" [44]. Concerning the chemical cycles required, "These are chemically very difficult reactions ... One needs, therefore, to postulate highly specific catalysts for these reactions. It is likely that such catalysts could be constructed by a skilled synthetic chemist, but questionable that they could be found among naturally occurring minerals or prebiotic organic molecules. The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to 'life-like' complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most non-enzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own"
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