Compared from person to person? I just want to make sure I understand.
I think I saw a graph explaining variants in a popular news article that said the ancestral strain is extinct. Is that correct?
I searched for a follow-up study as well and found nothing and maybe its because of these trends in Indiaâs Covid-19 situation:
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What Gil is doing is not surprising. It is the typical strategy of science deniers. Ignore the whole body of scientific evidence and cherry-pick studies that seem to support their claims.
This corroborates John Mercerâs claim that YEC hinders the practice of proper science. As long as the scientific claim is silent about or supportive of their beliefs, no qualms. Otherwise, its their interpretation of scripture or nothing else.
Yes, person to person. That is, if you sequence the virus from one person and sequence the virus from someone they transmitted it to, youâll find exactly the same dominant genome in both, roughly 60% of the time.
Did you check out the GISAID-Nextstrain link I supplied earlier? You can mouse over the entire phylogeny, including the ancestral strain at the root, and track the entire history with your very own eyes, including clad frequencies.
The âancestral strainâ is just the earliest sequence from a human patient. Undoubtedly, it descended from prior coronaviruses, and is related to SARS, MERS, and other zoonotic reservoirs.
If you want to unpack the genome, this NY Times article has the sequence and models for all the proteins in the COVID virus, along with functional descriptions.
Oh man, that rise in cases looks insane. Itâs MĂŒllerâs Rollercoaster!
Now compare and contrast what @Giltil said in this previous thread on Coronavirus in India and itâs putative relationship to Genetic Entropy:
âŠto what he has been arguing in this thread about MĂŒllerâs Ratchet as a vehicle causing Genetic Entropy of the Coronavirus.
How about when he created this thread?:
Dunno. Letâs take a look at Italy now:
@Giltil has more such similar threads making similarly ridiculous statements.
Now up above, Gilbert protests me characterizing Sanfordâs concept of GE as entailing the inevitable extinction of virtually all life on Earth by asserting (to my honest surprise) that Sanford is totally aware that his GE idea is dependent on factors such as population size, mutation rate, and so one. Yet Gilbert has wasted no time on this forum making statements such as the following many times before:
There are multiple others like it, but one should be enough. Of course, similar statements have been made by Paul Price and Valerie too. Nobody is under any illusions about what GE is supposedly about. Evolution is impossible because life should have gone extinct a long time ago, and is all currently headed for extinction (but Jesus will intervene before it happens).
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I donât know of any definitions of âstrainâ and âextinctâ that would make sense in the context that you are using them.
Valerie, are you aware that strains are about lineages, and that fixation of new variants in a strain doesnât make it a new strain?
Are you trying to rescue Sanfordâs GE, or might this be a product of not understanding the concept of nested hierarchy?
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I think sheâs trying to say that no current viruses have sequences identical to the originally sequences virus. Donât know if thatâs true, but thatâs what sheâs probably asking about.
Thanks for linking again. Very interesting.
Thanks! I feel like I would have guessed a much higher number. Obviously some selection at work.
I was looking at that last night. I had guessed a level of herd immunity was driving numbers down months ago, but would not have guessed tsunami waves. The U.S. I guess has had slow rolling waves. I wonder what makes the difference - more transmissible variants and higher population density and people not traveling very far? That curve is crazy, sad what it will translate to in terms of deaths.
No, thanks just used the wrong term.
No, I have already explained on the forum I think we wonât know anything for years about this virus and entropy. Sometimes a question is just a question.
You probably have a point here
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I want to know whether there are evidence that Mullerâs ratchet operates during some viral epidemics.
Well, as a proponent of the GE thesis, it is true that I am looking for supporting evidence and in the process, I am at risk to overlook contrary evidence. In this sense, I am grateful when experts like you take the time to consider my words and correct me when I am wrong. Now, it is not true that I only read the things that tell me what I want to believe. For example, regarding Mullerâs ratchet, bottlenecks and their effect on fitness, I intend to do some homework and read several interesting papers Iâve identified that not necessarily support my views.
You may be right here.
