The Elshamah mega-thread

[red]

Re: Rubisco is the most important enyzme on the planet.

The homology is most striking, except when it isnt..... and when it isnt, its time to make things up, and just assert that the subunits were  " eukaryotic additions ". Homology can well be explained through common design. Thats common practice. Examples which seem to fit evolutionary assumptions are  cited, while the  examples that do not fit are ignored, or baseless assertions are made, as above shows.

Except that it is not common practice (except amongst the ignorant).
How does a leaf look like a thorn? Not too well, yet they are homologous because we can track inherited characteristics. You merely confuse analogy with homology because you do not understand the difference.

The many similarities that exist among members of the animal kingdom is the result of the fact that a single designer created the basic kinds of living 'systems', then specially modified each type of life to enable it to survive in its unique environmental niche.

And we know you will present this evidence along with the evidence of your supposed designer in the fullness of time.

Structural similarities among automobiles, however, even similarities between older and newer models  are due to construction according to pre-existing patterns, i.e., to design. Ironically, even striking similarities are not sufficient to exclude design-based explanations. In order to demonstrate naturalistic evolution, it is necessary to show that the mechanism by which organisms are constructed (unlike the mechanism by which automobiles are constructed) does not involve design.

We know how DNA is responsible for inherited characteristics and we understand the mechanisms reasonably well. Equivocating over "design" does you no good here as your analogy is false.
Here's a take on your example which might help. Hopefully you realise you have a mother and a father. Which parent "designed" you?

 

[Mr_Wilford]

Re: Rubisco is the most important enyzme on the planet.

It's sad this spam is basically all that keeps this forum alive

 

[red]

Re: Rubisco is the most important enyzme on the planet.

Rumraket

you have conveniently avoided to address following :

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.

You have confused life with non life in the evolutionary context. To boot, adding abiogenesis to the mix makes your writings incoherent and nonsensical.

How did natural evolutionary processes find out how to do it ? Trial and error?

No, through the well established and time tested processes we call evolution. Somehow these steps led to you existing and being able to ask the very questions which let us test how organisms change over time. Not quite perfection, is it?

 

[Elshamah]

Re: Rubisco is the most important enyzme on the planet.

ahm.....

and this has also not been addressed....... :roll:

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 ? Thats precisely what happens in the cell . Evolution has no consciousness, and no forsight nor intelligence. But precisely that is required for PLANNING and make of blueprints. I cannot create a machine, without the precise drawing and project information in advance, which is required to make 1. the assembly tools 2. the subparts 2. the whole machine.

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.

 

[Rumraket]

Re: Rubisco is the most important enyzme on the planet.

ahm.....

and this has also not been addressed....... :roll:

Or how do proponents of evolution explain how natural selection would have favoured the emergence bla bla bla

Already been over this. Same fundamental mistake you make every time. Evolution demonstrably produces multi-component irreducibly complex structures, in fact we predict they will emerge through the evolutionary process and we have seen it happen in experiment without any guidance or design.

Irreducible complexity is not a successful argument against evolution for reasons already stated in your three other threads.

In fact we have observed the origin of an irreducibly complex pathway for the utilization of citrate under aerobic conditions in Richard Lenski's long-term evolution experiment with E coli.

A gene duplication spawned a copy of the citrate transporter in vicinity of a regulatory element that is only active under aerobic conditions. This allows the cells to use citrate when oxygen is present, which they normally cannot do.

If you remove the duplicate gene, the cell can no longer use citrate with oxygen present. If you remove the regulatory element, the citrate transporter fails to activate when oxygen is present, and the cell cannot use citrate and will die if there is no other food available. So there you go, a two-component, irreducibly complex system that requires both components to be present to work. If you remove one of the components, the system stops working. So it is irreducibly complex and it evolved.

If it is irreducibly complex it can still evolve. In fact we expect that the evolutionary process will create irreducibly complex structures. Do you understand this? If evolution is true, there should be irreducibly complex structures in living organism.

 

[red]

Re: Rubisco is the most important enyzme on the planet.

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?

A designer would do away with complexity and just make organic functions happen with the minimum of fuss.
If there were a designer capable of the complexity you propose, then surely that designer would be capable of omitting unnecessary steps!
The myriad of molecular functions you want to attribute to a designer should not have required insertion into DNA as your designer would not need a transport mechanism, nor a means of reproduction.
The fact is there is no designer, no magician, just natural processes which most people have been able to grasp.

 

[he_who_is_nobody]

Re: Rubisco is the most important enyzme on the planet.

A designer would do away with complexity and just make organic functions happen with the minimum of fuss.

Bingo!

What is more complex?

This:

Or this:

Now what is more advanced? Does complex equate to advanced? Obvousely not.

Simplicity is the key to good design.

