4 ms·

the claim is that there is no natural process that will result in the double argenine sequence. Adenine or adenosine can spontaneously [naturally] convert to a

by rolph 5y ago

the claim is that there is no natural process that will result in the double argenine sequence. Adenine or adenosine can spontaneously [naturally] convert to a guanidine, or cytosine. in addition recombination of two different RNA strands often occurs with RNA virus this is often evidenced by doubling of codons, often due to a "sticky end" break in the RNA strand. thus something like AGGCGG may naturally and spontaneously transvert to CGGCGG thanks for your interest gus have a look here re: sticky ends https://en.wikipedia.org/wiki/Sticky_and_blunt_ends#Overhangs_and_sticky_ends https://en.wikipedia.org/wiki/Sticky_and_blunt_ends#Overhang... sticky ends are most common with DNA however this is also an occurence with RNA complexed to double strand in physiological conditions. [ADNDM] it may be confusing to examine without this little bit; DNA is constructed of base pairs A-T and G-C and is double stranded as a central tendency RNA is composed of a sequence of A, U [uracil], G, and C but is often interpreted as a DNA sequence that would generate the RNA, espescially when speaking of [or working with] mRNA. RNA is not obligated to double strandedness however will form double strand complexes as part of its funtionality.

gus_massa 5y ago
Is there a famous case about duplication of a codon in an insertion? Looking at the paper that is linked in the article, the double codon is in Figure 1B. I really don't understand why that is a good alignment, the rest of the sequence looks very different. Is that usual or I'm missing something important? [I have an specialization in Chemistry during Secondary School, so I can distinguish polar and not polar and weird amino acids just looking at the formulas, but I never remember the names and I don't know by heat weird reactions.]
- rolph 5y ago
  important information: the genetic code is redundant, there are more than one codons corresponding to an amino acid. keep in mind a codon is three "letters" https://en.wikipedia.org/wiki/File:GeneticCode21-version-2.svg https://en.wikipedia.org/wiki/File:GeneticCode21-version-2.s... [start at centre find first letter move to ring 2 find second move to ring 3 find third, find amino acid coded] notice that there is more than one codon corresponding to most amino acids, and some codons are control words. also you needto look at 2 things, regarding Fig1b there is comparison between two different coronavirus CoV-ZXC21 [upper sequence] vs. the 2019-nCoV [lowersequence] the regions are different 651-661 in the first case, and the region 676-690 in the second case[2019CoV] these are different coronavirus so this is expected however they both correspond to a domain of the Spike protien [S] what is being demonstrated is that there is a region in the 2019-CoV spike protien that is "novel" ; 2019-CoV predecessors dont have this sequence. this sequence is a cleavage recognition site. this in basic terms "arms" the coronavirus to fuse with a cell when cloven at the sequence by "furin" this means the 2019-CoV is more likely to initiate fusion functions inside of a host rather than elsewhere, thus more viral copies would be capable of actually causing infection before being disrupted by the surroundings. the basis of many gain of function research gone wrong concerns is the presence of this cleavage recognition sequence. The Double codon insertion is being used to bolster the idea that this is engineered, the major fault in the premise is that there is no natural way for such insertion to occur. look at TABLE1 below Fig1 and you will see that other coronavirus as well as conspecific virus have such a cleavage site thus a natural origin for the sequence is not impossible. i have mentioned recombination, and transversion as completely plausible natural phenomenon that have been recognized for some time, thus the statement that there is no natural way for this [insertion] to occur is fallacious.
  - gus_massa 5y ago
    Can I ask for a favor? Can you look at this old withdraw preprint of 2020? https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.... (HN discussion https://news.ycombinator.com/item?id=22204866 https://news.ycombinator.com/item?id=22204866 ) Rebuttal?: https://theprepared.com/blog/no-the-2019-ncov-genome-doesnt-actually-seem-engineered-from-hiv/ https://theprepared.com/blog/no-the-2019-ncov-genome-doesnt-... (Tiny HN discussion https://news.ycombinator.com/item?id=22211992 https://news.ycombinator.com/item?id=22211992 ) My question is about Figure 2, where they show the insertions of Covid-19 compare with other variants. Why do they have more coincidences than in the figure 1 of the OP? I don't think that the old article is correct. I'm just curios because I see the tables in the old preprint and the sequences look similar, but in the new paper they don't look similar at all.
    - rolph 5y ago
