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AGelbert

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Virologists Doth Protest Too Much
« Reply #180 on: May 07, 2020, 02:24:01 pm »
TWiEVO 55: Coronavirus evolution from soup to nuts
2,257 views•May 6, 2020


Vincent Racaniello
51.1K subscribers

👨‍🔬 Nels and 👨‍🔬 Vincent continue their discussion of SARS-CoV-2 evolution, with a report that the coronavirus proofreading enzyme stimulates RNA recombination, and debunking the conclusion that a change in the 🔬 viral spike glycoprotein is associated with increased human to human transmission.
Category Science & Technology

Agelbert COMMENT: It is interesting that the S protein that codes for the spike protein (change in one amino acid) that enables the SARS-CoV-2 coronavirus to dock with and block the ACE2 receptor on human cells is produced near the 3' end. This would make sense if that mutation came about accidently on purpose in a virology lab somewhere. Redesigning a virus in a lab is easier near the 3 prime end of the RNA genome strand. Think about that. Considering all the tinkering with viruses in labs constantly going on here and there, why isn't the possibility that this mutation was a lab tinkering mistake, NOT a random point mutation, taken seriously by virologists in such a big hurry to claim it was a completely random example of viral mutation?  Vincent himself makes it crystal clear that this particular coronavirus has an EXTREMELY LOW mutation rate. Think about that.

It is the virologists in labs that, to use the phrase favored by Nels, are TURNING UP THE VIRAL MUTATION VOLUME FROM TEN TO ELEVEN. That is NOT "natural selection", Vincent. That is NOT "random evolution" in any way, shape or form. There is a LOT OF SCIENTIFIC EVIDENCE for THAT, even though Vincent rushes to claim there is "no scientific evidence" for that, pointing to  coronavirus viral genome studies as "scientific proof" that "it's all natural, not from some lab". Nels and Vincent are ones that descend into the "it's the religion of lack of science" tropes that are operating on faith, not science.

Agelbert COMMENT: Viral mutation is always confused by virologists as an example of evolution. It is not. It is an example of ADAPTATION. Adaptation does not produce a new species. Therefore, no evolution is going on.  Viral diversity is the result of adaptation, NOT "evolution". For over 30 years I have observed the word "adaptation" scrubbed from the scientific literature and replaced, erroneously, with the word "evolution". Viral mutations ARE NOT an example of natural selection, unless they result in the selecting out of existence of a dysfunctional virus. Natural selection is exclusively a subtractive process. Entropy is the constant, unavoidable rule in this universe, not the Darwinian happy talk about increased complexity though "beneficial" mutations brought about by natural selection. Viruses adapt, but they do not evolve. No Virus ever becomes a prokaryote through adaptive mutations. Anyone claiming otherwise is pushing empty, unscientific speculation. Viruses do not "evolve", they DEVOLVE, period.

Agelbert COMMENT: Vincent, the rather intractable problem that you do not wish to address is the issue of probabilty and statistics based on irrefutable factorial math in a random universe. You cannot get around that factorial math with your theory of how random protein synthesis produced, not simply the rather complex amino acids (all left handed, by the way, which adds a gigantic amount of time needed for the random production of 21 of them, all coming into existence at the same time, and all persisting abundantly and in sufficiently stable forms, rain or shine, millenia after millenia, until the first virus is formed as a functioning unit), but the three dimensional folding that defines their function, from primary all the way to quaternary folding. You've had lots of fun denaturing proteins in those virology labs, but how effective have you been at building one from scratch (i.e. elements)?   

You don't say a thing about the incredibly complex protein folding specificity in the first 9 lectures of virology, even though it's obvious from your excellent three dimensional presentations of viral proteins (and phospholipids and sugars and so on) that improper folding can interfere with function to the point of dysfunction. Yes, I know they bend and twist to hairpin this and invade that. They are enzymes. Enzymes do that to enable biochemical reactions without themselves being changed. I get that. I know you do, of course, but that isn't the point.

