4 ms·

What's the chance of hitting all 4 of them though? This is a good step in verification but you are awfully too quick to reject their claim.

folli 7y ago
Read the paper, they actually only match 2 inserts, the other two inserts are modified by the authors in such a way that they are made to match (Table 1). Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are. Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for its mutation rate (especially in these two proteins gp120 and gag, as they are under pressure to mutate in order to evade the immunesystem). So in such a large library of protein sequences one is bound to find a match of a short 6 letter (amino acid) sequence. That's why E values exist to make a statement about the statistical significance.
- folli 7y ago
  For posteriority, here's the link to the Blast results for the second insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV3014 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV...
  - im3w1l 7y ago
    Hello posteriority here! I wanted to reference these comments in a discussion but the links expired :/
- Palptine 7y ago
  Large HIV database inflating matches is indeed a big concern. But dismissing one miss matches sounds arbitrary: these segments were not arbitrarily selected, but real insertions on tops of sars.
  - folli 7y ago
    Again, take any random six letter amino acid sequence and chances are high that it matches to some HIV protein. I just did the experiment with my first name that is coincidentally 6 letters long, and lo and behold: a match to HIV env protein! Has my first name now been designed by a bioweapons facility?
    - AnimalMuppet 7y ago
      > Has my first name now been designed by a bioweapons facility? No, of course not. Your parents were designed by a bioweapons facility, so that they would choose that name. ;-)
      - folli 7y ago
        You revealed my secret

folli 7y ago

Read the paper, they actually only match 2 inserts, the other two inserts are modified by the authors in such a way that they are made to match (Table 1). Both inserts 1 and 2 also match to Streptococcus phage, but a bacteriophage would of course not be such a bold claim as HIV matches are. Also, be aware that because of the scientific interest in HIV, there are hundreds of HIV strains sequenced, a virus known for its mutation rate (especially in these two proteins gp120 and gag, as they are under pressure to mutate in order to evade the immunesystem). So in such a large library of protein sequences one is bound to find a match of a short 6 letter (amino acid) sequence. That's why E values exist to make a statement about the statistical significance.

folli 7y ago
For posteriority, here's the link to the Blast results for the second insert: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV3014 https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=39ACRKV...
- im3w1l 7y ago
  Hello posteriority here! I wanted to reference these comments in a discussion but the links expired :/
Palptine 7y ago
Large HIV database inflating matches is indeed a big concern. But dismissing one miss matches sounds arbitrary: these segments were not arbitrarily selected, but real insertions on tops of sars.
- folli 7y ago
  Again, take any random six letter amino acid sequence and chances are high that it matches to some HIV protein. I just did the experiment with my first name that is coincidentally 6 letters long, and lo and behold: a match to HIV env protein! Has my first name now been designed by a bioweapons facility?
  - AnimalMuppet 7y ago
    > Has my first name now been designed by a bioweapons facility? No, of course not. Your parents were designed by a bioweapons facility, so that they would choose that name. ;-)
    - folli 7y ago
      You revealed my secret