## mRNA Vaccines and UNIX

mRNA Vaccines and UNIX

How mRNA vaccines use UNIX modularity to help humanity.

by Christoph Lohmann <20h@r-36.net>
Specialist Doctor in Common and Family Medicine

## What is this talk about?

* There will be no deep dive into genetics and evolution.

* Everyone should be able to use this as an introduction why UNIX
  thinking is not just in computers and helps humanity.

* The topics are cut down for reuse in your daily life and
  adapted to UNIX users.

* This helps you to easily defend yourself against fake news around
  the mRNA vaccines.

## What is mRNA?

RNA is one of the oldest information technology in nature.

Depending on which (biological) lifeform you are, your source code is
stored in RNA or DNA.

One popular depiction of RNA and DNA are whirlwinds.

RNA in humans is normally generated from DNA.

m(essenger) RNA is RNA sent around in cells for communication and
gets automatically garbage collected.

mRNA (by nature) cannot be transformed into your DNA.

There are many other kinds of RNA, all described using some lower
case ASCII chars before the "RNA".

## How do vaccines work?

1. Inject some part of the virus/bacteria/pathogen into the bloodline
   of the human.

2. Certain cells of the immune system learn how to easily fight this
   virus/bacteria/pathogen.

3. Depending on which learning method of the immune system is used,
   refreshing/booster vaccinations are required.

## Virus attacking a human without vaccination.

1. Some virus gets coughed into you by a non-mask wearer.

2. The virus slowly infects cells, those cells die and show abnormal
   behaviour.

3. Your body police first starts small controls in the remote. The
   bigger the threat gets, the more police and/or specialized police
   is sent.

4. Depending on how fast the virus can spread and into which organs,
   is the police able to defend the body. HIV for example slowly
   infects the police and makes it unusable.

5. The body survives or dies.

## Virus attacking a human with vaccination.

1. Some virus gets coughed into you by a non-mask wearer.

2. The virus slowly infects cells, those cells die and show abnormal
   behaviour.

3. The by then vaccination-trained specialized police is directly
   dispatched to the first occurences of the first infections.

4. The virus infected cells and or the virus is caughted on the
   blood line streets and fast killed / arrested(1).

5. The body survives more often because less resources were used to
   defend against the virus.

(1) For arresting see how BCG (tuberculosis) vaccine worked and did
not work.

## Recapitulation: Vaccines and mRNA

We need to get mRNA into a body to the right immune cells so the
body is able to create the specialized response.

But mRNA is naturally garbage collected and will not go into the
cells on its own.

How do we get into the cells?

Here comes the modularity.

## Parts of a mRNA vaccine.

1. mRNA (easy to produce)

2. some lipid bubble around the mRNA so the mRNA does not get destroyed

3. some molecule to attract immune cells to the injection point

4. chemicals to stabilize the vaccination doses / vials


All of these levels can be replaced, modernized, interchanged.
Where do you see a similarity? In UNIX philosophy.

Outlook: Scientists are working on multi-level vaccines with more
         layers.

## UNIX interpretation

mrna-encode -d dendritic ${target} \
	| add-lipid-bubble \
	| stabilize \
	| vaccine-print

$target ... Some proteine of SARS-CoV-2 for example.

-d gives currently the target as "dendritic cells", which we need to
produce specialized actions against a virus like SARS-CoV-2.

Different targets, by giving specific information to specific
cells can help us with other diseases. See one example at the
end with cancer.

## The -d flag or destination.

mRNA used has three parts.

	${cap} ${information} ${endsequence}

$cap ... A cap sequence with some additions to tell where the information
         should go.
$information ... What should be pushed into the destination cell.
$endsequence ... Required buffer so the mRNA survives longer and gets
                 more easily read out by the destination cell.

So -d defines which kind of $cap we will need to target a specific
cell.

## Lipid bubble

This is pretty simple, but quiet complex. It required many years to
develop them.

