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
@mugecevik is an excellent scientist and a responsible professional. She likely read the paper more carefully than most. She grasped some of its strengths and weaknesses that are not apparent from a cursory glance. Below, I will mention a few points some may have missed.
1/
The paper does NOT evaluate the effect of school closures. Instead it conflates all ‘educational settings' into a single category, which includes universities.
2/
The paper primarily evaluates data from March and April 2020. The article is not particularly clear about this limitation, but the information can be found in the hefty supplementary material.
3/
The authors applied four different regression methods (some fancier than others) to the same data. The outcomes of the different regression models are correlated (enough to reach statistical significance), but they vary a lot. (heat map on the right below).
4/
The effect of individual interventions is extremely difficult to disentangle as the authors stress themselves. There is a very large number of interventions considered and the model was run on 49 countries and 26 US States (and not >200 countries).
5/
1/
I've recently come across a disinformation around evidence relating to school closures and community transmission that's been platformed prominently. This arises from flawed understanding of the data that underlies this evidence, and the methodologies used in these studies. pic.twitter.com/VM7cVKghgj
— Deepti Gurdasani (@dgurdasani1) February 1, 2021
The paper does NOT evaluate the effect of school closures. Instead it conflates all ‘educational settings' into a single category, which includes universities.
2/
The paper primarily evaluates data from March and April 2020. The article is not particularly clear about this limitation, but the information can be found in the hefty supplementary material.
3/
The authors applied four different regression methods (some fancier than others) to the same data. The outcomes of the different regression models are correlated (enough to reach statistical significance), but they vary a lot. (heat map on the right below).
4/
The effect of individual interventions is extremely difficult to disentangle as the authors stress themselves. There is a very large number of interventions considered and the model was run on 49 countries and 26 US States (and not >200 countries).
5/
Localized Surface Plasmon Resonance - an overview | ScienceDirect Topics
https://t.co/mzS7vVSREJ
https://t.co/353PdAX2fa
https://t.co/3yBImjOdd4
In some cases, almost 100% of the light energy can be converted to the second harmonic frequency. These cases typically involve intense pulsed laser beams passing through large crystals, and careful alignment to obtain phase matching.
https://t.co/mzS7vVSREJ
https://t.co/353PdAX2fa
https://t.co/3yBImjOdd4
In some cases, almost 100% of the light energy can be converted to the second harmonic frequency. These cases typically involve intense pulsed laser beams passing through large crystals, and careful alignment to obtain phase matching.
It's another stunning Malagasy #dartfrog/#poisonfrog for today's #FrogOfTheDay, #42 Mantella cowani Boulenger, 1882! A highly threatened, actively conserved and managed frog from the highlands of central #Madagascar
#MadagascarFrogs
📸D.Edmonds/CalPhotos
This thread will cover only a tiny fraction of the work on Mantella cowanii because, being so charismatic and threatened, it has received quite a bit of attention.
#MadagascarFrogs
We start at the very beginning: the first specimens, two females, were collected by Reverend Deans Cowan in East Betsileo, Madagascar, and sent to London, where George Albert Boulenger described the species in 1882.
#MadagascarFrogs
Boulenger placed the species in his new genus, Mantella, along with ebenaui, betsileo, and madagascariensis. He recognised that the other Malagasy poison frogs were distinct from the Dendrobates of the Americas, although he did keep them in the Dendrobatidae.
#MadagascarFrogs
As more specimens were collected, it became clear that the species was highly variable. In 1978, Jean Guibé wrote with interest about this variability, describing a new subspecies, M. cowani nigricans—today a full species. #MadagascarFrogs
https://t.co/dwaHMbrYbj
#MadagascarFrogs
📸D.Edmonds/CalPhotos
This thread will cover only a tiny fraction of the work on Mantella cowanii because, being so charismatic and threatened, it has received quite a bit of attention.
#MadagascarFrogs
We start at the very beginning: the first specimens, two females, were collected by Reverend Deans Cowan in East Betsileo, Madagascar, and sent to London, where George Albert Boulenger described the species in 1882.
#MadagascarFrogs
Boulenger placed the species in his new genus, Mantella, along with ebenaui, betsileo, and madagascariensis. He recognised that the other Malagasy poison frogs were distinct from the Dendrobates of the Americas, although he did keep them in the Dendrobatidae.
#MadagascarFrogs
As more specimens were collected, it became clear that the species was highly variable. In 1978, Jean Guibé wrote with interest about this variability, describing a new subspecies, M. cowani nigricans—today a full species. #MadagascarFrogs
https://t.co/dwaHMbrYbj
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