Rubisco is the most important enyzme on the planet.
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17-08-2015, 09:24 PM
Rubisco is the most important enyzme on the planet.
Rubisco is the most important enyzme on the planet.

http://reasonandscience.heavenforum.org/...esign#2337

virtually all the organic carbon in the biosphere derives ultimately from the carbon dioxide that this enzyme fixes from the atmosphere. Without it, advanced life would not be possible. And we would not be able to debate our origins. All inquiry and quest about if we are ultimatively the result of a powerful creator, or just random natural chemical reactions and emerging properties of lifeless matter, if biodiversity is due to evolution, or a intelligent designer, is second to the inquiry of how Rubisco came to be. Through my research i gained remarkable insight about Rubisco's complex structure, functioning and synthesis process, how many cell parts , enzymes, proteins and pathways are involved and required to assemble it, how the unfinished sub units require co and post-translational modifications, specific proteins that help like assembly robots in the manufacturing process,sophisticated pathways and mechanisms of protein import and targeting in chloroplasts through large multiprotein translocon complexes in the stroma, and andvanced protein communication and information systems. All this is of bewildering complexity, where dozens of individual interconnected and finely tuned parts are required, a web of interlocked extremely complex advanced molecular machines where if one is missing, nothing goes, that defy the intelligence of the best scientists for decades to find out their structure, mechanisms and functions. Could all this be due to natural processes ?

RuBisCO is a multi-subunit plant protein essential to photosynthesis. It catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere. In the C3 pathway, RuBisCO is responsible for initiating the first step in carbon dioxide fixation, a process by which atmospheric carbon dioxide is converted by plants to energy-rich molecules such as glucose. This step of the Calvin Cycle plays a crucial role in providing energy for the cell.

http://reasonandscience.heavenforum.org/...nson-cycle

Rubisco is also the most abundant enzyme on earth. It is present in every plant and photosynthetic organism, from the smallest cyanobacteria and plankton to palm trees and giant sequoias. Rubisco is a complex composed by eight large subunits and eight small subunits

Synthesized RuBisCO does not have a fully functional active site. It needs to be activated by a CO2 molecule that carbamylates its catalytic Lys to bind Mg2+ that completes the activation process. . The carboxylation involves at least four, perhaps five discrete steps and at least three transition states;

The origin of these highly specific , regulated and coordinated steps, which are essential for the activation of Rubisco, are best explained through a planning mind, which all set it up. Natural mechanisms are extremely unlikely to be capable to produce these sofisticated metabolic multistep pathways and assembly lines to make Rubisco in the first place . No wonder, that no mainstream scientific papers are able to provide compelling evolutionary scenarios. As long as the enzyme is not fully functional, nothing goes, and ultimatively, advanced life on earth would not be possible .How did the correct insertion of the correct metal cation Mg2+ surrounded by three H2O/OH molecules emerge ? Trial and error ? The genome needs the right information in order to get the right materials, the right shape and quantity of each subunit co-factors and metal clusters,how to position them at the right active site, and how to mount these parts in the right order . That seems to me only being explained in a compelling manner by the wise planning of a super intelligent engineer, which knew how to invent and build this highly sophisticated and complex machine and make it fully functional right from scratch. A step wise unguided emergence seems to be extremely unlikely.This mechanism seems to be the result of a intelligence, which set it all up through power, will and information.

The eight large subunits of rubisco are coded by the chloroplast DNA, and the eight small subunits by nuclear DNA. The small subunit of Rubisco and all the other Calvin cycle enzymes are encoded by nuclear genes and must be transported and travel to the chloroplast site after their synthesis in the cytosol.

http://reasonandscience.heavenforum.org/...loroplasts

The precursor forms of these stromal proteins contain an N-terminal stromal-import sequence. This transit peptide allows transfer of the small subunits synthesized in the cytosol through the chloroplast envelope translocon complexes into the plastid. These are highly complex molecular gates in the chloroplast inner and outer membrane, which filter which molecules go in. After the unfolded precursor enters the stromal space, it binds transiently to a stromal Hsc70 chaperone and the Nterminal sequence is cleaved.