I disagree. Firstly, I think Sanfordâs paper on H1N1 provides supporting evidence to GE. Second and foremost, it is false to claims that GE is an unscientific hypothesis. GE may be false, but by all mean, it is a scientific hypothesis.
In Nigeria, we would say âmad oâ. Seriously though, thatâs one worrying steep rise in new cases. I donât like it, but it rubbishes Gilâs claim of Mullerâs ratchet extinguishing hCoV19 in India.
Its not surprising Rum. He is engaging in apologetics.
Say no more. It is finished (Iâm Jesusâs voice).
Exactly. You are rejecting the scientific method.
If you were following the scientific method, you would have looked for all the evidence before labeling yourself as a proponent of a particular conclusion. After advancing a hypothesis, you would actively look for contrary evidence INSTEAD OF looking for supporting evidence.
Firstly, Sanfordâs paper grossly misrepresents the evidence provided by others. It might be fruitful for you to go and look at the papers he cites instead of pretending that Sanford is the one providing evidence.
Secondly, H1N1 is a subtype, not a strain. It is not a lineage. Thatâs all one really needs to know to understand that Sanfordâs paper is ridiculous.
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This is interesting. Do you have some references for this result?
And you also wrote:
When I read more molnupiravir after seeing the headline, it seemed like the kind of antiviral that Sanford and Carter were advocating would be helpful especially in a pandemic. If it continues to do well in trials, that might be better evidence of GE than anything weâll see in the immediate future.
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Fair enough. However, note that I was presenting things as a hypothesis which I realized was foolhardy, which is why I felt the need to ask the readers of this blog what they thought about it.
Alright, I think thatâs a fair point.
The estimate assumes that the number of mutations in the secondary case is Poisson-distributed. For the mean number of mutations expected per transmission, I give the calculation and the sources of the data in the Methods section of this paper, under âAnalysis of Superspreading Eventsâ.
In the cluster of P.1 cases that turned up on Cape Cod in the last couple of weeks, 28 out of 45 cases in the cluster had identical genomes, i.e. were separated by zero mutations. It is quite possible that the substitution rate is lower for the more transmissible variants, since they may experience less severe transmission bottlenecks.
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Yes, to completely clarify, I meant that because we wonât know anything about the natural progression of GE in the immediate future (meaning, as I said, we wonât know anything about it for years), Sanford making a testable prediction that these kinds of drugs would be helpful in a pandemic, would help back his claim about genetic entropy. Let me explain why I think that:
From what Iâve read, it seems these drugs are controversial among scientists yet, or maybe a better way to say it, is that there has been skepticism that they are safe, but instead may be mutagenic, or even that theyâre just not effective. I donât understand enough how the drugs work to weigh in on that. But if they were deemed safe, and for instance, if you saw, with this drug, that the dominant genome was transferred less than 60% of the time, and that subsequent infections were less transmissible or mild, that should obviously give their proposal some credibility. Up to others I guess if they donât think that has anything to do with natural progression of the virus.
(Many run-on sentences there, sorry, just not feeling like editing.)
No, it is completely irrelevant to his claim. Itâs preposterous. If a virus requires its own replicase or polymerase or capping enzyme to replicate its genome, inhibiting those enzymes will inhibit viral replication. That is obvious and says nothing about evolution, Valerie.
Oh, and in science we test our hypotheses to try to falsify them. Your resort to rhetoric about backing claims is a tacit admission that this is pseudoscience.
Let me explain why you are grasping at straws:
Thatâs just an absurd concoction, because there are multiple antivirals that target viral RNA polymerases. One example is ribavirin.
Thatâs not a better way to say it. They may not be safe, they may be mutagenic, and they may be ineffective, but none of that has anything to do with Sanford or with GE. Those things are determined by data produced by the people who, unlike Sanford, actually do science.
If Sanford agrees with your wishful thinking, why isnât he doing experiments in cultured cells?
I can tell. But you are weighing in anyway.
No. It obviously says nothing about natural evolution or GE. Itâs obvious that inhibiting replication of the viral genome inhibits replication of the virus that needs it.
Again, to support Sanford, you are misrepresenting the very essence of science.
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