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Invention of DNA "page numbers" opens up possibilities for the bioeconomy

caltech.edu

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Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#51

Earlier quoted context omitted.

pcr amplifies all sequences, correct or wrong, no? and as I understand it, it works on short snippets the best.

It amplifies sequences that contain the two primer sequences on each end of the target. So if you had synthesized sequence XYZ with some mistakes like YZX, then you could target X and Z and purify. You're correct that PCR has a limited max length, but it is longer and cheaper than vanilla DNA synthesis.

Kary B. Mullis Nobel Prize lecture Nobel Lecture, December 8, 1993

The Polymerase Chain Reaction

https://www.nobelprize.org/prizes/chemistry/1993/mullis/lect...

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#52

That page numbers in books were only invented 50 years after the printing press is a fun snippet from the article

Sometime after 685 AD, they invented spaces between words. All text - in Latin to that point, mostly - was written in scriptio continua. All sorts of ambiguity and hilarity would ensue; to be a good writer, you needed to ensure that words didn't bleed together and form incorrect meanings in unintended combinations. If you lost your place when reading, you'd have to know generally where you were in a scroll, and resta…

Also kind of crazy how long “but that’s the way we’ve always done it” can remain the dominant system, despite a revolutionary change being so trivially achievable. This required absolutely no technological advancement, literally just putting a little more space between letters to reduce ambiguity.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#55
post #13

This is probably the only way "humans" are going to colonize any planets other than Earth. And probably lots of new places on Earth too. Just include the genes for extreme-cold or extreme-arid climates. Or the genes for low oxygen environments, or even for metabolizing useful things from eating rocks. Or from spending 24 hours a day in salt water.

Imagine if we could turn our bodies into perfect spheres, and then adjust genetic beauty preferences to match it.

Seems like a heat dissipation problem

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#56

This is probably the only way "humans" are going to colonize any planets other than Earth. And probably lots of new places on Earth too. Just include the genes for extreme-cold or extreme-arid climates. Or the genes for low oxygen environments, or even for metabolizing useful things from eating rocks. Or from spending 24 hours a day in salt water.

The ease of this "just" is the most concerning thing in the context of humankind's survival.

>The ease of this "just" is the most concerning thing in the context of humankind's survival.

Right? I wouldn't expect genes for heat/cold tolerance in other organisms to necessarily be useful in humans. They work by mechanisms that are useful for that organism, but humans have our own set of problems.

It's like saying you can strap a jet engine on to a tractor and expect farm work to massively speed up. No: the machinery doesn't translate for a clean swap like that.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#57

For someone in Software what is a good way to learn the fundamentals of this?

Possibly not what you're asking for, but I wrote a generally-accessible intro to why it can be tricky to assemble many DNA fragments with "Golden Gate Assembly", a mainstream method which relies on short sequence overhangs. The Sidewinder method discussed in this thread aims to solve that "short overhang" problem.

https://zulko.github.io/bricks_and_scissors/posts/overhangs/

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#58

That page numbers in books were only invented 50 years after the printing press is a fun snippet from the article

Sometime after 685 AD, they invented spaces between words. All text - in Latin to that point, mostly - was written in scriptio continua. All sorts of ambiguity and hilarity would ensue; to be a good writer, you needed to ensure that words didn't bleed together and form incorrect meanings in unintended combinations. If you lost your place when reading, you'd have to know generally where you were in a scroll, and resta…

Hittite was putting spaces between words in the 17th century BCE. And if we're just interested in Latin, it used the interpunct as a word divider hundreds of years before the use of the space as word divider happened. The use of scriptio continua despite knowledge of word dividers was a choice.

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#59
post #11

Earlier quoted context omitted.

The ease of this "just" is the most concerning thing in the context of humankind's survival.

Then I recommend you don't find out what "Project Molecule" intends to do.

Thanks for the heads-up!

Re: Invention of DNA "page numbers" opens up possibilities for the bioeconomy

#60

For someone in Software what is a good way to learn the fundamentals of this?

If you live near a community bio lab see if you can join up and take some classes to learn some basic lab techniques. And some sort of intro bio class via mooc/textbook/local college class whatever if you can but community lab is honestly a great place to start if you have one.

The main thing to keep in mind is that all the stuff that involves analogies between software and biology is almost universally a bullshit oversimplification that you can safely ignore. It's just that software is so profitable and there's so much vc money in it that there's a ton of pressure to be like "oh we can program biology like we program computers." We can't - we invented computers but didn't invent biology. Biology is the end result of 4 billion years of unchecked entropy - it's a chaos system, non deterministic in the wildest ways, impossibly complicated, and yet something we are getting astonishingly good at understanding and engineering.

Basically, all the biologists that started companies that were like "we can program biology like we can program computers" are bankrupt now.

On the other hand, the computer scientists that respected the nature of biology and pushed the limits of computing to develop Alphafold - giant models trained on the full complexity of biological data - finally created computer systems that could handle biological systems like protein folding at an extraordinary level of capability. They won a nobel.

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