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Can be seen as a cheap form of DNA sequencing that only test for a few hits. Some major applications:
- gene expression profiling
- single-nucleotide polymorphism: specificity is high enough to detect snips
Experiments that involve sequencing bulk DNA found in a sample to determine what species are present, as opposed to sequencing just a single specific specimen. Examples of samples that are often used:
- river water to determine which bacteria are present, notably to determine if the water is free of dangerous bacteria. A concrete example is shown at: Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it".
- sea water biodiversity: ocean-microbiome.embl.de/companion.html
- food, including searching for desirable microorganisms such as in cheese or bread yeast
- poo, e.g. to study how the human microbiome influences health. There are companies actively working on this, e.g.: www.microbiotica.com/
One related application which most people would not consider metagenomics, is that of finding circulating tumor DNA in blood to detect tumors.
- techcrunch.com/2022/05/31/ultima-genomics-claims-100-full-genome-sequencing-after-stealth-600m-raise/ Ultima genomics TODO technology? Promises 100 USD genome, 600M funding out of stealth...
oriC = Origin of Chromosomal replication.
Caused by slipped strand mispairing.
This is an extremely widely used technique as of 2020 and much earlier.
If allows you to amplify "any" sequence of choice (TODO length limitations) between a start and end sequences of interest which you synthesize.
If the sequence of interest is present, it gets amplified exponentially, and you end up with a bunch of DNA at the end.
You can then measure the DNA concentration based on simple light refraction methods to see if there is a lot of DNA or not in the post-processed sample.
Even Ciro Santilli had some contact with it at: Section "How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it", see: PCR!
One common problem that happens with PCR if you don't design your primers right is: en.wikipedia.org/wiki/Primer_dimer
Sometime it fails: www.reddit.com/r/molecularbiology/comments/1kouomw/when_your_pcr_fails_again_and_you_start/and a comment:
Nothing humbles you faster than a bandless gel. One minute you’re a scientist, the next you’re just a pipette-wielding wizard casting spells that don’t work. Meanwhile, physicists are out there acting like gravity always behaves. Smash that upvote if your reagents have ever gaslit you.
PCR = Pray, Cry, Repeat
Our definition of fog computing: a system that uses the computational resources of individuals who volunteer their own devices, in which you give each of the volunteers part of a computational problem that you want to solve.
Electronic Ink such as that found on Amazon Kindle is the greatest invention ever made by man.
Once E Ink reaches reasonable refresh rates to replace liquid crystal displays, the world will finally be saved.
It would allow Ciro Santilli to spend his entire life in front of a screen rather in the real world without getting tired eyes, and even if it is sunny outside.
Ciro stopped reading non-code non-news a while back though, so the current refresh rates are useless, what a shame.
OMG, this is amazing: getfreewrite.com/
Predicted by the Dirac equation.
Can be easily seen from the solution of Equation "Expanded Dirac equation in Planck units" when the particle is at rest as shown at Video "Quantum Mechanics 12b - Dirac Equation II by ViaScience (2015)".
Predicted by the Dirac equation.
We've likely known since forever that photons are created: just turn on a light and see gazillion of them come out!
Photon creation is easy because photons are massless, so there is not minimum energy to create them.
The creation of other particles is much rarer however, and took longer to be discovered, one notable milestone being the discovery of the positron.
TODO, including why the Schrodinger equation is not.
The Dirac equation can be derived basically "directly" from the Representation theory of the Lorentz group for the spin half representation, this is shown for example at Physics from Symmetry by Jakob Schwichtenberg (2015) 6.3 "Dirac Equation".
The Diract equation is the spacetime symmetry part of the quantum electrodynamics Lagrangian, i.e. is describes how spin half particles behave without interactions. The full quantum electrodynamics Lagrangian can then be reached by adding the internal symmetry.
As mentioned at spin comes naturally when adding relativity to quantum mechanics, this same method allows us to analogously derive the equations for other spin numbers.
Bibliography:
Deriving The Dirac equation by Andrew Dotson (2019)
Source. Bibliography:
- www.youtube.com/watch?v=Fu1BGGeyqHQ&list=PL54DF0652B30D99A4&index=63 "K6. The Pauli Equation" by doctorphys
A relativistic version of the Schrödinger equation.
Correctly describes spin 0 particles.
The most memorable version of the equation can be written as shown at Section "Klein-Gordon equation in Einstein notation" with Einstein notation and Planck units:
Has some issues which are solved by the Dirac equation:
- it has a second time derivative of the wave function. Therefore, to solve it we must specify not only the initial value of the wave equation, but also the derivative of the wave equation,As mentioned at Advanced quantum mechanics by Freeman Dyson (1951) and further clarified at: physics.stackexchange.com/questions/340023/cant-the-negative-probabilities-of-klein-gordon-equation-be-avoided, this would lead to negative probabilities.
- the modulus of the wave function is not constant and therefore not always one, and therefore cannot be interpreted as a probability density anymore
- since we are working with the square of the energy, we have both positive and negative value solutions. This is also a features of the Dirac equation however.
Bibliography:
- Video "Quantum Mechanics 12a - Dirac Equation I by ViaScience (2015)" at youtu.be/OCuaBmAzqek?t=600
- An Introduction to QED and QCD by Jeff Forshaw (1997) 1.2 "Relativistic Wave Equations" and 1.4 "The Klein Gordon Equation" gives some key ideas
- 2011 PHYS 485 lecture videos by Roger Moore from the University of Alberta at around 7:30
- www.youtube.com/watch?v=WqoIW85xwoU&list=PL54DF0652B30D99A4&index=65 "L2. The Klein-Gordon Equation" by doctorphys
- sites.ualberta.ca/~gingrich/courses/phys512/node21.html from Advanced quantum mechanics II by Douglas Gingrich (2004)
- youtu.be/tR6UebCvFqE?t=23 particle at rest
- youtu.be/tR6UebCvFqE?t=322 unidirectional movement without a potential
- youtu.be/tR6UebCvFqE?t=507 shows that observers in different frames of reference also see different spin. We are reminded of how magnetism is just a side effect of special-relativity.
- youtu.be/tR6UebCvFqE?t=549 Dirac equation solution for the hydrogen atom, final result only + mentions fine structure prediction.
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 2. You can publish local OurBigBook lightweight markup files to either OurBigBook.com or as a static website.
Figure 3. Visual Studio Code extension installation.
Figure 5. . You can also edit articles on the Web editor without installing anything locally. Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact