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Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

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Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#21

Post by pests »

TheJoeMan wrote: post #20
frongpik wrote: post #7

Sounds like a new field of software engineering in the near future. And I like how the author casually mentions that there's an unexplained "linker" code in the AAA sequence that controls the number of copies to be made, with an implicit assumption that everyone's acting in a good faith. Frankly, if I noticed a strange 20 byte sequence inside the tail of zeros in an executable file, I'd instantly assume it's opcode i…

I can't say with certainty, but I learned the DNA printer makes shorter sequences that then self-assemble into the final strand. So if you have too many repeating AAA's, you can't control if there's 20 or 100 because new AAA sequences will keep latching on to the end of the strand. So, you break it up every so often with some other nucleotides.

Correct they are pattern builders and in repetitive sequences they have trouble terminating similar to recursion without an endcase.

Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#22

Post by rantwasp »

Love it. The explanation is amazing and strikes the right balance when it comes to introducing the things needed by the uninitiated to grok the gist of the vaccine.

How far we have come, as a species, by looking at what this vaccine is, is both inspiring and scary

Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#24

Post by amirkdv »

Great post!

A non-technical detail that the post misses is the human story here. Katalin Kariko, the biochemist that pioneered the idea of delivering vaccines in mRNA form, got nothing but rejections for her grant applications for this very idea and was eventually demoted from tenure track at U Penn.

Whatever you think of this, it's a misleading understatement to describe it as:

> As with other fundamental scientific research we are now reaping the benefits of, the discoverers of this technique had to fight to get their work funded and then accepted.

From the article[0] the post itself cites:

> By 1995, after six years on the faculty at the University of Pennsylvania, Karikó got demoted. She had been on the path to full professorship, but with no money coming in to support her work on mRNA, her bosses saw no point in pressing on.

[0]: https://www.statnews.com/2020/11/10/the-story-of-mrna-how-a-...

Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#25

Post by zevv »

My knowledge of modern genetic engineering is limited to some popsci literature, so I understand only parts of this story. I was surprside by this part though:

"Over many years of experimentation, it was found that if the U in RNA is replaced by a slightly modified molecule, our immune system loses interest. For real. [...] The really clever bit is that although this replacement Ψ placates (calms) our immune system, it is accepted as a normal U by relevant parts of the cell."

This sounds like a serious backdoor or attack vector to me - would there be any risk in introducing this Ψ, allowing some natural occuring permutations to turn wild or dangerous?

Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#26

Post by fierarul »

zevv wrote: post #25

My knowledge of modern genetic engineering is limited to some popsci literature, so I understand only parts of this story. I was surprside by this part though: "Over many years of experimentation, it was found that if the U in RNA is replaced by a slightly modified molecule, our immune system loses interest. For real. [...] The really clever bit is that although this replacement Ψ placates (calms) our immune system,…

Thank you! I came here to ask the same question.

Now that we are producing and injecting industrial quantities of Ψ, any chance this will get incorporated in actual viruses or maybe teach the immune system not to ignore it (or maybe even go crazy about it)?

Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#27

Post by scotty79 »

fierarul wrote: post #26
zevv wrote: post #25

My knowledge of modern genetic engineering is limited to some popsci literature, so I understand only parts of this story. I was surprside by this part though: "Over many years of experimentation, it was found that if the U in RNA is replaced by a slightly modified molecule, our immune system loses interest. For real. [...] The really clever bit is that although this replacement Ψ placates (calms) our immune system,…

Thank you! I came here to ask the same question. Now that we are producing and injecting industrial quantities of Ψ, any chance this will get incorporated in actual viruses or maybe teach the immune system not to ignore it (or maybe even go crazy about it)?

I think there's no risk since cells can't make Ψ, and probaby Ψ is not super durable as a chemical.

Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#28

Post by flobosg »

scotty79 wrote: post #27
fierarul wrote: post #26

Earlier quoted context omitted.

Thank you! I came here to ask the same question. Now that we are producing and injecting industrial quantities of Ψ, any chance this will get incorporated in actual viruses or maybe teach the immune system not to ignore it (or maybe even go crazy about it)?

I think there's no risk since cells can't make Ψ, and probaby Ψ is not super durable as a chemical.

> cells can't make Ψ

Pseudouridine is the most common RNA modification in cells, actually. They produce it all the time.

> and probaby Ψ is not super durable as a chemical.

Quite the opposite. Pseudouridine usually increases the stability of the RNA molecule it modifies.

Re: Reverse Engineering the Source Code of the BioNTech/Pfizer SARS-CoV-2 Vaccine

#30

Post by bionhoward »

pizza wrote: post #23

Is there a book or textbook that approaches genetics from a source-code hacking point of view? It's quite interesting and I'd like to learn more

Synthetic Biology: A Primer

Wetware: A Computer in Every Living Cell

(the second for systems biology)

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