Folding of the small and large Rubisco subunit proteins is mediated by the amazing GroEL–GroES chaperonin system. Protein folding mediated by chaperonins is the process by which newly synthesized polypeptide chains acquire the three-dimensional structures necessary for biological function. For many years, protein folding was believed to occur spontaneously. But it has become apparent that large proteins frequently fail to reach native state, forming nonfunctional aggregates instead. They need the aid of these sophisticated barrel shaped proteins.

http://reasonandscience.heavenforum.org/...chaperones

That raises interesting questions : How should and could natural non guided natural mechanisms forsee the necessity of chaperones in order to get a specific goal, that is the right precise 3 dimensional folding resulting in functional proteins to make living organisms ? Non living matter has no natural " drive " or purpose or goal to become living. The make of proteins to create life however is a multistep process of many parallel acting complex metabolic pathways and production-line like processes to make proteins and other life essential products like nucleotides, amino acids, lipids , carbohydrates etc. The right folding of proteins is just one of several other essential processes in order to get a functional protein. But a functional protein by its own has no function, unless correctly embedded through the right assembly sequence and order at the right functional place.

Eight S subunits combine with the eight L subunits to yield the active rubisco enzyme. At least three chloroplast outer-membrane proteins, including a receptor that binds the stromal-import sequence and a translocation channel protein, and five inner-membrane proteins are known to be essential for directing proteins to the stroma. Import into the stroma depends on ATP hydrolysis catalyzed by a stromal Hsc70 chaperone. Chloroplasts cannot generate an electrochemical gradient (proton-motive force) across their inner membrane. Thus protein import into the chloroplast stroma is powered solely by ATP hydrolysis. Within the stroma, the S-subunits undergo further posttranslational modification (transit peptide cleavage, Met-1 aN- methylation) prior to assembly into final L8S8 Rubisco complexes. How did natural evolutionary processes find out how to do it ? Trial and error?

In order to make and assemble Rubisco, at least 25 parts, most of them essential and irreducible, are directily involved in Rubisco function , activation, and synthesis:

http://reasonandscience.heavenforum.org/...esign#3899

Could these parts have evolved separately and gradually ? Most of them are specifically used as assembly tools of Rubisco, as for example the specialized chaperone RbcX, used during the synthesis process, and once Rubisco assembly has finished, these enzymes are discarted. Even one subunit missing renders Rubisco useless.

How do proponents of evolution explain how natural selection would have favoured a protein complex the function of which was to prevent a still-useless Rubisco small subunit from folding outside the chloroplast? Before it evolved a way to get the protein inside, there would be no benefit from keeping it unfolded outside. How could blind chance ‘know’ it needed to cause large subunit polypeptides to fold ‘correctly’ and to keep them from clumping? It could not ‘anticipate’ the ‘correct’ conformation before the protein became useful. And evolution would need to be clever indeed to chemically modify something not yet useful so that it could be folded ‘correctly’ when even the ‘correctly’ folded polypeptide would not yet become useful.

Only a designer would know why it would be necessary to produce a specialized protease, target it to the chloroplast, and program it to clip off the targeting sequence of the small subunit at just the right place. And what about the assembly of a collection of meaningless rubisco parts in just one certain way? In order to design a sophisticated set of tools to make something else useful in the future that had, as yet, no function, evolution (as ‘designer’) would have had to have detailed knowledge of the future usefulness of the protein it was so cleverly engineering. If evolution managed to generate any one of these chaperone protein complexes (and it would not), it would still be useless for generating rubisco unless all the other chaperones were also present. Without any one of them, the sixteen-unit complex could not be generated.
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17-08-2015, 09:40 PM
RE: Rubisco is the most important enyzme on the planet.
(17-08-2015 09:24 PM)Godexists Wrote:  Rubisco is the most important enyzme on the planet.

http://reasonandscience.heavenforum.org/...esign#2337

virtually all the organic carbon in the biosphere derives ultimately from the carbon dioxide that this enzyme fixes from the atmosphere. Without it, advanced life would not be possible. And we would not be able to debate our origins. All inquiry and quest about if we are ultimatively the result of a powerful creator, or just random natural chemical reactions and emerging properties of lifeless matter, if biodiversity is due to evolution, or a intelligent designer, is second to the inquiry of how Rubisco came to be. Through my research i gained remarkable insight about Rubisco's complex structure, functioning and synthesis process, how many cell parts , enzymes, proteins and pathways are involved and required to assemble it, how the unfinished sub units require co and post-translational modifications, specific proteins that help like assembly robots in the manufacturing process,sophisticated pathways and mechanisms of protein import and targeting in chloroplasts through large multiprotein translocon complexes in the stroma, and andvanced protein communication and information systems. All this is of bewildering complexity, where dozens of individual interconnected and finely tuned parts are required, a web of interlocked extremely complex advanced molecular machines where if one is missing, nothing goes, that defy the intelligence of the best scientists for decades to find out their structure, mechanisms and functions. Could all this be due to natural processes ?

