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AGelbert

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David Berlinski Atheism and its Scientific Pretensions
570,917 views•Sep 1, 2011


HooverInstitution
271K subscribers
Recorded on April 25, 2011,

To comment please go to
https://www.hoover.org/research/david-berlinski-atheism-and-its-scientific-pretensions

David Berlinski is the author of a number of books, including the recent volumes One, Two, Three:  Absolutely Elementary Mathematics and The Devil's Delusion:  Atheism and Its Scientific Pretensions.

Berlinski asserts that "a great many men and women have a dull, hurt, angry sense of being oppressed by the sciences. They are frustrated by endless scientific boasting.  They suspect that ... the scientific community holds them in contempt.  They are right to feel this way." With Darwin's theory of evolution as a point of departure, he takes scientists to task for their antireligious assumptions and explores the conflict between the scientific community and those with firmly held religious beliefs.

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Category News & Politics


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

AGelbert

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Virology Lectures 2020 #4: Structure of Viruses
50,910 views•Feb 4, 2020



👨‍🔬 Vincent Racaniello
50K subscribers

Virus particles are constructed in three ways: with helical, icosahedral, or complex symmetry. We discuss the principles of helical and icosahedral symmetry and how larger and larger viruses are assembled. Some particles are wrapped with a lipid envelope, derived from the host cell, which is embedded with viral glycoproteins.

Category Science & Technology


Agelbert COMMENT: There is a logical paradox involved in Vincent Racaniello's view that viruses, which are obligate parasites, as correctly defined by Vincent Racaniello, are "more ancient in the evolutionary ladder" than ribosome containing living cells. According to Modern Evolutionary Theory, which I am sure Vincent Racaniello does not question, prokaryotes were the only form of life on Earth for millions of years until more complicated eukaryotic cells came into being through the process of evolution.

Considering the prevailing view in the scientific community of the Darwinian evolutionary sequence stated above, viruses initially were parasitical exclusively of bacteria (i.e. prokaryotes). Vincent Racaniello's belief that viruses, always obligate parasites, "PRECEDED" bacteria, which have the complex machinery that the obligate parasite must access to reproduce, is a logical fallacy. It is putting the virus parasite "cart" before the bacterial host "horse". 

The more likely evolutionary scenario, one that most, if not all, virologists have unfortunately rejected, is that viruses devolved from prokaryotes that were subjected to several essentially simultaneous mutations that were both faulty and advantageous.

👉 The faulty mutation produced the obligate parasite, lacking the ribosome and other cell machinery that is sine qua non for perpetuation of the species through replication.

👉 The evolutionary advantage of the bacterial mutation to a virus (which had to have happened simultaneously with the loss of cell machinery for replication, or else there would be no viruses today), was an amazing toolbox of specific proteins beneficially mutated  to facilitate attacking and hijacking a bacterium in order to reproduce. There is no other logical way to view this. Any other way to view this is unscientific straw grasping.

Viruses are an example of Devolution, not Evolution. No OBLIGATE parasite, be it a virus or any example of the highly complex species of parasites from the subphylum Chelicerata, has ever existed PRIOR to the existence of the host that said parasite requires, do not pass go, do not avoid extinction, for the survival of that species. There is no random "evolutionary pressure" that can be pseudo-scientifically speculated about, even with lots of hand waving and charts, that would constitute "evidence" of the PRIOR existence of a parasite to some, not yet evolved, life form said parasite exists to target. No host, no host parasite that lives from targeting the host, PERIOD.

Furthermore, Vincent Racaniello's claim that viroids, that have a limited ability to self assemble, are the RNA spark that got the (added to his speculation that all those transposones in our genome are "evolutionary evidence" that we were "something else" before) evolution of life ball (i.e capsid ;D) rolling is more unscientific straw grasping.

WHY? While it is true that the T1 icosahedral capsid could certainly have come about randomly from this self assembling property of protein fragments, that does not even remotely begin to scientifically explain, steps by thousands of SIMULTANEOUSLY REQUIRED random steps (SEE: Factorial math mind boggling numbers), the amazingly specific viral machinery existing for the purpose of protecting some RNA (be it +RNA or whatever) inside that capsid and, within a limited amount of time from the moment the virus was formed and ejected into the intercellular environment, seeking to gain entry into a specifically targeted host through a specifically targeted receptor site, at which point even more specifc, finely tuned tools to hijack the host machinery are used for replication.

The point is that a capsid made of self assembling proteins is not the relevant evolutionary issue. The relevant evolutionary issue is that a virus, being an obligate parasite, that lacks even one of the tools I just listed above (in an overly simplistic fashion), goes extinct, period.

NOTE: I recognize that 👨‍🔬 Vincent Racaniello 👍 is, without a doubt, an expert in viruses, and explains their structure and function elegantly, clearly and beautifully. If he stayed away from the logically flawed speculation about the "evolutionary importance of viruses", he would be better off.

