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Hard agree. And if this is useful, let me share something that often gets omitted (not by @kakape).
Variants always emerge, & are not good or bad, but expected. The challenge is figuring out which variants are bad, and that can't be done with sequence alone.
You can't just look at a sequence and say, "Aha! A mutation in spike. This must be more transmissible or can evade antibody neutralization." Sure, we can use computational models to try and predict the functional consequence of a given mutation, but models are often wrong.
The virus acquires mutations randomly every time it replicates. Many mutations don't change the virus at all. Others may change it in a way that have no consequences for human transmission or disease. But you can't tell just looking at sequence alone.
In order to determine the functional impact of a mutation, you need to actually do experiments. You can look at some effects in cell culture, but to address questions relating to transmission or disease, you have to use animal models.
The reason people were concerned initially about B.1.1.7 is because of epidemiological evidence showing that it rapidly became dominant in one area. More rapidly that could be explained unless it had some kind of advantage that allowed it to outcompete other circulating variants.
Variants always emerge, & are not good or bad, but expected. The challenge is figuring out which variants are bad, and that can't be done with sequence alone.
Feels like the next thing we're going to need is a ranking system for how concerning "variants of concern\u201d actually are.
— Kai Kupferschmidt (@kakape) January 15, 2021
A lot of constellations of mutations are concerning, but people are lumping together variants with vastly different levels of evidence that we need to worry.
You can't just look at a sequence and say, "Aha! A mutation in spike. This must be more transmissible or can evade antibody neutralization." Sure, we can use computational models to try and predict the functional consequence of a given mutation, but models are often wrong.
The virus acquires mutations randomly every time it replicates. Many mutations don't change the virus at all. Others may change it in a way that have no consequences for human transmission or disease. But you can't tell just looking at sequence alone.
In order to determine the functional impact of a mutation, you need to actually do experiments. You can look at some effects in cell culture, but to address questions relating to transmission or disease, you have to use animal models.
The reason people were concerned initially about B.1.1.7 is because of epidemiological evidence showing that it rapidly became dominant in one area. More rapidly that could be explained unless it had some kind of advantage that allowed it to outcompete other circulating variants.
It was great to talk about reproducible workflows for @riotscienceclub @riotscience_wlv. You can watch the recording below, but if you don't want to listen to me talk for 40 minutes, I thought I would summarise my talk in a thread:
My inspiration was making open science accessible. I wanted to outline the mistakes I've made along the way so people would feel empowered to give it a go. Increased accountability is seen as a barrier to adopting open science practices as an ECR
It also comes across as all or nothing. You are either fully open science or your research won't get anywhere. However, that can be quite intimidating, so I wanted to emphasise this incremental approach to adapting your workflow
There are two sides to why you should work towards reproducibility. The first is communal. It's going to help the field if you or someone else can reproduce your whole pipeline.
There is also the selfish element of it's just going to help you do your work. If you can't remember what your work means after a lunch break, you're not going to remember months or years down the line
Thank you again @JamesEBartlett for a fantastic talk (with a really nice personal touch) on reproducible workflows!
— RIOT Science Club Wolverhampton (@riotscience_wlv) February 16, 2021
Thanks especially for the co-leads @IMLahart for co-hosting and @DrManiBhogal for nabbing James!
Slides: https://t.co/CNqxzOhch1
Video: https://t.co/YjHEHuRJlz
My inspiration was making open science accessible. I wanted to outline the mistakes I've made along the way so people would feel empowered to give it a go. Increased accountability is seen as a barrier to adopting open science practices as an ECR
It also comes across as all or nothing. You are either fully open science or your research won't get anywhere. However, that can be quite intimidating, so I wanted to emphasise this incremental approach to adapting your workflow
There are two sides to why you should work towards reproducibility. The first is communal. It's going to help the field if you or someone else can reproduce your whole pipeline.
