[Thread] In-silico molecular overclocking of RaTG13.
TLDR: 191-nt RdRp segments of SARS-CoV-2, RaTG13 and Ra7896 show an unexpected molecular clock behavior. In-silico synonym mutations is one probable explanation.

Assuming SARS-CoV-2 is an ancestor of Ra7896 (used in RaTG13) does not fully explain it. Implied evolutionary rate would be in the order of 10^-2 substitutions/site/year in a well-conserved part of the genome, far from a normal ~10^-3 for a complete genome
https://t.co/5blQ4IxsxY
So, it is not only SARS-CoV-2 having its molecular clock frozen, but also RaTG13 molecular clock running more than expected.
@Nerdhaspower and @Quay_Dr have already noted strange patterns of synonym mutations along the genome of RaTG13
I always make this assumption: WIV ability of faking sequences is not unrestricted. They would never fake aa seqs, due to the protein folding problem. In a few months or years, they would be discovered
https://t.co/13athRfPIa
So, in silico, WIV would never make:
- non-synonymous mutations
- splicing within genes
But they could make:
- synonymous mutations
- swap genes or the complete genome from other real viruses
Why fabricating RaTG13?: To make it appear more distant than it really is. You probably never heard of that 98.65% identity between SARS-CoV-2 RdRp and Ra4991 RdRp. It was very dangerous!
https://t.co/WurzUVwW0W
But, if you want to make one virus appear more distant to another one without being noticed, you cannot just make orthogonal synonymous mutations, because you can get caught with the phylogenetic trees if you do not do it wisely
WIV forgot that they would eventually publish 7896 RdRp that could serve as a close outer group for SARS-CoV-2 and RaTG13.
Imagine Fig. 1 is real/base situation, A is fixed and you want B more distant.
Note: A is SARS-CoV-2, B is RaTG13 and O is the outer group (clade 7896)
If you just add orthogonal synonymous mutations to B, the clock is distorted (Fig 2, A & B not contemporaries). Correct way of faking would have been making a few backward synonymous mutations towards the outgroup (Fig 3), and then a few orthogonal synonym mutations (Fig 4)
It seems that WIV forgot the backward mutations!
I was thinking if it was better to keep this secret until WIV publish their next paper of the clade 7896 to let them commit the error again. But it clearly shows up in any tree. Their problem was not checking it this short segment

More from All

॥ॐ॥
अस्य श्री गायत्री ध्यान श्लोक:
(gAyatri dhyAna shlOka)
• This shloka to meditate personified form of वेदमाता गायत्री was given by Bhagwaan Brahma to Sage yAgnavalkya (याज्ञवल्क्य).

• 14th shloka of गायत्री कवचम् which is taken from वशिष्ठ संहिता, goes as follows..


• मुक्ता-विद्रुम-हेम-नील धवलच्छायैर्मुखस्त्रीक्षणै:।
muktA vidruma hEma nIla dhavalachhAyaiH mukhaistrlkShaNaiH.

• युक्तामिन्दुकला-निबद्धमुकुटां तत्वार्थवर्णात्मिकाम्॥
yuktAmindukalA nibaddha makutAm tatvArtha varNAtmikam.

• गायत्रीं वरदाभयाङ्कुश कशां शुभ्रं कपालं गदाम्।
gAyatrIm vardAbhayANkusha kashAm shubhram kapAlam gadAm.

• शंखं चक्रमथारविन्दयुगलं हस्तैर्वहन्ती भजै॥
shankham chakramathArvinda yugalam hastairvahantIm bhajE.

This shloka describes the form of वेदमाता गायत्री.

• It says, "She has five faces which shine with the colours of a Pearl 'मुक्ता', Coral 'विद्रुम', Gold 'हेम्', Sapphire 'नील्', & a Diamond 'धवलम्'.

• These five faces are symbolic of the five primordial elements called पञ्चमहाभूत:' which makes up the entire existence.

• These are the elements of SPACE, FIRE, WIND, EARTH & WATER.

• All these five faces shine with three eyes 'त्रिक्षणै:'.
1. Mini Thread on Conflicts of Interest involving the authors of the Nature Toilet Paper:
https://t.co/VUYbsKGncx
Kristian G. Andersen
Andrew Rambaut
Ian Lipkin
Edward C. Holmes
Robert F. Garry

2. Thanks to @newboxer007 for forwarding the link to the research by an Australian in Taiwan (not on

3. K.Andersen didn't mention "competing interests"
Only Garry listed Zalgen Labs, which we will look at later.
In acknowledgements, Michael Farzan, Wellcome Trust, NIH, ERC & ARC are mentioned.
Author affiliations listed as usual.
Note the 328 Citations!
https://t.co/nmOeohM89Q


4. Kristian Andersen (1)
Andersen worked with USAMRIID & Fort Detrick scientists on research, with Robert Garry, Jens Kuhn & Sina Bavari among


5. Kristian Andersen (2)
Works at Scripps Research Institute, which WAS in serious financial trouble, haemorrhaging 20 million $ a year.
But just when the first virus cases were emerging, they received great news.
They issued a press release dated November 27, 2019:

You May Also Like

Department List of UCAS-China PROFESSORs for ANSO, CSC and UCAS (fully or partial) Scholarship Acceptance
1) UCAS School of physical sciences Professor
https://t.co/9X8OheIvRw
2) UCAS School of mathematical sciences Professor

3) UCAS School of nuclear sciences and technology
https://t.co/nQH8JnewcJ
4) UCAS School of astronomy and space sciences
https://t.co/7Ikc6CuKHZ
5) UCAS School of engineering

6) Geotechnical Engineering Teaching and Research Office
https://t.co/jBCJW7UKlQ
7) Multi-scale Mechanics Teaching and Research Section
https://t.co/eqfQnX1LEQ
😎 Microgravity Science Teaching and Research

9) High temperature gas dynamics teaching and research section
https://t.co/tVIdKgTPl3
10) Department of Biomechanics and Medical Engineering
https://t.co/ubW4xhZY2R
11) Ocean Engineering Teaching and Research

12) Department of Dynamics and Advanced Manufacturing
https://t.co/42BKXEugGv
13) Refrigeration and Cryogenic Engineering Teaching and Research Office
https://t.co/pZdUXFTvw3
14) Power Machinery and Engineering Teaching and Research
“We don’t negotiate salaries” is a negotiation tactic.

Always. No, your company is not an exception.

A tactic I don’t appreciate at all because of how unfairly it penalizes low-leverage, junior employees, and those loyal enough not to question it, but that’s negotiation for you after all. Weaponized information asymmetry.

Listen to Aditya


And by the way, you should never be worried that an offer would be withdrawn if you politely negotiate.

I have seen this happen *extremely* rarely, mostly to women, and anyway is a giant red flag. It suggests you probably didn’t want to work there.

You wish there was no negotiating so it would all be more fair? I feel you, but it’s not happening.

Instead, negotiate hard, use your privilege, and then go and share numbers with your underrepresented and underpaid colleagues. […]