Finally, there is the issue of proper protein folding, an indispensable part of successful protein synthesis. Every one of the those self assembling T units Vincent Racaniello beautifully described, that make up the non-covalent icosahedral structure that forms a virus capsid, MUST be folded a very specific way. Even with exactly the same proportion of atoms from different elements, bonded in exactly the same way in these capsid assembly molecules, they will not function properly if they are not folded properly.

Viruses do not have Ribosomes and Chaperonins. They never did have Ribosomes and Chaperonins.

What that means to people who don't see a problem with the claim that the "self assembly" ability of capsid proteins in viruses is "proof" that viruses "started the evolution of life" is that without Ribosomes, which are key to the complex process of synthesizing proteins to be later folded by Chaperonins (Chaperonins are any of a family of large chaperone proteins that function chiefly to assist in the folding of newly synthesized proteins), NONE of those viral capsid forming T units will be folded properly.

That's right, they DO NOT "self fold" properly. That's right. They self assemble to form a capsid ONLY when their T units are PREVIOUSLY folded properly. That's right. Randomly, the exact same capsid protein molecules will have thousands, if not millions, of possible three dimensional arrangements, of which ONLY ONE ARRANGEMENT, specific to each and every member of any given family of T units, WILL WORK. Even the tiniest 60 facet capsid requires that all of its T units be folded in exactly the same way in order to self assemble.

Viruses are an example of Devolution, not Evolution.
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

AGelbert

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Unscientific Ivory Tower Arrogance
« Reply #182 on: May 07, 2020, 02:14:54 pm »

Study 4+ years for a degree.
Study 4+ more for a PhD or MD.
Join a lab and start working.
Spend years studying the problem.
Form hypothesis and gather evidence.
Test hypothesis and form conclusions.
Report findings and have it peer reviewed.
Publish the findings and have it reported in the press.

Guy on YouTube: "Bullshit."

I don't know what that was all about, and I don't know who the guy on YouTube was or what, specifically, he criticized. However, I see nothing humerous about the appeal to authority fallacious debating technique displayed above. It is a rather obvious attempt to classify anyone criticizing a scientist as someone who does not understand any science and operates on whim and ignorance. IOW, the above is a thoroughly UNSCIENTIFIC cheap shot that has a germ of truth in it, only if you apply it to propagandist emotional button pushers for profit (e.g. Alex Jones). To apply it accross the board to everyone out there is an example of ivory tower arrogance in the extreme, as well as being factually incorrect, it being that when one of their own steps outside the NOMENKLATURA required "peer reviewed" Dogma, they get locked out of the club. Nobel Prize Winner Biochemist Kary Mullis, who invented the PCR (Polymerase Chain Reaction to identify virus presence) technique, was ostracized for calling bullshit on some unscientific assumptions labelled as HIV "science". He was NOT allowed to publish papers afterwards, even though he was MORE QUALIFIED to write and publish scientific study papers than the peer reviewers locking him out. That is NOT an "isolated example". 

Calling bullshit on bad science is, according to the above cheap shot, unscientific and worthy of disdain IF YOU ARE NOT PART OF THE SCIENTIFIC NOMENKLATURA. Of course, who are we underedumacated lower life forms with zero peer reviewer credibility to question such loyal servants, the evolutionary apex of Homo sapiens, the pinnacle evolution, populating those hallowed halls of high wisdom and Darwinian certainty? After all, from Darwin until now, it is quite clear how highly evolved the scientists, that have brought about all that wonderful technology that killed more people in a century than any century in human history and trashed enough of the planet to trigger the Sixth Mass Extinction, are. 

« Last Edit: May 07, 2020, 05:12:29 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

AGelbert

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Virologists Doth Protest Too Much
« Reply #183 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

AGelbert

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👨‍🔬 James Tour: The Mystery of the Origin of Life
341,723 views•Mar 18, 2019


Discovery Science
63.7K subscribers

UPDATE: This lecture has obviously hit a nerve. For Prof. Tour's response to his critics, see http://www.jmtour.com/wp-content/uplo.... Tour in his response apologizes for using the word "lying" with regard to Jack Szostak, but he goes on to explain in detail why his substantive criticisms of Szostak's article were correct. To read the criticisms leveled at Tour, see https://stonesnbones.blogspot.com/201....

Dr. Tour is one of the world’s top synthetic organic chemists. He has authored 680 scientific publications and holds more than 120 patents (here is a partial list). In 2014, Thomson Reuters named him one of “The World’s Most Influential Scientific Minds,” and in 2018 Clarivate Analytics recognized him as one of the world’s most highly cited researchers. Tour is also fearless. He joined more than a thousand other scientists in signing the “Scientific Dissent from Darwinism.” More recently, he has become a thorn in the side of the origin of life research community, offering blunt assessments of the current state of origin of life research. Read more on this controversy here: https://evolutionnews.org/2019/05/pro...