      the old [withdrawn] paper apparantly was withdrawn, due to manipulation of data. there is the issue of sequence similarity, not only to some domains of an HIV protien, but also similarity to a number of other entities. it was this paper that drove the misinfo regarding 2019-CoV being chimeric with HIV [UNTRUE] one must take convergent selection into account. this means many unrelated organisms evolve the same solution to a problem because it is the only solution to the problem that doesnt produce disadvantage. i took a look at Steven Quays back story , and it is not to his credit regarding any declaration about the origin of 2019-CoV. his research consists of a bayesian analysis of sequence data, no wet work is produced. the paper in question here: https://zenodo.org/record/4642956 https://zenodo.org/record/4642956 is not published in an accredited journal, despite modifications. this smells like duck seems to walk like a duck, i have yet to recieve any corresponence so i dont know if it sounds like a duck, but im hunching it would. there is more to this, but i think the direction this is going should be implict by now.
- rolph 5y ago
  [reply] also, duplication of a codon is usually associated with some sort of damage to the molecule, is implicated in the genetic basis of numerous cancer outcomes, and is usually accompanied by a 16 base pair insertion in the case of DNA, as an artefact of the repair. the CoV has a different enzyme that does similar repair task in addition to reading out the code thus incurring small span insertions, that are later proof read to clean up alignment mismatches. there are cases such as influenza, corresponding to a single point insertion, rather than codon duplication that correspond to a jump in lethality such as the Heamagglutinin of influenza virus, leading to the 1918 Flu gaining lethality after pandemic distribution in a "second wave" this insertion point is a cleavage site for the protien.
spadez 5y ago
>the claim is that there is no natural process that will result in the double argenine sequence. I think the claim is that it is very unlikely to happen naturally, and the article makes it very clear. So I wonder why you assume that it claims "there is no natural process". And the final suggestion of the article appears NOT to be that lab leak is the final conclusion, but only that it should be the leading hypothesis among the existing ones, if one goes by science and science alone.
- rolph 5y ago
  i am not assuming, the claim is made very clearly multiple times through the article , and the WSJ article , has cherry picked the publication. there is no basis to the claim that 2 arginine codons adjacent to each other is a rare, engineered event, this [codon duplication]is a very common artefect of natural nucleotide repair mechanisms, also the article suffers from a deficiency of understanding, as the duplication of a lesion associated codon is also accompanied with a guide segment of nucleotide so the feature is more than just a duplicated codon. there is also the case of transversion and this has not been addressed, but could be illuminated with radio phosphorous labeling and restriction fragment analysis.
- gus_massa 5y ago
  > if one goes by science and science alone The press article is not very technical. The research paper is more interesting, but IIUC it is mostly about how this "furin cleavage" is very important and why it's important that is has two amino acids, but the discussion about the possible mutation to reach it is very shallow. I'd like to see an accurate model of all the known ways the virus can mutate, tweaked to model origin of the current known species of coronavirus, and then use the model to get an estimation of the origin that is impossible, and then "use science" to conclude that the handmade origin is likely.
  - rolph 5y ago
    if you look around at the back story for Steven Quay, and Richard Muller, it gets interesting. https://medium.com/beingwell/dr-steven-quay-to-brief-u-s-congress-on-origin-of-the-covid-19-pandemic-ccc857d951c4 https://medium.com/beingwell/dr-steven-quay-to-brief-u-s-con... "He is the author of a book on surviving the pandemic, “Stay Safe: A Physician’s Guide to Survive Coronavirus”. He has seen his fair share of controversy during the pandemic. His book, published in June of 2020 was removed from Kindle by Amazon, hours after its launch. His outspoken views on treatments for Covid-19 have often conflicted with the official narrative. For instance, in his book, he offers the following advice for dealing with Covid-19, and it's not difficult to see why the book was removed by Amazon. One 2-minute step you can take every time you come home to kill coronavirus before it enters your lungs A quick, free home test for COVID-19 that is as good as the FDA-approved nasal swab The one exercise you won’t learn in the gym that can save your life How NOT to die of COVID-19 (Make your lungs younger) What to do if you have early-stage COVID-19 so that you can stay out of the hospital The #1 most effective way to prevent the spread of coronavirus as we reopen society (Hint: it’s the one thing the CDC said was “NOT effective” when coronavirus hit the U.S.) Why a vaccine won’t be the solution, and what YOU can do to protect yourself, now and in the future What to eat and drink (and what to avoid), so you can prevent and beat this coronavirus The best supplements I have found from clinical trial research for immune health during this pandemic The coronavirus’ “Diabolic Trait” and how it helped the virus spread so fast An easy DIY step that takes your face mask from a viral barrier to a virus killer, giving you over 100-times the protection of an untreated mask The one blood test to ask for if you are hospitalized that can keep you off a ventilator Three steps to take to thrive during the next epidemic Learn about gain-of-function research and why we must ban it to prevent future pandemics"