RuBisCO is a multi-subunit plant protein essential to photosynthesis. It catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere. In the C3 pathway, RuBisCO is responsible for initiating the first step in carbon dioxide fixation, a process by which atmospheric carbon dioxide is converted by plants to energy-rich molecules such as glucose. This step of the Calvin Cycle plays a crucial role in providing energy for the cell.

http://reasonandscience.heavenforum.org/...nson-cycle

Rubisco is also the most abundant enzyme on earth. It is present in every plant and photosynthetic organism, from the smallest cyanobacteria and plankton to palm trees and giant sequoias. Rubisco is a complex composed by eight large subunits and eight small subunits

Synthesized RuBisCO does not have a fully functional active site. It needs to be activated by a CO2 molecule that carbamylates its catalytic Lys to bind Mg2+ that completes the activation process. . The carboxylation involves at least four, perhaps five discrete steps and at least three transition states;

The origin of these highly specific , regulated and coordinated steps, which are essential for the activation of Rubisco, are best explained through a planning mind, which all set it up. Natural mechanisms are extremely unlikely to be capable to produce these sofisticated metabolic multistep pathways and assembly lines to make Rubisco in the first place . No wonder, that no mainstream scientific papers are able to provide compelling evolutionary scenarios. As long as the enzyme is not fully functional, nothing goes, and ultimatively, advanced life on earth would not be possible .How did the correct insertion of the correct metal cation Mg2+ surrounded by three H2O/OH molecules emerge ? Trial and error ? The genome needs the right information in order to get the right materials, the right shape and quantity of each subunit co-factors and metal clusters,how to position them at the right active site, and how to mount these parts in the right order . That seems to me only being explained in a compelling manner by the wise planning of a super intelligent engineer, which knew how to invent and build this highly sophisticated and complex machine and make it fully functional right from scratch. A step wise unguided emergence seems to be extremely unlikely.This mechanism seems to be the result of a intelligence, which set it all up through power, will and information.

The eight large subunits of rubisco are coded by the chloroplast DNA, and the eight small subunits by nuclear DNA. The small subunit of Rubisco and all the other Calvin cycle enzymes are encoded by nuclear genes and must be transported and travel to the chloroplast site after their synthesis in the cytosol.

http://reasonandscience.heavenforum.org/...loroplasts

The precursor forms of these stromal proteins contain an N-terminal stromal-import sequence. This transit peptide allows transfer of the small subunits synthesized in the cytosol through the chloroplast envelope translocon complexes into the plastid. These are highly complex molecular gates in the chloroplast inner and outer membrane, which filter which molecules go in. After the unfolded precursor enters the stromal space, it binds transiently to a stromal Hsc70 chaperone and the Nterminal sequence is cleaved.

Folding of the small and large Rubisco subunit proteins is mediated by the amazing GroEL–GroES chaperonin system. Protein folding mediated by chaperonins is the process by which newly synthesized polypeptide chains acquire the three-dimensional structures necessary for biological function. For many years, protein folding was believed to occur spontaneously. But it has become apparent that large proteins frequently fail to reach native state, forming nonfunctional aggregates instead. They need the aid of these sophisticated barrel shaped proteins.

http://reasonandscience.heavenforum.org/...chaperones

That raises interesting questions : How should and could natural non guided natural mechanisms forsee the necessity of chaperones in order to get a specific goal, that is the right precise 3 dimensional folding resulting in functional proteins to make living organisms ? Non living matter has no natural " drive " or purpose or goal to become living. The make of proteins to create life however is a multistep process of many parallel acting complex metabolic pathways and production-line like processes to make proteins and other life essential products like nucleotides, amino acids, lipids , carbohydrates etc. The right folding of proteins is just one of several other essential processes in order to get a functional protein. But a functional protein by its own has no function, unless correctly embedded through the right assembly sequence and order at the right functional place.