There is also the selfish element of it's just going to help you do your work. If you can't remember what your work means after a lunch break, you're not going to remember months or years down the line
Why are lunch breaks important for #code?
— Dr Rebecca Hirst (@HirstRj) February 11, 2021
If you can't remember what your variable names refer to after lunch, you sure as hell won't remember in 3 months.
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Joshua Hawley, Missouri's Junior Senator, is an autocrat in waiting.
His arrogance and ambition prohibit any allegiance to morality or character.
Thus far, his plan to seize the presidency has fallen into place.
An explanation in photographs.
🧵
Joshua grew up in the next town over from mine, in Lexington, Missouri. A a teenager he wrote a column for the local paper, where he perfected his political condescension.
2/
By the time he reached high-school, however, he attended an elite private high-school 60 miles away in Kansas City.
This is a piece of his history he works to erase as he builds up his counterfeit image as a rural farm boy from a small town who grew up farming.
3/
After graduating from Rockhurst High School, he attended Stanford University where he wrote for the Stanford Review--a libertarian publication founded by Peter Thiel..
4/
(Full Link: https://t.co/zixs1HazLk)
Hawley's writing during his early 20s reveals that he wished for the curriculum at Stanford and other "liberal institutions" to change and to incorporate more conservative moral values.
This led him to create the "Freedom Forum."
5/
His arrogance and ambition prohibit any allegiance to morality or character.
Thus far, his plan to seize the presidency has fallen into place.
An explanation in photographs.
🧵
Joshua grew up in the next town over from mine, in Lexington, Missouri. A a teenager he wrote a column for the local paper, where he perfected his political condescension.
2/
By the time he reached high-school, however, he attended an elite private high-school 60 miles away in Kansas City.
This is a piece of his history he works to erase as he builds up his counterfeit image as a rural farm boy from a small town who grew up farming.
3/
After graduating from Rockhurst High School, he attended Stanford University where he wrote for the Stanford Review--a libertarian publication founded by Peter Thiel..
4/
(Full Link: https://t.co/zixs1HazLk)
Hawley's writing during his early 20s reveals that he wished for the curriculum at Stanford and other "liberal institutions" to change and to incorporate more conservative moral values.
This led him to create the "Freedom Forum."
5/
1/ Here’s a list of conversational frameworks I’ve picked up that have been helpful.
Please add your own.
2/ The Magic Question: "What would need to be true for you
3/ On evaluating where someone’s head is at regarding a topic they are being wishy-washy about or delaying.
“Gun to the head—what would you decide now?”
“Fast forward 6 months after your sabbatical--how would you decide: what criteria is most important to you?”
4/ Other Q’s re: decisions:
“Putting aside a list of pros/cons, what’s the *one* reason you’re doing this?” “Why is that the most important reason?”
“What’s end-game here?”
“What does success look like in a world where you pick that path?”
5/ When listening, after empathizing, and wanting to help them make their own decisions without imposing your world view:
“What would the best version of yourself do”?
Please add your own.
2/ The Magic Question: "What would need to be true for you
1/\u201cWhat would need to be true for you to\u2026.X\u201d
— Erik Torenberg (@eriktorenberg) December 4, 2018
Why is this the most powerful question you can ask when attempting to reach an agreement with another human being or organization?
A thread, co-written by @deanmbrody: https://t.co/Yo6jHbSit9
3/ On evaluating where someone’s head is at regarding a topic they are being wishy-washy about or delaying.
“Gun to the head—what would you decide now?”
“Fast forward 6 months after your sabbatical--how would you decide: what criteria is most important to you?”
4/ Other Q’s re: decisions:
“Putting aside a list of pros/cons, what’s the *one* reason you’re doing this?” “Why is that the most important reason?”
“What’s end-game here?”
“What does success look like in a world where you pick that path?”
5/ When listening, after empathizing, and wanting to help them make their own decisions without imposing your world view:
“What would the best version of yourself do”?