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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

#81

Post by wat10000 »

datsci_est_2015 wrote: post #52
observationist wrote: post #39

Earlier quoted context omitted.

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.

Imagine if it Turned Out that Capitalizing Various Words made Things more Readable. How Quickly Would That be Adopted?

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

#82

Post by vee-kay »

melagonster wrote: post #18
vee-kay wrote: post #12

Earlier quoted context omitted.

Science has never been constrained by ethics. The same scientists who cry about ethics, have happily experimented on mice and guinea pigs in their labs, even if it causes the deaths or distress of those little sentient beings. Mutations/mutatives like Halo's Master Chief and Marvel's Super Soldier serum won't remain sci-fi for much longer, methinks.

And save human life at the same time? Experiments are not just about torturing animals; people spend a lot of time optimizing for experiment design.

Hey, did you hear about the Volkswagen Monkeys?

Volkswagen (the same megacorp that did the infamous Dieselgate/Emissionsgate scams) forced monkeys to inhale exhaust from its automobiles, to try to show that fumes from current models (the cars, not the monkeys) were less noxious than previous models.

https://www.msn.com/en-us/science/sociology/20-of-the-most-u...

https://en.wikipedia.org/wiki/Volkswagen_emissions_scandal

I guess this cannot be termed as "torturing animals" in the "name of science".

We humans also inhale vehicular exhaust fumes, don't we?

Oh wait, I forgot. Monkeys don't drive cars.

Or do they? https://m.youtube.com/watch?v=XW5NLeGEo94

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

#83

Post by duskwuff »

HappMacDonald wrote: post #78
Ekaros wrote: post #74

Earlier quoted context omitted.

English is good example. It has not been fixed for long while. Even if there would be so many better ways to write certain words.

I feel like Mathematical notation is also a great example (since Math is ultimately a separate language: the language of measurement) It's been built up over centuries where new innovations and shifts in perspective often create new kinds of notation, but those most frequently just get tacked onto whatever else is already standard and the new notations almost never actually supplant the old. AFAICT we haven't really…

> AFAICT we haven't really had a big shift in fundamental mathematical notation in Europe (and its colonies) since Roman Numerals (CXXIII) gave way to Arabic (123) numerals four hundred years ago. 8I

Your history is a little confused. Arabic numerals came into use in Europe as early as the 13th century (introduced by Leonardo Fibonacci), but most other mathematical notation like "=" or or "√" didn't show up until the 16th or 17th century.

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

#84

Post by duskwuff »

observationist wrote: post #67
wl wrote: post #58

Earlier quoted context omitted.

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.

I wonder, how much was gatekeeping, keeping things hard on purpose, how much waas inertia, "that's just the way things are done", and how much was a kind of despairing "holy shit, it'd be so much work to have to go through and recopy everything in the new format, literally decades of effort, and there's other things we want to do with our lives". The whole context of written words had so much implicit process and kno…

Also probably a bit of "good parchment is expensive, why would we waste it on blank space?"

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

#85

Post by koeng »

I work in DNA assembly and synthesis. Here is my take:

They don't use oligo pools - "This capacity may be adapted to use large oligo pools to substantially reduce the cost per construct45 but requires further engineering to account for the formation of the unintended Sidewinder heteroduplexes before assembly and the higher truncation rate of pooled oligos"

This absolutely destroys any unit economics when it comes to DNA synthesis. Oligo pool synthesis isn't 10x cheaper, it's 100x to 1000x cheaper than individual oligo synthesis.

So what they really have is a good way to do DNA assembly from synthesized oligos; fair. But we have that: GoldenGate can do 40 part assemblies, hell it can do 52 part assemblies, and you CAN use oligo pools - https://pmc.ncbi.nlm.nih.gov/articles/PMC10949349/ (there are a couple enzymatic properties which allow this, mainly that you can use full doublestranded DNA, which you can make with a PCR. Can't make these overhang guys with a PCR).

We've even found that with some GoldenGate enzymes, the biology somehow breaks the current models of the physics of ligation by being so efficient - https://www.biorxiv.org/content/10.64898/2026.01.31.702778v1

Their gels do look really good, I'll admit. I can imagine circumstances (exception cases) where this would be better. But not only is this kind of thing for 99% of cases has already been available for many years while being orders of magnitude cheaper (plural).

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

#87

Post by mmooss »

ssivark wrote: post #32
trebligdivad wrote: post #14

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

The early printing press was probably focused on short few page documents (an increasing scale), and it wouldn't be surprising if page numbers were a solution to help printers not mix up pages.

> it wouldn't be surprising if page numbers were a solution to help printers not mix up pages.

It's an interesting idea. Remember they printed large sheets containing many 'pages', I think even in different orientations, which were then folded and the ends cut to produce a nice orderly codex for the reader. They were printing in a different order than the one you read in.

I do think they numbered the large sheets or similar, and you can find old books that retain that number, but I don't recall what it is called.

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

#88

Post by mmooss »

vee-kay wrote: post #80
9dev wrote: post #72

Earlier quoted context omitted.

These files are a never ending quell of evilness. It’s really fascinating. One day people are going to realise the upper 1% are just that—very few….

[flagged]

For the most part, they only have the power others give them.

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

#90

Post by Metacelsus »

nullbyte808 wrote: post #17

Such a simple concept took this long to discover? Now we just need a way of packing the DNA strings into blank cells reliably.

It was known in 2006 but rediscovered recently: https://patents.google.com/patent/US20060281113A1/en
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