Sponsor updates by Ciro Santilli 35 Updated +Created
Previously, updates were being done with more focus to sponsors in the format of the child sections to this section. That format is now retired in favor of the more direct Section "Updates" format.
Intrinsic termination by Ciro Santilli 35 Updated +Created
Transcription unit by Ciro Santilli 35 Updated +Created
A sequence of mRNA that can actually be transcribed.
Multiple different transcription units can be produced by a single operon, see: operon vs transcription unit.
Operon by Ciro Santilli 35 Updated +Created
Sequence of genes under a single promoter. For an example, see E. Coli K-12 MG1655 operon thrLABC.
A single operon may produce multiple different transcription units depending on certain conditions, see: operon vs transcription unit.
RNA half-life prediction by Ciro Santilli 35 Updated +Created
GitHub Sponsors by Ciro Santilli 35 Updated +Created
Adenine methylation by Ciro Santilli 35 Updated +Created
Synthetic chromosome by Ciro Santilli 35 Updated +Created
Basically a synonym for doing a large chunk of de novo DNA synthesis.
Pre-sequencing preparation by Ciro Santilli 35 Updated +Created
One cool thing we did in this procedure was to use magnetic separation with magnetic beads to further concentrate the DNA: Figure 1. "GE MagRack 6 pipetting.".
The beads are coated to stick to the DNA, which allows us to easily extract the DNA from the rest of the solution. This is cool, but bio people are borderline obsessed by those beads! Go figure!
Figure 1.
GE MagRack 6 pipetting.
Source.
Figure 2.
GE MagRack 6 eppendorf with magnetic beads mounted.
Source.
Then we prepared the DNA for sequencing with the Oxford Nanopore specific part: Oxford Nanopore SQK-LSK109 Ligation Sequencing Kit.
Here some of the steps required a bit more of vortexing for mixing the reagents, and for this we used the VELP Scientifica WIZARD IR Infrared Vortex Mixer which appears to be quicker to use and not as strong as the Vortex Genie 2 previously used to break up the cells:
Figure 3.
VELP Scientifica WIZARD IR Infrared Vortex Mixer running.
Source.
After all that was done, the DNA of the several 400 ml water bottles and hours of hard purification labour were contained in one single Eppendorf!
Nuclear weapon by Ciro Santilli 35 Updated +Created
Figure 1.
A weapons-grade ring of electrorefined plutonium, typical of the rings refined at Los Alamos and sent to Rocky Flats for fabrication
. Source. The ring has a purity of 99.96%, weighs 5.3 kg, and is approx 11 cm in diameter. It is enough plutonium for one bomb core. Which city shall we blow up today?
Ciro Santilli is mildly obsessed by nuclear reactions, because they are so quirky. How can a little ball destroy a city? How can putting too much of it together produce criticality and kill people like in the Slotin accident or the Tokaimura criticality accident. It is mind blowing really.
More fun nuclear stuff to watch:
Video 1.
Tour of a nuclear misile silo from the 60's by Arizona Highways TV (2019)
Source.
Video 2.
The Ultimate Guide to Nuclear Weapons by hypohystericalhistory (2022)
Source. Good overall summary. Some interesting points:
2019-12 Bikehut bicycle repair stand by Ciro Santilli 35 Updated +Created
Maybe I'm an idiot and should have bought a much smaller rear wheel stand, only thought of that later, e.g.: www.amazon.co.uk/dp/B00G7ZO3GE or www.amazon.co.uk/dp/B00SD7NL44
Rope attached to rear rack + door knob: www.youtube.com/watch?v=teUsJt1WL1g
Use the Internet by Ciro Santilli 35 Updated +Created
If you give a course in a classroom, you reach 10 people (the others were sleeping).
If you make a perfect course online, and answer questions online, you reach 10 thousand.
Not doing things online is a waste of time.
You are a highly trained professional, and your time is extremely valuable.
Even if it takes twice as long to create the material than giving course, you are still more efficient by a factor of 500.
It is as if there were 500 little copies of you working full time. It is a superpower.
Pilus by Ciro Santilli 35 Updated +Created
Can either be a cell's dick used during bacterial conjugation, or little attachment anchors.
Nucleoid by Ciro Santilli 35 Updated +Created
Defining properties of elementary particles by Ciro Santilli 35 Updated +Created
A suggested at Physics from Symmetry by Jakob Schwichtenberg (2015) chapter 3.9 "Elementary particles", it appears that in the Standard Model, the behaviour of each particle can be uniquely defined by the following five numbers:
E.g. for the electron we have:
  • mass:
  • spin: 1/2
  • electric charge:
  • weak charge: -1/2
  • color charge: 0
Once you specify these properties, you could in theory just pluck them into the Standard Model Lagrangian and you could simulate what happens.
Setting new random values for those properties would also allow us to create new particles. It appears unknown why we only see the particles that we do, and why they have the values of properties they have.
Prokaryotic small ribosome subunit by Ciro Santilli 35 Updated +Created
Prokaryotic ribosome by Ciro Santilli 35 Updated +Created
Phase-space formulation by Ciro Santilli 35 Updated +Created
An "alternative" formulation of quantum mechanics that does not involve operators.
Pinned article: ourbigbook/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!
Video 1.
Intro to OurBigBook
. Source.
We have two killer features:
  1. 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-calculus
    Articles 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/derivative
    Video 2.
    OurBigBook Web topics demo
    . Source.
  2. 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:
    • 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
    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.
    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.
    Video 4.
    OurBigBook Visual Studio Code extension editing and navigation demo
    . Source.
  3. https://raw.githubusercontent.com/ourbigbook/ourbigbook-media/master/feature/x/hilbert-space-arrow.png
  4. Infinitely deep tables of contents:
    Figure 6.
    Dynamic article tree with infinitely deep table of contents
    .
    Descendant pages can also show up as toplevel e.g.: ourbigbook.com/cirosantilli/chordate-subclade
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