Recently I learned something about DNA that blew my mind, and in this thread, I'll attempt to blow your mind as well. Behold: Chargaff's 2nd Parity Rule for DNA N-Grams.
If you are into cryptography or reverse engineering, you should love this.
Thread:
T G T C A G T
A C A G T C A
(note how the other strand is upside down - this matters!)
This is called Chargaff's 1st parity rule.
https://t.co/jD4cMt0PJ0
This is called Chargaff's 2nd parity rule.
For N=2, this says that percentage of CC (%CC) and %GG are also equal, as are %AG and %CT (complemented AND reversed) etc.
More from Science
https://t.co/hXlo8qgkD0
Look like that they got a classical case of PCR Cross-Contamination.
They had 2 fabricated samples (SRX9714436 and SRX9714921) on the same PCR run. Alongside with Lung07. They did not perform metagenomic sequencing on the “feces” and they did not get
A positive oral or anal swab from anywhere in their sampling. Feces came from anus and if these were positive the anal swabs must also be positive. Clearly it got there after the NA have been extracted and were from the very low-level degraded RNA which were mutagenized from
The Taq. https://t.co/yKXCgiT29w to see SRX9714921 and SRX9714436.
Human+Mouse in the positive SRA, human in both of them. Seeing human+mouse in identical proportions across 3 different sequencers (PRJNA573298, A22, SEX9714436) are pretty straight indication that the originals
Were already contaminated with Human and mouse from the very beginning, and that this contamination is due to dishonesty in the sample handling process which prescribe a spiking of samples in ACE2-HEK293T/A549, VERO E6 and Human lung xenograft mouse.
The “lineages” they claimed to have found aren’t mutational lineages at all—all the mutations they see on these sequences were unique to that specific sequence, and are the result of RNA degradation and from the Taq polymerase errors accumulated from the nested PCR process
Look like that they got a classical case of PCR Cross-Contamination.
They had 2 fabricated samples (SRX9714436 and SRX9714921) on the same PCR run. Alongside with Lung07. They did not perform metagenomic sequencing on the “feces” and they did not get
A positive oral or anal swab from anywhere in their sampling. Feces came from anus and if these were positive the anal swabs must also be positive. Clearly it got there after the NA have been extracted and were from the very low-level degraded RNA which were mutagenized from
The Taq. https://t.co/yKXCgiT29w to see SRX9714921 and SRX9714436.
Human+Mouse in the positive SRA, human in both of them. Seeing human+mouse in identical proportions across 3 different sequencers (PRJNA573298, A22, SEX9714436) are pretty straight indication that the originals
Were already contaminated with Human and mouse from the very beginning, and that this contamination is due to dishonesty in the sample handling process which prescribe a spiking of samples in ACE2-HEK293T/A549, VERO E6 and Human lung xenograft mouse.
The “lineages” they claimed to have found aren’t mutational lineages at all—all the mutations they see on these sequences were unique to that specific sequence, and are the result of RNA degradation and from the Taq polymerase errors accumulated from the nested PCR process
#DDDD $LBPS $LOAC
A thread on the potential near term catalysts behind why I have increased my position in 4d Pharma @4dpharmaplc (LON: #DDDD):
1) NASDAQ listing. This is the most obvious.
The idea behind this is that the huge pool of capital and institutional interest in the NASDAQ will enable a higher per-share valuation for #DDDD than was achievable in the UK.
Comparators to @4dpharmaplc #DDDD (market capitalisation £150m) on the NASDAQ and their market capitalisation:
Seres Therapeutics: $2.33bn = £1.72bn (has had a successful phase 3 C. difficile trial); from my previous research (below) the chance of #DDDD achieving this at least once is at least
Kaleido Biosciences: $347m = £256m. 4 products under consideration, compared to #DDDD's potential 16. When you view @4dpharmaplc's 1000+ patents and AI-driven MicroRx platform (not to mention their end-to-end manufacturing capability), 4d's undervaluation is clear.
A thread on the potential near term catalysts behind why I have increased my position in 4d Pharma @4dpharmaplc (LON: #DDDD):
1) NASDAQ listing. This is the most obvious.
The idea behind this is that the huge pool of capital and institutional interest in the NASDAQ will enable a higher per-share valuation for #DDDD than was achievable in the UK.
Comparators to @4dpharmaplc #DDDD (market capitalisation £150m) on the NASDAQ and their market capitalisation:
Seres Therapeutics: $2.33bn = £1.72bn (has had a successful phase 3 C. difficile trial); from my previous research (below) the chance of #DDDD achieving this at least once is at least
While looking at speculative pharmaceutical stocks I am reminded of why I am averse to these risky picks.#DDDD was compelling enough, though, to break this rule. The 10+ treatments under trial, industry-leading IP portfolio, and comparable undervaluation are inescapable.
— Shrey Srivastava (@BlogShrey) December 16, 2020
Kaleido Biosciences: $347m = £256m. 4 products under consideration, compared to #DDDD's potential 16. When you view @4dpharmaplc's 1000+ patents and AI-driven MicroRx platform (not to mention their end-to-end manufacturing capability), 4d's undervaluation is clear.
The endangered whales must contend with up to 1,000 boats moving daily through an important feeding area in the eastern South Pacific, according to research published in the scientific journal Nature.@WeDontHaveTime
#ForNature @JohnKerry
#ForNature @JohnKerry
Blue whales threatened by ship collisions in busy Patagonia waters
— James Mitchell \u24cb\U0001f42c (@MesMitch) February 1, 2021
Endangered giants face potentially fatal encounters with the 1,000 daily fishing vessels moving through main feeding area off Chile, scientists warn\U0001f43b\u200d\u2744\ufe0f@WeDontHaveTime
#ForNature @JohnKerry
1/ Automobiles and Intake Fraction. Since cars are back in the news I thought I would retweet this model result I offered in early April 2020. I focused only on 1 micron particles & accounted for windows completely closed & cracked slightly open.
2/ Related air exchange rates were based on experimental results in literature for mid-sized sedans. Particle deposition to indoor surfaces were accounted for, as the surface to volume ratio in a 3 m3 cab is large. An important outcome was the intake fraction (IF)
3/ Here, IF is the number of particles (or virions in collective particles) inhaled by a receptor DIVIDED BY the number or particles (or virions in collective particles) emitted by an infector.
4/ Integrated over the two hour drive (in this example) the IF for all windows closed & a receptor at rest is 0.08 (8% of what comes out of the infectors respiratory system ends up in the respiratory system of the receptor). 8%! That is a very high intake factor.
5/ With additional ventilation from cracking a window open drops the IF to 0.012 (1.2%) still relatively high. Can get lower by opening more windows.
Simulation: Riding in car for 120 min w/ infected passenger who seems fine other than a cough every few mins. (1) a lot of SARS-CoV-2 virus (in fine aerosol particles) accumulation in car cabin w/ windows closed; (2) cracking window open slightly = dramatic reduction. #COVID19 pic.twitter.com/bCmrmnLUPG
— Dr. Richard Corsi (@CorsIAQ) April 4, 2020
2/ Related air exchange rates were based on experimental results in literature for mid-sized sedans. Particle deposition to indoor surfaces were accounted for, as the surface to volume ratio in a 3 m3 cab is large. An important outcome was the intake fraction (IF)
3/ Here, IF is the number of particles (or virions in collective particles) inhaled by a receptor DIVIDED BY the number or particles (or virions in collective particles) emitted by an infector.
4/ Integrated over the two hour drive (in this example) the IF for all windows closed & a receptor at rest is 0.08 (8% of what comes out of the infectors respiratory system ends up in the respiratory system of the receptor). 8%! That is a very high intake factor.
5/ With additional ventilation from cracking a window open drops the IF to 0.012 (1.2%) still relatively high. Can get lower by opening more windows.
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👨💻 Last resume I sent to a startup one year ago, sharing with you to get ideas:
- Forget what you don't have, make your strength bold
- Pick one work experience and explain what you did in detail w/ bullet points
- Write it towards the role you apply
- Give social proof
/thread
"But I got no work experience..."
Make a open source lib, make a small side project for yourself, do freelance work, ask friends to work with them, no friends? Find friends on Github, and Twitter.
Bonus points:
- Show you care about the company: I used the company's brand font and gradient for in the resume for my name and "Thank You" note.
- Don't list 15 things and libraries you worked with, pick the most related ones to the role you're applying.
-🙅♂️"copy cover letter"
"I got no firends, no work"
One practical way is to reach out to conferences and offer to make their website for free. But make sure to do it good. You'll get:
- a project for portfolio
- new friends
- work experience
- learnt new stuff
- new thing for Twitter bio
If you don't even have the skills yet, why not try your chance for @LambdaSchool? No? @freeCodeCamp. Still not? Pick something from here and learn https://t.co/7NPS1zbLTi
You'll feel very overwhelmed, no escape, just acknowledge it and keep pushing.
- Forget what you don't have, make your strength bold
- Pick one work experience and explain what you did in detail w/ bullet points
- Write it towards the role you apply
- Give social proof
/thread
"But I got no work experience..."
Make a open source lib, make a small side project for yourself, do freelance work, ask friends to work with them, no friends? Find friends on Github, and Twitter.
Bonus points:
- Show you care about the company: I used the company's brand font and gradient for in the resume for my name and "Thank You" note.
- Don't list 15 things and libraries you worked with, pick the most related ones to the role you're applying.
-🙅♂️"copy cover letter"
"I got no firends, no work"
One practical way is to reach out to conferences and offer to make their website for free. But make sure to do it good. You'll get:
- a project for portfolio
- new friends
- work experience
- learnt new stuff
- new thing for Twitter bio
If you don't even have the skills yet, why not try your chance for @LambdaSchool? No? @freeCodeCamp. Still not? Pick something from here and learn https://t.co/7NPS1zbLTi
You'll feel very overwhelmed, no escape, just acknowledge it and keep pushing.
1/ 👋 Excited to share what we’ve been building at https://t.co/GOQJ7LjQ2t + we are going to tweetstorm our progress every week!
Week 1 highlights: getting shortlisted for YC W2019🤞, acquiring a premium domain💰, meeting Substack's @hamishmckenzie and Stripe CEO @patrickc 🤩
2/ So what is Brew?
brew / bru : / to make (beer, coffee etc.) / verb: begin to develop 🌱
A place for you to enjoy premium content while supporting your favorite creators. Sort of like a ‘Consumer-facing Patreon’ cc @jackconte
(we’re still working on the pitch)
3/ So, why be so transparent? Two words: launch strategy.
jk 😅 a) I loooove doing something consistently for a long period of time b) limited downside and infinite upside (feedback, accountability, reach).
cc @altimor, @pmarca
4/ https://t.co/GOQJ7LjQ2t domain 🍻
It started with a cold email. Guess what? He was using BuyMeACoffee on his blog, and was excited to hear about what we're building next. Within 2w, we signed the deal at @Escrowcom's SF office. You’re a pleasure to work with @MichaelCyger!
5/ @ycombinator's invite for the in-person interview arrived that evening. Quite a day!
Thanks @patio11 for the thoughtful feedback on our YC application, and @gabhubert for your directions on positioning the product — set the tone for our pitch!
Week 1 highlights: getting shortlisted for YC W2019🤞, acquiring a premium domain💰, meeting Substack's @hamishmckenzie and Stripe CEO @patrickc 🤩
2/ So what is Brew?
brew / bru : / to make (beer, coffee etc.) / verb: begin to develop 🌱
A place for you to enjoy premium content while supporting your favorite creators. Sort of like a ‘Consumer-facing Patreon’ cc @jackconte
(we’re still working on the pitch)
3/ So, why be so transparent? Two words: launch strategy.
jk 😅 a) I loooove doing something consistently for a long period of time b) limited downside and infinite upside (feedback, accountability, reach).
cc @altimor, @pmarca
4/ https://t.co/GOQJ7LjQ2t domain 🍻
It started with a cold email. Guess what? He was using BuyMeACoffee on his blog, and was excited to hear about what we're building next. Within 2w, we signed the deal at @Escrowcom's SF office. You’re a pleasure to work with @MichaelCyger!
5/ @ycombinator's invite for the in-person interview arrived that evening. Quite a day!
Thanks @patio11 for the thoughtful feedback on our YC application, and @gabhubert for your directions on positioning the product — set the tone for our pitch!
