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Discovery of 7 times higher complexity of protein folding!


Can protein folding complexity be formed by stochastic processes? With 14 intermediate steps?
JILA Team Discovers Many New Twists in Protein Folding

Biophysicists at JILA have measured protein folding in more detail than ever before, revealing behavior that is surprisingly more complex than previously known. . . .
They fold into three-dimensional shapes that determine their function through a series of intermediate states, like origami. Accurately describing the folding process requires identifying all of the intermediate states.
The JILA research revealed many previously unknown states by unfolding an individual protein. For example, the JILA team identified 14 intermediate states—seven times as many as previously observed—in just one part of bacteriorhodopsin, a protein in microbes that converts light to chemical energy and is widely studied in research.
The increased complexity was stunning,” said project leader Tom Perkins, a National Institute of Standards and Technology (NIST) biophysicist working at JILA, a partnership of NIST and the University of Colorado Boulder. “Better instruments revealed all sorts of hidden dynamics that were obscured over the last 17 years when using conventional technology.”
If you miss most of the intermediate states, then you don’t really understand the system,” he said.
Knowledge of protein folding is important because proteins must assume the correct 3-D structure to function properly. Misfolding may inactivate a protein or make it toxic. Several neurodegenerative and other diseases are attributed to incorrect folding of certain proteins.

Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins. 2017. H. Yu, M.G.W. Siewny, D.T. Edwards, A.W. Sanders and T.T. Perkins. Science. March 3. Vol. 355, Issue 6328, pp. 945-950, DOI: 10.1126/science.aah7124

Pulling apart protein unfolding
Elucidating the details of how complex proteins fold is a longstanding challenge. Key insights into the unfolding pathways of diverse proteins have come from single-molecule force spectroscopy (SMFS) experiments in which proteins are literally pulled apart. Yu et al. developed a SMFS technique that could unfold individual bacteriorhodopsin molecules in a native lipid bilayer with 1-µs temporal resolution (see the Perspective by Müller and Gaub). The technique delivered a 100-fold improvement over earlier studies of bacteriorhodopsin and revealed many intermediates not seen before. The authors also observed unfolding and refolding transitions between intermediate states.

Excellent post, DLH. Thank you. Truth Will Set You Free
Even before this revelation it was for the atheistic Darwinists like defending the notion that a fully automated factory with robotic equipment being directed by digitally stored information somehow came about mindlessly and accidentally. It is obvious they have lost all objectivity and the real basis for their position is that it is what they desperately want to be true -- and nothing more. harry
UB: Try this link. Again, Comment #189, especially the middle to end part, re the "Blob." PaV
PAV, your link appears to be broken. Upright BiPed
PaV, I share much of your sentiment. A little reflection by the honest seeker of even average intelligence is sufficient for them to come to understand the reality of design in biology and the complete failure of the materialistic narrative. It isn't even a close call. The continued insistence by so many in clinging desperately to the materialist narrative is certainly not based on the evidence . . . or even on rational thought. Such individuals will rarely, if ever, be willing to take a hard look in the mirror and examine their preconceptions and presumptions and biases. Absent a personal crisis of some kind that forces deep reflection and introspection, most will continue merrily along their way, oblivious to the absurdity and incoherence of their position. I guess some of the reasons I stay engaged (though my level of engagement greatly ebbs and flows, depending on life's other obligations) are the following: 1. This is an incredibly interesting topic, both scientifically and philosophically: Where did we come from? Why are we here? Is it all just an accident, or is there any reason to think there is a plan or purpose behind our existence? 2. The engineering behind biological systems is extremely fascinating and instructive. Just keeping up on the bench part of the science in its own right is worth a fair amount of attention. Even if everyone in the world were to someday accept the reality of design in biology to the point that there were no more debate, delving into the details of these designed systems would still keep me very interested. 3. By discussing and debating I stay sharp and hone my own understanding and arguments. 4. There are many, many people (including young people) who are where I was many years ago -- wondering what this debate is all about, whether this intelligent design thing is meaningful, what the Darwinian mechanism can really do, whether the materialist creation narrative has any legs? Such individuals should of course do their own research and there is plenty of material out there. But it is also helpful to hear from someone who has been through the process and the analysis; someone who has seen most of the latest evolutionary claims and arguments, not just what was written in some books years ago. I hope that in some small way for some small handful of individuals my participation in the debate can help fill that role. ----- Anyway, I certainly understand where you are coming from and agree that debating with committed materialists is often less than productive. I have definitely enjoyed your thoughts and interactions over the years and hope you'll continue to weigh in as your time permits! Eric Anderson
So the more we learn, the more we realize that it isn't just the sequence of amino acids that results in a particular fold and three-dimensional shape. There have been hints of this for a long time, but it is high time we stop describing the process as though it were a chemical necessity. Yet another important step in the process that is moderated, controlled, prepared. The idea that things just happen by dint of chemistry in biology is such nonsense. Eric Anderson
There are very few OPs that I post here anymore simply because over the years the evidence science has unearthed has completely demolished the Darwinian narrative. This 17 step (how many more steps will they find in the future?) process of protein folding is just one more example of "hidden" complexity. The overall level of complexity of cellular function is now so high that one can no longer be intellectually honest and still adhere to Darwinian mumbo-jumbo. Only "bias"--materialistic, atheistic bias--can account for this adherence. In the case of "Christian" Darwinists, it is a case of: "I spent my whole life studying this, and this is the only way I can make money" sort of 'bias.' Years ago, I argued with Darwinists and tried to understand their arguments, and I awaited someone---anyone--to make a sensible case for Darwinism. It never happened. They never got close. Meanwhile, I awaited scientific discovery. I said to myself (and posted it) that sequencing data would prove pivotal in the debate, one way or the other. It is now so overwhelmingly obvious that Darwinism is almost completely wrong (it MAY be right at the 'edges'), I really have very little interest in debating it any more. It's the same, unpersuasive arguments, over and over, again. In a hundred years, after so much more will have been discovered--all of which will discredit their theory, the Darwinists will still use the same arguments. (see Comment #189 here) PaV
An interesting program on Nova. The Origami phenomenon highlighted in this program is narrated for the most part by very intelligent designers with PhDs. I wonder how many of them are aware of the parallels and similarities Origami has with protein folding? http://www.pbs.org/wgbh/nova/physics/origami-revolution.html ayearningforpublius
Did he say "the system"? Is that teleological language? See also Levinthal's paradox es58
DLH, Excellent paper reference! Thanks! We ain't seen nothin' yet. The best is still to come. :) The first time I heard about protein folding, I was having lunch with a biology researcher who was actually working on this. At one point in the middle of his fascinating description of that fantastic process, he suddenly stopped and asked me if I didn't like the food, adding that I could request a different dish. He had noticed that I had stopped eating. I told him that while listening to his detailed description of the protein folding I simply had completely forgotten about the food. He laughed. Needless to say that I have not recovered from that amazement yet. Perhaps it's gotten even worse lately. :) Dionisio

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