The point is that there is nothing wishy washy about how all this happens, especially when the overlall function of a virus is viewed as a unit. For the evolution of loose proteins, sugars and phospholipids to become a virus, you can't just have future capsid proteins floating around capturing a stray amino acid here and there, randomly becoming a viroid (you need a LOT of identical amino acid sequence viroids to evolve into existence within a very brief amount of hours or the factorial math kicks in again because there weren't enough fragments or some of the fragments degraded and no capsid could self assemble - I.e. back to evolutionary square one),  and then randomly "deciding" (as you correctly say, "WHY does not apply to evolution") that bouncing against a rock or a bunch of photons is a great way to replicate.

What I am taking way too long to say is that the occurrence of those events needed to form a unit called a virus are statistically impossible in one single generation in your RNA world full of viroid fragments (never mind how all those left handed amino acids got there to put them together). There is no "random step by step" argument here that works. You are a scientist. Don't tell me that in the pre-life world, temperature, pressure, pH and so on where "friendly" to the laboratory level stability required to randomly build the first virus. That world was extremely environmentally violent  Ask any geologist if you think that primordial soup was chemically stable in any way, shape or form. It was not. That said,  the pre-life planet earth environment is not the main issue here. The main issue here is protein synthesis.

You defend your evolution of viruses hypothesis pointing to the self assembling structural proteins from the icosahedral virus capsid. As I mentioned in a previous post, and you are well aware of, viral capsid proteins, even in a T1 arrangement, are specifically folded a primary, secondary, tertiary and, depending on the virus, quaternary way. You don't talk about how incredibly complex the process of folding those proteins is. Your RNA world hypothesis does not explain that in any way. Some cell machinery has to do that folding.

At present, none of that folding happens randomly. Yet, you assume that the first virus ball capsid that sparked life on earth came into existence randomly. And that's just the capsid, the simplest part of a virus! I find it breathtaking that you, an eminent scientist, can believe, through Darwinian faith, that we have enough time in a 14 billion year universe to go from your rather conveniently complex "RNA  world" to the prokaryotes, never mind those pesky, and extremely complex, eukaryotes that somehow came later on. Spare me the billions of years argument. Factorial math makes a joke out of it, even for the T1 icosahedral capsid, never mind the RNA strand code for replication inside it.

I know, you think I'm some kind of pathetic fundy that "doesn't undertand science". Listen Prof, back in 1986 when I was majoring in biology late in life, I told my Profs that the assumption that we have "junk" DNA was baloney. They were not impresed. Well, though I have no credentials, it turns out that a made a good guess, eh? Yeah, I know, it doesn't count because it was not science based (I didn't prove it with a study). To me, it was simply logical that the part of the cell where the business of jealously guarded reproduction with all sorts of policing going on to keep the species from deviating from the template is place is no place for "junk". My theory, then which was another good guess, is tht "junk" DNA had genes in it that could be activated by environmental pressures. But, enough of that.

As to who actually did create all this life, including the obligate parasites called viruses, that is an issue for faith, not scientific inquiry. Although I do believe God exists and created the three dimensional unverse, this is not about God; this is about your refusal to do the factorial math which is sine qua non for your viral proteins to evolve to do what they specifically do.

If you want to be an atheist, go for it, but don't pretend randomly formed proteins became a virus until you can prove that in a lab by throwing all the elements required for said proteins, lipids and sugars together and coming up with FIRST, simple proteins, lipids and sugars, and THEN folding the proteins correctly all the way to their quaternary structure, and FINALLY getting them to self assemble and function as a unit in a virus.

Yes, capsids "self assemble" AFTER some ribosome and a chaperonin built them and folded them. There is, as you know, NOTHING random about how ribosomes or chaperonins function.

You have not convinced me that viruses, never mind the viroids in your "RNA world" hypothesis, existed before prokaryotes. However, I enjoy your lectures and plan to wath them all. You are an excellent teacher. I have several videos of yours to watch, since I'm only at number 10, but I'm an old man with lots of time. 😊

If you have the time please watch this video from an expert in protein synthesis.

👨‍🔬 James Tour: The Origin of Life Has Not Been Explained



« Last Edit: May 07, 2020, 03:38:11 pm by AGelbert »
Rob not the poor, because he is poor: neither oppress the afflicted in the gate:
For the Lord will plead their cause, and spoil the soul of those that spoiled them. Pr. 22:22-23

 

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