 

[Elshamah]

Re: Rubisco is the most important enyzme on the planet.

ahm.....

and this has also not been addressed....... :roll:

Or how do proponents of evolution explain how natural selection would have favoured the emergence bla bla bla

Already been over this. Same fundamental mistake you make every time. Evolution demonstrably produces multi-component irreducibly complex structures, in fact we predict they will emerge through the evolutionary process and we have seen it happen in experiment without any guidance or design.

Irreducible complexity is not a successful argument against evolution for reasons already stated in your three other threads.

In fact we have observed the origin of an irreducibly complex pathway for the utilization of citrate under aerobic conditions in Richard Lenski's long-term evolution experiment with E coli.

A gene duplication spawned a copy of the citrate transporter in vicinity of a regulatory element that is only active under aerobic conditions. This allows the cells to use citrate when oxygen is present, which they normally cannot do.

If you remove the duplicate gene, the cell can no longer use citrate with oxygen present. If you remove the regulatory element, the citrate transporter fails to activate when oxygen is present, and the cell cannot use citrate and will die if there is no other food available. So there you go, a two-component, irreducibly complex system that requires both components to be present to work. If you remove one of the components, the system stops working. So it is irreducibly complex and it evolved.

If it is irreducibly complex it can still evolve. In fact we expect that the evolutionary process will create irreducibly complex structures. Do you understand this? If evolution is true, there should be irreducibly complex structures in living organism.

ahm.. dodging the issues raised..... congrats !!

 

[Elshamah]

Re: Rubisco is the most important enyzme on the planet.

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?

A designer would do away with complexity and just make organic functions happen with the minimum of fuss.
If there were a designer capable of the complexity you propose, then surely that designer would be capable of omitting unnecessary steps!
The myriad of molecular functions you want to attribute to a designer should not have required insertion into DNA as your designer would not need a transport mechanism, nor a means of reproduction.
The fact is there is no designer, no magician, just natural processes which most people have been able to grasp.

Ahm... so you understand the systems described, and know how to make them in a less complex way. Congrats. You must be a genious then......

 

[SpecialFrog]

Re: Rubisco is the most important enyzme on the planet.

So Elshamah, how could such complexity come from the simple god you allege?

 

[red]

Re: Rubisco is the most important enyzme on the planet.

Ahm... so you understand the systems described, and know how to make them in a less complex way. Congrats. You must be a genious then......

Yes I understand the systems described and would have avoided them if I were a designer.
For example, I would never have designed a human rib cage (essentially the "chassis" for our form) such that it allows our organs to slump out of it, rather than use gravity to hold them in place. That's a classic design failure. Well it is for bipeds, but not for our four legged friends who evolved and inherited that morphology fit for purpose.
With regard to Rubiscon - your topic of choice here, we know that Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO2 and NH3 and the consumption of energy during photorespiration. Another example of poor design. However through genetic engineering we might be able to do a bit better for Rubisco and enable crops to deliver more with the same input.
Why is your designer sitting on the fence when over billion people are starving?

 

[MarsCydonia]

Re: Rubisco is the most important enyzme on the planet.

So Elshamah, how could such complexity come from the simple god you allege?

Magic

 

[Elshamah]

Re: Rubisco is the most important enyzme on the planet.

So Elshamah, how could such complexity come from the simple god you allege?

Magic

How do proponents of naturalism explain how natural mechanisms 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.

magic

 

[Collecemall]

Re: Rubisco is the most important enyzme on the planet.

How do proponents of naturalism explain how natural mechanisms 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.

magic

Let's play hypothetical for a min. I'll pretend there was a designer with the ability to confound us and made all the intricacies and complexity involved in cellular interaction and creation and you reconcile that with the rest of the story.

How do you reconcile that entity with the one who decided putting testicles outside the abdomen was a feature? Because THAT was a brilliant decision. I'm by no means a mental giant but there are hundreds if not thousands of these "design features" in every species that even I couldn't have missed and only make sense in light of evolution. Some of which we can't even say the creator didn't know about because it IS done in other species. So which is this entity? The one that "created" the intricacies and complexity or the moron who didn't realize balls get smashed? Or do you propose that he/she/it had their brains sucked out once the cell was complete and hasn't been heard from since?

 

[Dragan Glas]

Re: Rubisco is the most important enyzme on the planet.

Greetings,

Magic

How do proponents of naturalism explain how natural mechanisms 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.

magic

As typical of creationists, you continue to believe that natural mechanisms are "blind chance".

Natural selection is not chance - speciation is shaped by the environment, non-lethal traits are selected against by a given environment.

You are conflating development of separate proteins as if they had to occur simultaneously - by design.

There are only four possible combinations of these where they're either both outside or inside, or where one is outside and the other inside. All could have occurred but the only one that "worked" - kept the organism alive - was the one that has survived and propagated over time.

This is what happens where a chance mutation happens to "work" for that individual organism in a given environment, and is passed on, perhaps creating a new species.

It's a trial-and-error process - no fore-sight or planning required: whatever trait doesn't kill is passed on

Kindest regards,

James:

 

[Rumraket]

Re: Rubisco is the most important enyzme on the planet.

How do proponents of naturalism explain how natural mechanisms 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.

magic

Already been over this. Same fundamental mistake you make every time. Evolution demonstrably produces multi-component irreducibly complex structures, in fact we predict they will emerge through the evolutionary process and we have seen it happen in experiment without any guidance or design.

Irreducible complexity is not a successful argument against evolution for reasons already stated in your three other threads.

In fact we have observed the origin of an irreducibly complex pathway for the utilization of citrate under aerobic conditions in Richard Lenski's long-term evolution experiment with E coli.

A gene duplication spawned a copy of the citrate transporter in vicinity of a regulatory element that is only active under aerobic conditions. This allows the cells to use citrate when oxygen is present, which they normally cannot do.

If you remove the duplicate gene, the cell can no longer use citrate with oxygen present. If you remove the regulatory element, the citrate transporter fails to activate when oxygen is present, and the cell cannot use citrate and will die if there is no other food available. So there you go, a two-component, irreducibly complex system that requires both components to be present to work. If you remove one of the components, the system stops working. So it is irreducibly complex and it evolved.

If it is irreducibly complex it can still evolve. In fact we expect that the evolutionary process will create irreducibly complex structures. Do you understand this? If evolution is true, there should be irreducibly complex structures in living organism.

 

[MarsCydonia]

Re: Rubisco is the most important enyzme on the planet.

How do proponents of naturalism explain how natural mechanisms 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.

magic

You use this word, magic, but I do not think you understand what it means.

You are proposing that we rule out natural processes (because of a combination of ignorance and personal incredulity from what I have seen) and that we go with a "simple God spoke and poof, there it was" explanation.

We can call it a miracle instead of magic if calling it magic upsets your sensitivities but that does not change the explanation, does it?

 

[he_who_is_nobody]

Re: Rubisco is the most important enyzme on the planet.

How do proponents of naturalism explain how natural mechanisms 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.

magic

You use this word, magic, but I do not think you understand what it means.

You are proposing that we rule out natural processes (because of a combination of ignorance and personal incredulity from what I have seen) and that we go with a "simple God spoke and poof, there it was" explanation.

We can call it a miracle instead of magic if calling it magic upsets your sensitivities but that does not change the explanation, does it?

This is something that has always baffled me. Even if the intelligent design creationists were correct in their assertion that we believe [insert process/organ] came about because of random chance, that would still be a better explanation than magic/miracles. We have evidence that random events do happen and can create things. We have no evidence that magic/miracles have ever occurred.

 

[MarsCydonia]

Re: Rubisco is the most important enyzme on the planet.

This is something that has always baffled me. Even if the intelligent design creationists were correct in their assertion that we believe [insert process/organ] came about because of random chance, that would still be a better explanation than magic/miracles. We have evidence that random events do happen and can create things. We have no evidence that magic/miracles have ever occurred.

Think what the state of science would be today if inquiry into phenomenon was stiffled by dismissing the possibility of natural processes and everything was attributed to magic:

- "Look at this rainbow, I wonder why we observe them following a rainfall. Could there be a natural explanation for it linked to the rain?"

- "Natural explanation? Of course there is not. Rainbows are a gift from God, just like it says in the bible. If they appear after rainfall it's because it is God that makes them magically appear, to reassure us he will not drown the whole world again".

History is filled with phenomenoms that appeared magical but were found to have a natural explanation. Instead of ruling natural processes out of incredulity, cdesign proponentsists should try ruling God in, by actually providing evidence of magic/miracles.

 

[Dragan Glas]

Re: Rubisco is the most important enyzme on the planet.

Greetings,

How endosymbionts escape dead tubeworms and repopulate live specimens

Abstract
Theory predicts that horizontal acquisition of symbionts by plants and animals must be coupled to release and limited dispersal of symbionts for intergenerational persistence of mutualisms. For deep-sea hydrothermal vent tubeworms (Vestimentifera, Siboglinidae), it has been demonstrated that a few symbiotic bacteria infect aposymbiotic host larvae and grow in a newly formed organ, the trophosome. However, whether viable symbionts can be released to augment environmental populations has been doubtful, because (i) the adult worms lack obvious openings and (ii) the vast majority of symbionts has been regarded as terminally differentiated. Here we show experimentally that symbionts rapidly escape their hosts upon death and recruit to surfaces where they proliferate. Estimating symbiont release from our experiments taken together with well-known tubeworm density ranges, we suggest a few million to 1.5 billion symbionts seeding the environment upon death of a tubeworm clump. In situ observations show that such clumps have rapid turnover, suggesting that release of large numbers of symbionts may ensure effective dispersal to new sites followed by active larval colonization. Moreover, release of symbionts might enable adaptations that evolve within host individuals to spread within host populations and possibly to new environments.

Kindest regards,

James