Taped at the 2019 Dallas Science and Faith Conference at Park Cities Baptist Church in Dallas sponsored by Discovery Institute’s Center for Science and Culture.

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Category Science & Technology
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

AGelbert

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👨‍🔬 James Tour: The Mystery of the Origin of Life
341,723 views•Mar 18, 2019
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

AGelbert

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The wicked worketh a deceitful work: but to him that soweth righteousness shall be a sure reward. -- Proverbs 11:18
Virology Lectures 2020 #21: Evolution
9,960 views•Apr 18, 2020


Vincent Racaniello
51.5K subscribers

Viral evolution is the change of a viral population in the face of selection pressures . This process occurs faster than in other organisms because viruses produce so many progeny harboring many genome mutations. In this lecture we consider the four main drivers of viral evolution: large numbers of progeny, mutation, selection, and quasispecies effects, and discuss where viruses came from and where they are going.

Agelbert COMMENT: Wonderful. ::) Now people have Darwin Happy Talk Tatoos. What next, a statue to leave offerings to in Vincent's office? Nothing like "objective scientic inquiry", eh, Vincent? The above lecture is so full of evidence free conjecture that only a true believer in the Darwinian Religion would accept the assertions made by Vincent as "facts".

THIS is how complex a cell membrane IS:

WHY doesn't Vincent ever mention those pesky INTERACTOMES? Maybe it is because they don't fit in his "RNA world" pet theory.

THIS is the way Vincent operates:

THIS is what evolution theory true believers like Vincent want YOU to believe happened in prebiotic Earth:

THIS is what Vincent and his co-religionist true believers refuse to do, but MUST DO if they expect anyone with critical thinking skills to take their bold assertions seriously:

Viral mutation is ADAPTATION, not "evolution". Mr. Virologist Vincent cannot seem to tell the difference between those two processes, rather conveniently supporting his claims about "irrefutable evidence of rapid viral evolution". Vincent jumped right in there to assert that viruses "evolve faster than anything else out there, from bacteria to cows", RIGHT? Well, if that is true, how come you cannot show evidence of a virus becoming a bacterium? THAT would be EVOLUTION. But gee, these viruses that "Darwin would love because they evolve so fast", that have been around practically forever, even giving the dinosaurs herpes (that was a good one, Vincent),  just can't seem to "EVOLVE" into anything ELSE but a VIRUS!

Finally, please fact check Vincent's ASSUMPTIONS (START AT: 1:07:20 for several, one after another, evidence free leaps of protein synthesis logic, leaving out how those sugars needed for capsid glycoproteins were "randomly" synthesized) about the synthesis of the pre-virus molecules by viewing the video referenced in the graphics I just posted. Vincent provides NO explanation for the "evolution" of the first RNA Reverse Transcriptase molecule. Perhaps he rushed through that FUNDAMENTALLY IMPORTANT PROCESS (if that does not happen, nothing happens) because, understanding how factorial math IMPOSSIBLE it is for that to occur randomly, AND remain stable for a long enough time to proceed to the next step, he just does not want to talk about it.

Then he glosses over the "random" synthesis of other incredibly complex molecules, indispensable for the existence of a virus, (i.e. structural ENZYMES), as if they just popped randomly into the "RNA world" primordial soup. NO FACTS, just CONJECTURE dressed up as, 'WE THINK' "facts".

Notice the, "WE CAN SEE THE ACQUISITION OF CAPSID PROTEINS"  CONJECTURE. Hello, Vincent. WHY don't you spend some time explaining to your students that CAPSID PROTEINS, even in the T1 arrangement, all must be chiral IN THE SAME WAY and all must be folded, from the primary to quaternary structure, IDENTICALLY for them to self assemble into a capsid? YOU did not do that because you KNOW that only a Ribosome and a Chaperonin, neither of which existed in the prebiotic Earth, can DO THAT. Yes, friends, it cannot happen randomly because of the factorial math, something that Vincent avoids like the COVID--19 plague unless he wants to talk up viral mutation "evolutionary" diversity.

Listen closely to Vincent in the above happy talk, fact free pitch about the synthesis of the first virus as he says, in a KEY part of that process, "We don't know how that happened". No kidding, Vincent. You sure DON'T. Until you adequately explain, through Darwinian Theory RANDOM processes, HOW THAT HAPPPENED, you cannot assert, with any objective scientific credibility, that it happened "randomly". YET, we have to take your FAITH that SEVERAL sine qua non processes needed for viral particle evolution  "just happpened" as "FACT"?

YOU are the one that said "you do not care for beliefs, just facts". If it is good for goose, it is good for the scientist gander, Vincent. Below, please find,  some Darwinian Primordial Soup to add to your "evolution soup to nuts" theatrics. It's less embarrasingly ignorant than the "evolution" of Homo sapiens graphic timeline as "evidence" that viruses will "do better than humans". Yeah, right...
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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