Does DNA have the equivalent of IF-statements, WHILE loops, or function calls? • Hacker News Board

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#201

Post by sjducb » Thu, Jan 11, 2024, 10:23 AM UTC

roughly wrote: post #164

sjducb wrote: post #134

Earlier quoted context omitted.

As a biologist who moved into software engineering I love working with actual machines. You can think of a design, build it and have it work as you expect. You can’t do that in biology. The reason is that we “understand” how computers work. Our understanding of biology is nowhere near that level. A high percentage of established knowledge is wrong or so incomplete that it’s not useful for designing new systems. This…

I think another reason is that biological systems are _fantastically_ complicated - for example, we're finding that the spatial distribution of molecules within the cell affect enzymatic processes in ways that may have implications for alzheimer's and dementia. For another, there's various bacterial communities where, if you want to trace the enzymatic pathway for a particular product, you're jumping between species…

I agree that biology is fantastically complicated.

When I say we “understand” everything that matters about a computer; I don’t mean one person understands. I mean each important part is understood by at least one person. Together humanity understands everything important about a computer.

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#202

Post by bibelo » Thu, Jan 11, 2024, 1:20 PM UTC

andreyvit wrote: post #123

bmartin13 wrote: post #110

I'm pretty sure something this complex came from a higher order being. That whole order from chaos argument is not holding water for me with this degree of complexity.

I'm afraid your intuition about complexity misleads you here. If you'd like to learn more, spend some time with say evolutionary algorithms. It's not a big time commitment; playing around for a couple days will likely be enough. You'll find how the crap an evolution-style search comes up with is really similar to how nature works: a few beautiful core finds + a big pile of hacks of varying craziness, some of them tot…

Where do these algorithms come from?

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#203

Post by pama » Thu, Jan 11, 2024, 3:55 PM UTC

dekhn wrote: post #192

pama wrote: post #152

Earlier quoted context omitted.

Thanks for the neat estimate. It would be hard to dehydrate DNA to a significant degree, so adding some water and counterions would probably reduce your estimate by a bit. (Error correction would also reduce things by a bit.) Overall the estimate of ~500 exabytes per gram seems reasonable to me.

I think there are worse ideas than cloning your data into a population of tardigrades using an error-correcting code, and then dehydrating them into the tun state. Not nearly the density of raw dry DNA (which itself can be stabilized using trehalose or PVA) but tardigrade tuns can resist harsh environments for ~millenia.

Agreed. I hope there will be commercial scale inexpensive solutions of this type in the next ten years.

Re: Does DNA have the equivalent of IF-statements, WHILE loops, or function calls?

#204

Post by samuell » Fri, Jan 12, 2024, 12:24 PM UTC

visarga wrote: post #20

Well, DNA might not have programming structures, but it acts like a neural network. See "Gene regulatory network" > Some proteins though serve only to activate other genes, and these are the transcription factors that are the main players in regulatory networks or cascades. By binding to the promoter region at the start of other genes they turn them on, initiating the production of another protein, and so on. Some tr…

In systems biology textbooks, these networks are typically described more as alike logic gates than as neural networks, although some similarities are there for sure.

The GRNs are a bit more dynamic than strictly on/off, but the fact they have multiple types of interaction, such as enhancers and inhibitors, means they can model logical gates better than I understand a typical neural network can.