10 ms·

This is a semi-interesting piece (because of how poorly written it is and how hilariously confident the writer is), but it is embarrassing that the person writi

by ausername42027 5y ago

This is a semi-interesting piece (because of how poorly written it is and how hilariously confident the writer is), but it is embarrassing that the person writing claims to have a PhD in at least something semi-related to molecular biology, yet is trying to convince people that we can use independent probability when dealing with protein amino acid sequences. Certain sequences are seen time and time again in nature, just like certain traits visible to the naked eye have evolved independently. More importantly, this author dismisses natural mixing of SARS and HIV1 as "ridiculous" and provides no other explanation. It is possible that SARS-CoV-2 was created in a lab, but it is also possible that HIV-1 and SARS-CoV-2 co-infected a host. Edit: to elaborate, certain amino acid sequences are seen again and again, and others are practically impossible to see in nature because amino-acids fold into 3D proteins...and each amino acid is like a Lego piece. There is a lot more detail needed to understand fully how tertiary and 4try protein structures form...but it is also possible to understand it decently well after an undergraduate degree in biology, chemistry, biochemistry, etc. A PhD in the field knows this inside and out. If I had to guess, the author of this post has a PhD in something like statistics or computer science, and thinks that they can apply high school level math to two fields (molecular biology and biochemistry) that they do not even have a high school level of understanding of. To make a very stretched analogy (I am a doctoral student in the life sciences and a hobby programmer), this blog post is like saying that some Java source code is stolen because four of the class names are the same between two projects, and then using the number of possible characters in the class names and the length of the name to run some statistics. The problem being that no one has class names like "AeNOQ92bA"...in fact the vast majority of 8 character sequences will never be class names. Just like the vast majority of amino acid sequences (likely) do not exist in nature. And then you dig deeper and find out the class name is something like "MainDashboardSupervisorTree" (I do not know Java so forgive me). Then you also find out that the author of both classes...is the same guy who moved companies and likes particular naming convection, but never meant to copy stuff word for word. Similar to how SARS-CoV-2 could have naturally incorporated HIV-1 RNA into its genome when co-infecting a host.

dnautics 5y ago
the HIV-1 protein sequence is the same but not the DNA sequence. The moderna DNA sequence is identical. The odds of HIV-1 mixing with bat coronavirus, and then somehow finding the moderna DNA sequence, while not astronomically low, are pretty low.
- nameless912 5y ago
  Well sure, but given that viruses mutate on the order of millions of times a day (since they replicate on the order of gazillions of times a day) it's not terribly unreasonable that this sequence could have developed by accident, even through the relatively winding path you described. Hell, the entire genetic code of every variant of COVID-19 exists somewhere in the digits of Pi, but that doesn't mean that mathematicians created COVID. This reeks of a slightly more advanced form of numerology to me.
  - dnautics 5y ago
    While viruses do mutate a lot, if the sequence were that labile, then you would expect there to be a lot of divergence around the furin cleavage site. We don't really see that, so the site is stable. So, is there something special about that DNA sequence (including the synonymous wobble pairs) that make this a random walk gradient descent minimum? Or is the mutation rate lower than you think.
    - nameless912 5y ago
      All I'm saying is when people say "this mutation is super rare therefore it MUST have been manmade!", I'm skeptical. Even the most stable DNA sequences have mutations occasionally, because mutations happen for a bunch of totally uncorrelated reasons. It could have been manmade, but it could have also been made by a stray cosmic ray. To say a particular sequence "proves" that the virus is manmade is...sketchy at best.
      - dnautics 5y ago
        Nobody is claiming proof. Don't move the goalposts.
timmytokyo 5y ago
The person who wrote the article is pseudonymous, so their credentials cannot be examined or questioned.
- Jimmc414 5y ago
  They are presenting verifiable evidence are they not? Why do their credentials matter outside of ad hominem attack?
  - Bud 5y ago
    The evidence, and more crucially, its meaning and significance are not "verifiable" by 99.999% of the population. That's why things like credentials, resumes, publication history, and peer review exist. That's why we care if someone has promulgated 50 hoaxes in the past, for instance. So yeah. Credentials do matter, and it matters that this person is not willing to say this out loud, in public, without using a pseudonym.
    - dnautics 5y ago
      Alright. I can verify the meaning and significance. I have a PhD in chemical biology, and have done (non-pathogenic) gain of function research. This is the sort of result that I would expect someone to have found if I were given the charge to insert a furin cleavage site into a virus. Proof: https://bmcbiochem.biomedcentral.com/articles/10.1186/1471-2091-15-10 https://bmcbiochem.biomedcentral.com/articles/10.1186/1471-2... ,in which I stack-overflow-copy-paste ideas for beneficial mutations from sequences in distant species.
    - WanderPanda 5y ago
      > So yeah. Credentials do matter, and it matters that this person is not willing to say this out loud, in public, without using a pseudonym. The problem is that we've come so far that him not saying this out loud is not necessarily hinting to him being a charlatan. Plausibly, the cost/benefit analysis by that individum might not make it worth speaking the truth given how heated up the matter is rn. If this sentiment propagates to other topics I fear that larger (and important) parts of the world might drift towards soviet era incompetence
dadboddilf2 5y ago
- vibrato2 5y ago
trembonator 5y ago
jesse_a_b 5y ago
An additionnal improbability is, from all the millions of patents, why one from MODERNA ?