by rolph 5y ago

gus_massa 5y ago

Is there a famous case about duplication of a codon in an insertion? Looking at the paper that is linked in the article, the double codon is in Figure 1B. I really don't understand why that is a good alignment, the rest of the sequence looks very different. Is that usual or I'm missing something important? [I have an specialization in Chemistry during Secondary School, so I can distinguish polar and not polar and weird amino acids just looking at the formulas, but I never remember the names and I don't know by heat weird reactions.]

rolph 5y ago
important information: the genetic code is redundant, there are more than one codons corresponding to an amino acid. keep in mind a codon is three "letters" https://en.wikipedia.org/wiki/File:GeneticCode21-version-2.svg https://en.wikipedia.org/wiki/File:GeneticCode21-version-2.s... [start at centre find first letter move to ring 2 find second move to ring 3 find third, find amino acid coded] notice that there is more than one codon corresponding to most amino acids, and some codons are control words. also you needto look at 2 things, regarding Fig1b there is comparison between two different coronavirus CoV-ZXC21 [upper sequence] vs. the 2019-nCoV [lowersequence] the regions are different 651-661 in the first case, and the region 676-690 in the second case[2019CoV] these are different coronavirus so this is expected however they both correspond to a domain of the Spike protien [S] what is being demonstrated is that there is a region in the 2019-CoV spike protien that is "novel" ; 2019-CoV predecessors dont have this sequence. this sequence is a cleavage recognition site. this in basic terms "arms" the coronavirus to fuse with a cell when cloven at the sequence by "furin" this means the 2019-CoV is more likely to initiate fusion functions inside of a host rather than elsewhere, thus more viral copies would be capable of actually causing infection before being disrupted by the surroundings. the basis of many gain of function research gone wrong concerns is the presence of this cleavage recognition sequence. The Double codon insertion is being used to bolster the idea that this is engineered, the major fault in the premise is that there is no natural way for such insertion to occur. look at TABLE1 below Fig1 and you will see that other coronavirus as well as conspecific virus have such a cleavage site thus a natural origin for the sequence is not impossible. i have mentioned recombination, and transversion as completely plausible natural phenomenon that have been recognized for some time, thus the statement that there is no natural way for this [insertion] to occur is fallacious.
- gus_massa 5y ago
  Can I ask for a favor? Can you look at this old withdraw preprint of 2020? https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.... (HN discussion https://news.ycombinator.com/item?id=22204866 https://news.ycombinator.com/item?id=22204866 ) Rebuttal?: https://theprepared.com/blog/no-the-2019-ncov-genome-doesnt-actually-seem-engineered-from-hiv/ https://theprepared.com/blog/no-the-2019-ncov-genome-doesnt-... (Tiny HN discussion https://news.ycombinator.com/item?id=22211992 https://news.ycombinator.com/item?id=22211992 ) My question is about Figure 2, where they show the insertions of Covid-19 compare with other variants. Why do they have more coincidences than in the figure 1 of the OP? I don't think that the old article is correct. I'm just curios because I see the tables in the old preprint and the sequences look similar, but in the new paper they don't look similar at all.
  - rolph 5y ago
    the old [withdrawn] paper apparantly was withdrawn, due to manipulation of data. there is the issue of sequence similarity, not only to some domains of an HIV protien, but also similarity to a number of other entities. it was this paper that drove the misinfo regarding 2019-CoV being chimeric with HIV [UNTRUE] one must take convergent selection into account. this means many unrelated organisms evolve the same solution to a problem because it is the only solution to the problem that doesnt produce disadvantage. i took a look at Steven Quays back story , and it is not to his credit regarding any declaration about the origin of 2019-CoV. his research consists of a bayesian analysis of sequence data, no wet work is produced. the paper in question here: https://zenodo.org/record/4642956 https://zenodo.org/record/4642956 is not published in an accredited journal, despite modifications. this smells like duck seems to walk like a duck, i have yet to recieve any corresponence so i dont know if it sounds like a duck, but im hunching it would. there is more to this, but i think the direction this is going should be implict by now.
rolph 5y ago
[reply] also, duplication of a codon is usually associated with some sort of damage to the molecule, is implicated in the genetic basis of numerous cancer outcomes, and is usually accompanied by a 16 base pair insertion in the case of DNA, as an artefact of the repair. the CoV has a different enzyme that does similar repair task in addition to reading out the code thus incurring small span insertions, that are later proof read to clean up alignment mismatches. there are cases such as influenza, corresponding to a single point insertion, rather than codon duplication that correspond to a jump in lethality such as the Heamagglutinin of influenza virus, leading to the 1918 Flu gaining lethality after pandemic distribution in a "second wave" this insertion point is a cleavage site for the protien.

