Ciro Santilli @cirosantilli 40

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.

In the case of the electron, we need to start with at least enough energy for the mass of the electron positron pair. This requires a photon with wavelength in the picometer range, which is not common in the thermal radiation of daily life.

This notation is not so common in basic mathematics, but it is so incredibly convenient, especially with Einstein notation as shown at Section "Einstein notation for partial derivatives":

This notation is similar to partial label partial derivative notation, but it uses indices instead of labels such as $x$, $y$, etc.

This is quite mind blowing. The laws of physics actually differentiate between particles and antiparticles moving in opposite directions!!!

Only the weak interaction however does it of the fundamental interactions.

Some historical remarks on Surely You're Joking, Mr. Feynman section "The 7 Percent Solution".

It gets worse of course with CP Violation.

Ciro Santilli lived in Paris for a few years between 2013 and 2016, and he can confirm the uncontroversial fact that "Paris is Magic".

Not just one type of magic though. Every quarter in Paris has its own unique personality that sets it apart and gives it a different mood.

Ciro knows Paris not from its historical facts, but from the raw feeling of endless walks through its streets in different times of the year. Ciro is a walker.

Maybe one day Ciro will expand this section to try and convey into words his feelings of love for the city, but maybe the effort would be pointless. Maybe such feelings can only be felt by other free-roaming walker souls living in the city, and that is both beautiful and a shame.

See also the legendary Cirodance bowl of soup episode at Place de la République.

Ciro had written the following in the past before he lived in smaller cities, started cycling and joined the Street reclamation movement he thought:Perhaps compared to São Paulo City, which is what he knew before that was true. But no, his standards have improved since. Paris has way too many cars. The noise of internal combustion engine vehicles is extremely annoying. And because there are too many personal vehicles, cars have to horn a lot to fight for space. Fuck cars. Paris has been making a big cycling push in the early 2020's, and that is great. But it is still far, far from good.

Often just called collimated light due to the collimator being the main procedure to obtain it.

However, you move very far away from the source, e.g. the Sun, you also get essentially parallel light.

Bibliography:

Outstanding scenery/filming locations and clothing! What are those places! Wikipedia says it was shot party in Shanxi.

Good music.

Appears to have widely modified the story unfortunately however.

They really love their pyrotechnics!

God, Ciro Santilli respects this guy.

Watching www.youtube.com/watch?v=-SbZZPX-y9g in 2022, who was one of his inspirations, made Ciro miss his guitar so much... one day, maybe, one day.

Their main innovation seems to be their 3D design which they call "Coaxmon".

Funding:

The normal navigation to them was paywalled, but the static files are served without login checks if you know their URL. One way to go about it is to search by prefix on the Wayback Machine: web.archive.org/web/*/https://www2.physics.ox.ac.uk/sites/default/files/contentblock/2011/06/03/*

The last handbooks we can find are 2020/2021, they might have move to a new more properly paywalled location after that year.

At the time of the experiment, Illumina equipment was cheaper per base pair and dominates the human genome sequencing market, but it required a much higher initial investment for the equipment (TODO how much).

The reusable Nanopore device costs just about 500 dollars, and about 500 dollars (50 unit volume) for the single usage flow cell which can decode up to 30 billion base pairs, which is about 10 human genomes 1x! Note that 1x is basically useless for one of the most important of all applications of sequencing: detection of single-nucleotide polymorphisms, since the error rate would be too high to base clinical decisions on.

Compare that to Illumina which is currently doing about an 1000 dollar human genome at 30x, and a bit less errors per base pair (TODO how much).

Other advantages of the MinION over Illumina which didn't really matter to this particular experiment are:

Now that's some basal shit! It's basically a fucking blob!!! Except that it is flat. No nervous system. Not even tissues. It is basically a multicellular

Inferior compared to self-directed learning, but better than the traditional "everyone gets the same" approach.

With all this ready, we opened the Nanopore flow cell, which is the 500 dollar consumable piece that goes in the sequencer.

We then had to pipette the final golden Eppendorf into the flow cell. My anxiety levels were going through the roof: Figure 4. "Oxford nanopore MinION flow cell pipette loading.".

At this point bio people start telling lab horror stories of expensive solutions being spilled and people having to recover them from fridge walls, or of how people threw away golden Eppendorfs and had to pick them out of trash bins with hundreds of others looking exactly the same etc. (but also how some discoveries were made like this). This reminded Ciro of: youtu.be/89UNPdNtOoE?t=919 Alfred Maddock's plutonium spill horror story.

Luckily this time, it worked out!

We then just had to connect the MinION to the computer, and wait for 2 days.

During this time, the DNA would be sucked through the pores.

As can be seen from Video 1. "Oxford Nanopore MinION software channels pannel on Mac." the software tells us which pores are still working.

Pores go bad sooner or later randomly, until there are none left, at which point we can stop the process and throw the flow cell away.

48 hours was expected to be a reasonable time until all pores went bad, and so we called it a day, and waited for an email from the PuntSeq team telling us how things went.

We reached a yield of 16 billion base pairs out of the 30Gbp nominal maximum, which the bio people said was not bad.

www.qiagen.com/us/products/discovery-translational-research/dna-rn-a-purification/dna-purification/dna-clean-up/qiaquick-pcr-purification-kit/#orderinginformation (archive)

Manual archive: web.archive.org/web/20190911100243/https://www.qiagen.com/us/resources/download.aspx?id=e0fab087-ea52-4c16-b79f-c224bf760c39&lang=en

Removes PCR byproducts from purified DNA.

Biology experiments are hard, and so they go wrong, a lot.

For this reason, it is wise to verify that certain steps are correct whenever possible.

And so this is the first thing we did on the second day!

Gel electrophoresis separates molecules by their charge-to-mass ratio. It is one of those ultra common lab procedures!

This allows us to determine how long are the DNA fragments present in our solution.

Since we know that we amplified the 16S regions which we know the rough size of (there might be a bit of variability across species, but not that much), we were expecting to see a big band at that size.

And that is exactly what we saw!

First we had to prepare the gel, put the gel comb, and pipette the samples into wells present in the gel:

To see the DNA, we added ethidium bromide to the samples, which is a substance that that both binds to DNA and is fluorescent.

Because it interacts heavily with DNA, ethidium bromide is a mutagen, and the biology people sure did treat the dedicated electrophoresis bench area with respect! Figure 4. "Gel electrophoresis dedicated bench area to prevent ethidium bromide contamination.".

The UV transilluminator we used to shoot UV light into the gel was the Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator. The fluorescent substance then emitted a light we can see.

As barely seen at Figure 8. "Fischer Scientific UVP LM-26E Benchtop 2UV Transilluminator illuminated gel." due to bad photo quality due to lack of light, there is one strong green line, which compared to the ladder matches our expected 16S length. What we saw it with the naked eyes was very clear however.