By having the full blueprint of this, it can be modified in case of
allergies, adapted for patients.

## Chemicals to attract immune cells.

Creating a bit bigger local reaction so more destination cells come
to that muscle or wherever the vaccine is injected so better learning
is done.

Sadly here we see allergies so far. Future research will reduce this.

One part can be aluminium complexes and are used in some vaccinations.
Concentrations are too low for any systematic effect.
Anti-vaxxers use this for strange theories. If you need help, we
have a huge summary in Germany that debunk such theories.

## Chemicals to stabilize the vaccinations.

This is required for transport, for the vials, for creating the
individual doses. Details are out of scope of this talk.

Over time this is modified and made better. See that Biontech/Comirnaty
can now be stored in refrigerator for 30 days instead of only at -80°C
in the beginning.

## Where can this whole infrastructe be reused?

* against other infectious diseases
	* It was used against Ebola!

* against cancer

* in individualized cancer therapy

* against multiple sclerosis / immun-based diseases

* Much more. See logic explained below.

## Many more usage cases?

The basic principle is to find some proteine which can be encoded in
mRNA and which is only in some (disease) target. Creating an immune
response against this proteine should not cause any (big) side-effects
in the body and attack non-target cells.

We need diff(1).

## Individualized Cancer Therapy: Introduction

* Some patient has colon cancer.

* The colon cancer is found and removed surgically.

* Colon cancers have the tendency to spread easily after being removed.
	* For now one option is chemotherapy / throw atom bomb onto
	  whole body of all growing cells.
	* Radiotherapy; send x-rays onto the region where the cancer
	  is supposed to be and (hope) the cells do not grow.

## Individualized Cancer Therapy: mRNA

This is being worked on _now_.

* The blood of the patient is taken and some probe of the cancer.
* A molecular diff(1) is run over cancer and patient DNA/RNA.
* The found diff(1) is analyzed withing four weeks(!) into some
  individualized mRNA vaccine.
* The body uses its own response against cancer cells and allows
  exact local destruction of cancer cells.
* A third way to destroy cancer is available to help patients.

Studies for colon cancer show very promising results.

## Individualized Cancer Therapy: For UNIX users.

dna-decode ${cancer-cell} > cancer_cell.dna
dna-decode ${normal-cell} > normal_cell.dna
dna-diff cancer_cell.dna normal_cell.dna > diff_cells.dna
mrna-convert diff_cells.dna > diff_cels.rna
mrna-encode -d t-lymphozyte $(<diff_cells.rna) \
	| add-lipid-bubble \
	| stabilize \
	| vaccine-print
# Inject into patient and save his/her life.

## Sidenote: The world is getting better.

Did you know that we can cure some cancer 100%?

* Scientists and doctors were able to create a medication which
  targets exactly the cause of some specialized lymphoma.
	* Patients can be cured for 100%.

Did you know, that we are already vaccinating cancer away?

* The vaccination against human papilloma virus reduced the
  cervix (female vagine) carcinoma cases by 70%, with only
  40% of the population being vaccinated in Germany.
	* It reduces penis carcinoma for all men and anal
	  carcinoma for (mostly) gay anal sex partners too.
	* Vaccines have many good uses.

Further virus targets are promising for reducing cancer in the
future.

## Summary: UNIX thinking.

* Replaceable modularity is helping the world.
	* To make it easy to understand and have more brains work on it.

* Modules need to be simple and reusable, so others can use it.
	* See sfeed and xml2tsv being reused to parse the web.

* Old technology (here: mRNA; in Unix: strings, tsv) can be easily
  reused in the future in ways we can not imagine now.

* Source code needs to be open for other research. All hidden code
  is lost code. Once you are dead, your not written down thoughts
  are dead too.

* We all need to work together for a better future. Domain thinking
  stops us.

## Questions?

Are there questions?


## Thanks

Thank you very much for listening.

If you have comments or further questions:

	Christoph Lohmann <20h@r-36.net>