A protein is created in the cell by copying its DNA gene, making any necessary edits to the copy, and passing the copy to the ribosome machine which uses the genetic code to translate the copy (a series of nucleotides) into the protein structure (a series of amino acids). But the story does not end here. The final step, after translation, is to fold the protein into its three dimensional structure. It is a step that is difficult to monitor and difficult to predict. The chain of amino acids folds up in a tiny fraction of a second and the final shape it assumes is not obvious. And sometimes the folding process is literally hidden as the nascent protein chain is hidden inside the cavity of a chaperonin machine with the lid shut.Chaperonins are large protein machines that help some proteins to fold into their proper shape. New research is reporting on the structure of a particular chaperonin, including the lid closing action. The results are fascinating and they raise the question of how and why such an intricate protein machine evolved.
The different types of chaperonins fall into the broader category of molecular machines that not only help new proteins to fold, but also help existing proteins recover from shock, help with the assembly of machines, and so forth.
The obvious question is: How could evolution just happen to produce such machines? After all, a long series of lucky mutations would be required. But a more subtle problem has to do with not how, but why evolution would produce such machines.
For instance, this chaperonin machine, even if somehow was created by the cell, helps fold proteins that don’t want to fold very often. So before the helper chaperonin machine was available, these reluctant proteins would be lying around in various useless forms. For all we know they might be unfolded, or they might be misfolded. In any case, they would be clogging the works.
According to evolution these reluctant proteins would decrease fitness and not be selected. They would be evolutionary dead ends.
But in that case the chaperonin helper machines, when they just happened to evolve, would have nothing to do. Again, according to evolution, they would be consuming energy, getting in the way, and generally not helping. They too would not be selected.
These are questions that young evolutionists are prone to ask (evolutionists are constantly probing and trying to falsify their own theory). In their lack of experience they miss the obvious solution: Evolution simultaneously evolved both the chaperonins and the proteins that need their help. The reluctant proteins were never clogging the works, and the chaperonins never lacked for something to do. Evolution’s timing was perfect. As usual evolution provides an answer that is simple, elegant and compelling. You can see why it is said to be a fact.
Evolution is so lucky, and then on top of this luck it also happens to be the only explanation allowed according to the "rules" of the game. Sometimes I wish I was as lucky as evolution, I would be a millionaire.
ReplyDelete--Johan--
I just don't have enough FAITH to be an evolutionist.
ReplyDeleteArchibald, Logsdon & Doolittle, Origin and Evolution of Eukaryotic Chaperonins: Phylogenetic Evidence for Ancient Duplications in CCT Genes, Molecular Biology and Evolution 2000.
ReplyDeleteApparently, extant chaperonins have evolutionary precursors.
Cornelius -
ReplyDeleteFirstly,
"(evolutionists are constantly probing and trying to falsify their own theory)."
This is how all science works. There is nothing suspicious ordamning about it. It is simple standard scientific practise to constantly try to falsify your theories.
Secondly - "How could evolution just happen to produce such machines? After all, a long series of lucky mutations would be required."
How is this logically any different from looking at any complex organ, say an eye, and saying 'How could evolution produce such a thing? A long series of lucky mutations would be required."
Isn't this just an argument from incredulity? You don't see how it could have happened, therefore it can't have?
Thirdly, I have to repeat a point you have ignored twice now - what conclusion do you want your readers to draw?
Even if, as you seem to be implying the explaination evolution provides is insufficient somehow, so what? All you are demonstrating is that there are mysteries in biology. Which I don't think anyone will disagree with.
Since you've already ignored this question twice, I hold out little hope you will actually address it this time, so allow me to tell you why I think you do it: this follows the pattern of many Intelligent Design arguments - point out just how complicated and complex life is, ideally accompanied by reasons why current science's explanations are insufficient (sometimes correctly, sometimes just a mangled confusion of the facts), and then conclude that these mysteries have beaten our greatest minds - we will never explain them rationally because they are obviously miracles. We should just declare them the work of a supernatural designer and be done with it.
Now admitedly you do not declare this final conclusion, but then you don't really declare any conclusion at all. You keep pushing the reader in this direction, and then stop just short of actually stating the conclusion yourself - presumably hoping the reader will draw this inference on their own.
But the fact that you do not openly state this obviously theological conclusion does not make the train of logic that got you there any more scientific or any less religious.
At best, all you are doing is pointing out mysteries.
Ritchie: "Thirdly, I have to repeat a point you have ignored twice now - what conclusion do you want your readers to draw?"
ReplyDeleteSimple. Force and information are congnizant entities. Only ID would have a chance at keeping their eye on the conceptual ball.
"Out of sight is not out of Mind".
Steve -
ReplyDeleteExactly how do you work that out? I think I'll need you to explain that one for me.
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ReplyDeleteRitchie:
ReplyDelete=========================
"(evolutionists are constantly probing and trying to falsify their own theory)."
This is how all science works. There is nothing suspicious ordamning about it. It is simple standard scientific practise to constantly try to falsify your theories.
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I guess my sarcasm was too subtle. Evolutionists do not genuinely seek falsification -- it is simply out of the question. They talk all about quandaries and issues with their theory, but genuine falsification is never in view. It is never a live option. Never. That's what religion does to science.