dnautics 5y ago

the HIV-1 protein sequence is the same but not the DNA sequence. The moderna DNA sequence is identical. The odds of HIV-1 mixing with bat coronavirus, and then somehow finding the moderna DNA sequence, while not astronomically low, are pretty low.

nameless912 5y ago
Well sure, but given that viruses mutate on the order of millions of times a day (since they replicate on the order of gazillions of times a day) it's not terribly unreasonable that this sequence could have developed by accident, even through the relatively winding path you described. Hell, the entire genetic code of every variant of COVID-19 exists somewhere in the digits of Pi, but that doesn't mean that mathematicians created COVID. This reeks of a slightly more advanced form of numerology to me.
- dnautics 5y ago
  While viruses do mutate a lot, if the sequence were that labile, then you would expect there to be a lot of divergence around the furin cleavage site. We don't really see that, so the site is stable. So, is there something special about that DNA sequence (including the synonymous wobble pairs) that make this a random walk gradient descent minimum? Or is the mutation rate lower than you think.
  - nameless912 5y ago
    All I'm saying is when people say "this mutation is super rare therefore it MUST have been manmade!", I'm skeptical. Even the most stable DNA sequences have mutations occasionally, because mutations happen for a bunch of totally uncorrelated reasons. It could have been manmade, but it could have also been made by a stray cosmic ray. To say a particular sequence "proves" that the virus is manmade is...sketchy at best.
    - dnautics 5y ago
      Nobody is claiming proof. Don't move the goalposts.

timmytokyo 5y ago

The person who wrote the article is pseudonymous, so their credentials cannot be examined or questioned.

Jimmc414 5y ago
They are presenting verifiable evidence are they not? Why do their credentials matter outside of ad hominem attack?
- Bud 5y ago
  The evidence, and more crucially, its meaning and significance are not "verifiable" by 99.999% of the population. That's why things like credentials, resumes, publication history, and peer review exist. That's why we care if someone has promulgated 50 hoaxes in the past, for instance. So yeah. Credentials do matter, and it matters that this person is not willing to say this out loud, in public, without using a pseudonym.
  - dnautics 5y ago
    Alright. I can verify the meaning and significance. I have a PhD in chemical biology, and have done (non-pathogenic) gain of function research. This is the sort of result that I would expect someone to have found if I were given the charge to insert a furin cleavage site into a virus. Proof: https://bmcbiochem.biomedcentral.com/articles/10.1186/1471-2091-15-10 https://bmcbiochem.biomedcentral.com/articles/10.1186/1471-2... ,in which I stack-overflow-copy-paste ideas for beneficial mutations from sequences in distant species.
  - WanderPanda 5y ago
    > So yeah. Credentials do matter, and it matters that this person is not willing to say this out loud, in public, without using a pseudonym. The problem is that we've come so far that him not saying this out loud is not necessarily hinting to him being a charlatan. Plausibly, the cost/benefit analysis by that individum might not make it worth speaking the truth given how heated up the matter is rn. If this sentiment propagates to other topics I fear that larger (and important) parts of the world might drift towards soviet era incompetence

dadboddilf2 5y ago

vibrato2 5y ago

trembonator 5y ago

jesse_a_b 5y ago

An additionnal improbability is, from all the millions of patents, why one from MODERNA ?