Eight S subunits combine with the eight L subunits to yield the active rubisco enzyme. At least three chloroplast outer-membrane proteins, including a receptor that binds the stromal-import sequence and a translocation channel protein, and five inner-membrane proteins are known to be essential for directing proteins to the stroma. Import into the stroma depends on ATP hydrolysis catalyzed by a stromal Hsc70 chaperone. Chloroplasts cannot generate an electrochemical gradient (proton-motive force) across their inner membrane. Thus protein import into the chloroplast stroma is powered solely by ATP hydrolysis. Within the stroma, the S-subunits undergo further posttranslational modification (transit peptide cleavage, Met-1 aN- methylation) prior to assembly into final L8S8 Rubisco complexes. How did natural evolutionary processes find out how to do it ? Trial and error?

In order to make and assemble Rubisco, at least 25 parts, most of them essential and irreducible, are directily involved in Rubisco function , activation, and synthesis:

http://reasonandscience.heavenforum.org/...esign#3899

Could these parts have evolved separately and gradually ? Most of them are specifically used as assembly tools of Rubisco, as for example the specialized chaperone RbcX, used during the synthesis process, and once Rubisco assembly has finished, these enzymes are discarted. Even one subunit missing renders Rubisco useless.

How do proponents of evolution explain how natural selection would have favoured a protein complex the function of which was to prevent a still-useless Rubisco small subunit from folding outside the chloroplast? Before it evolved a way to get the protein inside, there would be no benefit from keeping it unfolded outside. How could blind chance ‘know’ it needed to cause large subunit polypeptides to fold ‘correctly’ and to keep them from clumping? It could not ‘anticipate’ the ‘correct’ conformation before the protein became useful. And evolution would need to be clever indeed to chemically modify something not yet useful so that it could be folded ‘correctly’ when even the ‘correctly’ folded polypeptide would not yet become useful.

Only a designer would know why it would be necessary to produce a specialized protease, target it to the chloroplast, and program it to clip off the targeting sequence of the small subunit at just the right place. And what about the assembly of a collection of meaningless rubisco parts in just one certain way? In order to design a sophisticated set of tools to make something else useful in the future that had, as yet, no function, evolution (as ‘designer’) would have had to have detailed knowledge of the future usefulness of the protein it was so cleverly engineering. If evolution managed to generate any one of these chaperone protein complexes (and it would not), it would still be useless for generating rubisco unless all the other chaperones were also present. Without any one of them, the sixteen-unit complex could not be generated.

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17-08-2015, 09:45 PM (This post was last modified: 17-08-2015 10:05 PM by Unbeliever.)
RE: Rubisco is the most important enyzme on the planet.
(17-08-2015 09:24 PM)Godexists Wrote:  The genome needs the right information in order to get the right materials, the right shape and quantity of each subunit co-factors and metal clusters,how to position them at the right active site, and how to mount these parts in the right order . That seems to me only being explained in a compelling manner by the wise planning of a super intelligent engineer, which knew how to invent and build this highly sophisticated and complex machine and make it fully functional right from scratch. A step wise unguided emergence seems to be extremely unlikely.This mechanism seems to be the result of a intelligence, which set it all up through power, will and information.

Your entire argument is nothing but the argument from personal incredulity fallacy.

You fail.

"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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17-08-2015, 09:52 PM
RE: Rubisco is the most important enyzme on the planet.
(17-08-2015 09:45 PM)Unbeliever Wrote:  Your entire argument is nothing but the argument from personal incredulity fallacy.

You fail.

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17-08-2015, 10:34 PM
RE: Rubisco is the most important enyzme on the planet.
The good part is that scientific advances are forcing the incredulous to up their game with their arguments from incredulity.

This in turn forces the real scientists to up their game in dis-incredulising.

Ironically, this is the memetic version of the genetic 'arms race'.

In other words, the ignorant are helping to shape the questions and the quality of knowledge-delivery.

Yes

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17-08-2015, 11:04 PM
RE: Rubisco is the most important enyzme on the planet.
It genuinely amazes me that people like this can fail to grasp the very basic principle that ID/IC does not work when you assume that the way a chemical system operates now is the only way it could work, ever. The "knock out one portion" argument, first used by Behe with the blood clotting cascade example, is thoroughly debunked. (See the video posted in the other thread: https://www.youtube.com/watch?v=d4r2J6Y5AqE.)

They are dishonest to present evolution in that way, because it's just not how evolution works, and it's dishonest of the ID/IC people to continue to push that strawman version of how it works just to debunk it.