spadez 5y ago

>the claim is that there is no natural process that will result in the double argenine sequence. I think the claim is that it is very unlikely to happen naturally, and the article makes it very clear. So I wonder why you assume that it claims "there is no natural process". And the final suggestion of the article appears NOT to be that lab leak is the final conclusion, but only that it should be the leading hypothesis among the existing ones, if one goes by science and science alone.

rolph 5y ago
i am not assuming, the claim is made very clearly multiple times through the article , and the WSJ article , has cherry picked the publication. there is no basis to the claim that 2 arginine codons adjacent to each other is a rare, engineered event, this [codon duplication]is a very common artefect of natural nucleotide repair mechanisms, also the article suffers from a deficiency of understanding, as the duplication of a lesion associated codon is also accompanied with a guide segment of nucleotide so the feature is more than just a duplicated codon. there is also the case of transversion and this has not been addressed, but could be illuminated with radio phosphorous labeling and restriction fragment analysis.
gus_massa 5y ago
> if one goes by science and science alone The press article is not very technical. The research paper is more interesting, but IIUC it is mostly about how this "furin cleavage" is very important and why it's important that is has two amino acids, but the discussion about the possible mutation to reach it is very shallow. I'd like to see an accurate model of all the known ways the virus can mutate, tweaked to model origin of the current known species of coronavirus, and then use the model to get an estimation of the origin that is impossible, and then "use science" to conclude that the handmade origin is likely.
- rolph 5y ago
  if you look around at the back story for Steven Quay, and Richard Muller, it gets interesting. https://medium.com/beingwell/dr-steven-quay-to-brief-u-s-congress-on-origin-of-the-covid-19-pandemic-ccc857d951c4 https://medium.com/beingwell/dr-steven-quay-to-brief-u-s-con... "He is the author of a book on surviving the pandemic, “Stay Safe: A Physician’s Guide to Survive Coronavirus”. He has seen his fair share of controversy during the pandemic. His book, published in June of 2020 was removed from Kindle by Amazon, hours after its launch. His outspoken views on treatments for Covid-19 have often conflicted with the official narrative. For instance, in his book, he offers the following advice for dealing with Covid-19, and it's not difficult to see why the book was removed by Amazon. One 2-minute step you can take every time you come home to kill coronavirus before it enters your lungs A quick, free home test for COVID-19 that is as good as the FDA-approved nasal swab The one exercise you won’t learn in the gym that can save your life How NOT to die of COVID-19 (Make your lungs younger) What to do if you have early-stage COVID-19 so that you can stay out of the hospital The #1 most effective way to prevent the spread of coronavirus as we reopen society (Hint: it’s the one thing the CDC said was “NOT effective” when coronavirus hit the U.S.) Why a vaccine won’t be the solution, and what YOU can do to protect yourself, now and in the future What to eat and drink (and what to avoid), so you can prevent and beat this coronavirus The best supplements I have found from clinical trial research for immune health during this pandemic The coronavirus’ “Diabolic Trait” and how it helped the virus spread so fast An easy DIY step that takes your face mask from a viral barrier to a virus killer, giving you over 100-times the protection of an untreated mask The one blood test to ask for if you are hospitalized that can keep you off a ventilator Three steps to take to thrive during the next epidemic Learn about gain-of-function research and why we must ban it to prevent future pandemics"