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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

#51

Post by ahubert »

renaudg wrote: post #17

This was a compelling and inspiring read, thanks. The way the CS and genetics concepts map with each other is really fascinating and thought-provoking. How would a curious engineer go about learning more about this particular "computer architecture" ? Going further, is there a realistic career path for someone with a software engineering background to retrain, pivot and meaningfully contribute to research in this are…

So .. it is not easy to get into this field. From the outside we tend to see DNA as some freestanding thing that fascinates us. The biology people intertwine DNA with everything they do. The route to knowing about this stuff therefore goes via learning about biology first. One of my favorite books, Molecular Biology of the Cell, covers DNA thoroughly.. by spending time on it on almost every of its 1300 pages. But it is all in between "the rest of biology". In a way I can understand this of course, but it is very very hard work.

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

#52

Post by divbzero »

yread wrote: post #33

Nice article. There are more interesting things to say about RNA that makes it a bit less like code - for example that it too can fold to a 3d structure, with some cases that can cause problems - hairpins for example where the sequence is palindrome-like (in the complementing letters) ACG followed by CGU can fold onto itself. This caused the problems with the initial batch of CDC's PCR tests

And on top of that RNA can exhibit non-canonical base pairing like G-U. [1]

[1]: https://commons.wikimedia.org/wiki/File:Wobble.svg

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

#53

Post by kolinko »

ahubert wrote: post #14
andromaton wrote: post #11

The article reads very similar to articles about reverse engineering machine code in undocumented, obfuscated, or malicious software.

"life is a 4 billion year old software project" :-)

„written by interns who kept changing random stuff until bugs disappeared”

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

#54

Post by kolinko »

dbetteridge wrote: post #36

Fascinating article, Any suggestions where I could go to learn more specifically about this sort of genetic engineering and more generally about biology (University level and above).

I used: - Vincent’s Racaniello virology iTunesU course (viruses exploit all biology systems to hack the body) - introduction to Genetics on inkling

Many people also recommend the book „Cell”.

You will also want to start with a first few chapters of Organic Chemistry from any course/book

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

#55

Post by xg15 »

This was a really amazing and illustrative article. As a programmer, it definitely gave me a better understanding of the vaccine (or at least I believe so).

I was curious about a part that I haven't found a lot of writing on so far - namely, what happens with the artificial spike protein after the cell assembled it.

Does it, like, keep floating around inside the cell? Does it attach to the cell membrane like it would to the viroid? Does it leave the cell and enter the bloodstream or does it something altogether different?

I figure it can't really stay inside the cell as it has to interact with the immune system at some point.

However, if it attaches to the cell wall, wouldn't this cause risk that the immune system considers the whole cell a pathogen and attacks it? After all, teaching the immune system to destroy anything the spike is attached to is sort of the whole point of the exercise.

Finally, if the spike enters the bloodstream, could it wreak havoc with ACE2 receptors?

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

#56

Post by metta2uall »

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)?

They're injecting already-made Ψ, not any of the genetic instructions that would enable cells/viruses to make their own Ψ.

But the broader concern about advances in biotech being potentially very dangerous is I think a very good one..

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

#57

Post by giuscri »

ahubert wrote: post #51
renaudg wrote: post #17

This was a compelling and inspiring read, thanks. The way the CS and genetics concepts map with each other is really fascinating and thought-provoking. How would a curious engineer go about learning more about this particular "computer architecture" ? Going further, is there a realistic career path for someone with a software engineering background to retrain, pivot and meaningfully contribute to research in this are…

So .. it is not easy to get into this field. From the outside we tend to see DNA as some freestanding thing that fascinates us. The biology people intertwine DNA with everything they do. The route to knowing about this stuff therefore goes via learning about biology first. One of my favorite books, Molecular Biology of the Cell, covers DNA thoroughly.. by spending time on it on almost every of its 1300 pages. But it…

Hi Bert, what do you think of http://rosalind.info/problems/list-view/ ?

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

#58

Post by coldtea »

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 might not, but people can...

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

#59

Post by coldtea »

amirkdv wrote: post #24

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…

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

It might be an "understatement" but it's hardly misleading. You make it sound like the author intentionally dissed them by downplaying the story.

The technique eventually did end up funded and accepted. And she still made millions (from the license), will get a Nobel soon (I predict - there's alredy pressure for that), plus, her story will 99% be made into a movie sometime in the next 20-30 years (I also predict).

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

#60

Post by coldtea »

inglor_cz wrote: post #35
amirkdv wrote: post #24

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…

There is a common thread in many discussions (esp. on Reddit) creating a false dichotomy between the greedy private sector and the taxpayer-funded basic research that comes with all the important new ideas. While not an entirely false picture, the real situation is far from that clear and scientific struggles of Katalin Karikó, who finally left the academia for private sector (she is now a vice president in BioNTech,…

>There is a common thread in many discussions (esp. on Reddit) creating a false dichotomy between the greedy private sector and the taxpayer-funded basic research that comes with all the important new ideas.

Well, in the modern world we have both a greedy private sector and a greedy academia...

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