Pro Tip: if you're using the term/phrase "remove one part and...", then you are wrong. You are pretending that a gene or chemical in a cell does only one thing, by myopically focusing on the single process. Miller did a great job of showing the evolutionary "borrowing" basis for the often-used bacterial flagellum example (which the ID/IC people used in the Katzmiller case endlessly), where a series of proteins that are part of a bacterial "pump" were attached to other proteins for the base of the "flagellum motor".

"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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17-08-2015, 11:26 PM
RE: Rubisco is the most important enyzme on the planet.
Oh, and if one of the biology students here isn't around, the rest of you can save yourselves time... they've already indexed most of the claims Creationists, including this douchebag, are making:

http://www.talkorigins.org/indexcc/list.html

Most of it is a list of links to the appropriate scientific papers on the subject, so it does require a bit of knowledge to process, but for those who are curious, it's there. Most of what GE posts is in CB200, the biochemistry section, though some specifics (such as the above photosynthesis one) are in other sections, such as botany (CB510).

"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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17-08-2015, 11:38 PM
RE: Rubisco is the most important enyzme on the planet.
(17-08-2015 11:26 PM)RocketSurgeon76 Wrote:  Oh, and if one of the biology students here isn't around, the rest of you can save yourselves time... they've already indexed most of the claims Creationists, including this douchebag, are making:

http://www.talkorigins.org/indexcc/list.html

Most of it is a list of links to the appropriate scientific papers on the subject, so it does require a bit of knowledge to process, but for those who are curious, it's there. Most of what GE posts is in CB200, the biochemistry section, though some specifics (such as the above photosynthesis one) are in other sections, such as botany (CB510).

Thanks for that link. I actually spent some time searching for it when I first saw this thread, but it's been a while since I last got involved in a discussion on straight-up creationism, so I'd forgotten the precise place to find it. It's a great source.

It's worth noting, though, that you don't even need an elementary school level understanding of biology, chemistry, or even the underpinnings of the theory of evolution in order to refute Godexists' nonsense.

He doesn't understand a word of what he's parroting. He just knows that it sounds complicated, and seizes any mentions of complexity or the requirement for certain compounds to be present in order for some things to happen as evidence that it had to have been designed.

If it's complicated, it obviously had to have a designer, because obviously chemistry can't account for such things on its own. This is the argument from incredulity fallacy, as noted above.

If removing a part of it makes it stop working, it had to have a designer, because it's irreducibly complex. This completely ignores the whole point of the theory of evolution; the mechanisms involved did not necessarily serve that purpose earlier in their history. Godexists' insistence that his inability to think of a way for these systems to have evolved is, again, nothing but the argument from incredulity fallacy.

It really all just comes down to that. I encourage everyone reading this thread to do the research anyway, because it's fascinating stuff, but Godexists' arguments fall completely on their collective face whether or not you know the details.

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17-08-2015, 11:53 PM
RE: Rubisco is the most important enyzme on the planet.
(17-08-2015 11:04 PM)RocketSurgeon76 Wrote:  Pro Tip: if you're using the term/phrase "remove one part and...", then you are wrong. You are pretending that a gene or chemical in a cell does only one thing, by myopically focusing on the single process.


If you remove the ECU (engine control unit) from any modern automobile, the vehicle ceases to function. Simple as that, the ECU is critical to the maintenance and operation of modern vehicles; without one you cannot start the engine.


Model T's didn't have, nor need, ECU's.


Now just because a modern Honda Civic has an ECU, doesn't mean that they always had ECU's, or that it's not possible to have a model that operates perfectly fine without an ECU. Functions now handled by the ECU were once controlled by other devices, such as carburetors in place of electronically controlled fuel injectors.


ID and irreducible complexity amounts to claiming that God invented the Honda Civic, because if you removed the ECU the car no longer functions, and therefore the car is irreducibly complex and requires divine intervention to explain it's operation.


@ GodExists

Does that sound stupid to you GE? God being responsible for the Honda Civic and all other modern automobiles? It should, because it is stupid. And to those of us who actually understand evolutionary theory (because we haven't been indoctrinated into reactionary rejection of it), your 'arguments' are just as infantile.

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18-08-2015, 12:20 AM
RE: Rubisco is the most important enyzme on the planet.
I admit I don't know shit about chemistry.
I do know that I have seen this same article copypasta dumped in a few other atheist type places without comment from the poster. I guess if it looks "sciency" enough and it came from a christian source, its gotta be A-OK.
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