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Isn't this just an argument from incredulity? You don't see how it could have happened, therefore it can't have?
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But I didn't say that. I'm not arguing that it can't have. I'm arguing that we do not know for a fact that it did. As absurd as that is, that is what evolutionists claim.
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what conclusion do you want your readers to draw? ... At best, all you are doing is pointing out mysteries.
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That science is interesting. That there are important unanswered questions awaiting attention. That the religion evolutionists have imposed in inappropriate in science.
Cornelius Hunter: Evolutionists do not genuinely seek falsification -- it is simply out of the question.
ReplyDeleteThat's simply not correct. Nearly every published scientific research paper is a test of a hypothesis. This often results in falsification of one of the assumptions that make up the hypothesis. Indeed, falsification is one of the most important ways to push science forward. That's why it is so easy to quote-mine, because scientists are always trying to overturn this or that tenet of evolutionary theory.
Cornelius Hunter: How could evolution just happen to produce such machines? After all, a long series of lucky mutations would be required.
Ritchie: Isn't this just an argument from incredulity? You don't see how it could have happened, therefore it can't have?
Cornelius Hunter: I'm arguing that we do not know for a fact that it did.
It's a strawman based on a specific claim, that "a long series of lucky mutations would be required." Having built the straw man, you strike at it with your incredulity. In fact, selection sometimes makes the evolution of a structure inevitable, even though the source of the variation is random. (Consider that perfume molecules will soon permeate a room, even though their individual motions are random.) Whether this is applicable to the particular case or not is contingent on the specifics.
And yes, we know with reasonable scientific certainty that it evolved, even if we can't reconstruct its entire history. That's because of the bulk of the evidence we have repeatedly suggested you need to consider—starting with Common Descent.
But perfume in a room is not a structure with highly specified complexity, but rather a ramdom scattering of molecules.
ReplyDeleteIMHO, the problem comes down to a another chicken/egg scenario. Certain proteins depend on the chaperonin for their shape. But hat means that the chaperonin had to evovle before these proteins. But then the chaperonin itself serves no purpose. So it could not evolve. Unless, the cell knew that it would need the chaperonin in the future. There's a lot of these kinds of problems in biology.
laugh out loud: But perfume in a room is not a structure with highly specified complexity, but rather a ramdom scattering of molecules.
ReplyDeleteIf we look at sequence space, we see evolution as a process of expanding into the space from points it already occupies. Whether evolution is likely to discover a particular pathway depends on the topology of the local space and the distances involved. In some areas of the space, the results are predictable. For instance, the evolution of antibiotic resistance in the Lederberg Experiment is inevitable given sufficient populations of bacteria. On the other hand, citrate-utilization is not inevitable but contingent, given the environmental conditions of the Lenski Experiment.
laugh out loud: Certain proteins depend on the chaperonin for their shape. But hat means that the chaperonin had to evovle before these proteins.
That's the Irreducible Complexity Argument. It can be shown that evolutionary processes can evolve Irreducible Structures. A simple example is a complex, functional system A, which adds a helper B. A and B then optimize through functional polarization to become dependent on one another. Now we have a complex and irreducible structure A-B.
If Chaperonins evolved, we would predict they had evolutionary precursors. And that is what we find.
Archibald, Logsdon & Doolittle, Origin and Evolution of Eukaryotic Chaperonins: Phylogenetic Evidence for Ancient Duplications in CCT Genes, Molecular Biology and Evolution 2000.
But the chaperonin does not need the various proteins it folds. It serves no purpose until they exist. And the proteins cannot serve their purpose without the chaperonin to fold them. The only scenario I can think of is self foldding proteins evolving, then the chaperonin evolves to help them fold, then the proteins loose the ability to self fold. But then why would the chaperonins evolve, if they aren't necessary?
ReplyDeleteCornelius -
ReplyDelete"Evolutionists do not genuinely seek falsification -- it is simply out of the question. They talk all about quandaries and issues with their theory, but genuine falsification is never in view. It is never a live option. Never."
Zachriel is totally right. The idea that 'evolutionists' simply do not seek to falsify their theory is nonsense.
"But I didn't say that. I'm not arguing that it can't have. I'm arguing that we do not know for a fact that it did."
And what hypotheses would you suggest we test other than the hypotheses that they evolved naturally through natural selection? What other mechanism is there to test against? It is not bias or 'religious fundamentalism' to back the only horse in the race.
"That science is interesting. That there are important unanswered questions awaiting attention."
Those two are true. Yet you limit your scope to just evolution. You do not criticize other theories for not being perfectly, unassailably complete.
"That the religion evolutionists have imposed in inappropriate in science."
There is no religion! Science does not impose any theological views, inlcuding the scientists who support evolutionary theory!
I cannot see where you get this ridiculous idea from. Metaphysically the theory of evolution is treated no differently from any other scientific thoery. And yet you repeatedly insist it is imposing theology!
laugh out loud: It serves no purpose until they exist.
ReplyDeleteThat's not necessarily the case.
laugh out loud: The only scenario I can think of is self foldding proteins evolving, then the chaperonin evolves to help them fold, then the proteins loose the ability to self fold.
Most proteins can fold themselves; but chaparones increase the reliability and speed of the process and prevents aggregation in the crowded cellular environment. And yes, they can co-evolve so that the process becomes dependent.