Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

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

biology.stackexchange.com

Post reply on HN
Print view View original

101–110 of 204 posts

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

#101

Post by samplatt »

psyklic wrote: post #35

In grad school, I (briefly) researched synthetic DNA logic gates. Using these, you can build neural networks in DNA [1] and probabilistic switching circuits (my co-authored paper) [2]. To do this, you design DNA strands that bind to each other in designated regions when mixed. To make a logic gate, you just make some bindings conditional on other bindings. To detect that the gate is closed, you make the final binding…

Fascinating. Have you read the story story, The Moral Virologist? I've always been curious as to how close to realistic it was, and you seem a person that could answer that.

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

#102

Post by actionfromafar »

pelagicAustral wrote: post #97
gameman144 wrote: post #95

One really cool mechanism I didn't see listed there (at least directly) was riboswitches. Essentially, a segment of mRNA with a binding site for a molecule. Ribosomes that are transcribing the RNA will then branch into two separate flows depending on whether the molecule is bound or not. https://en.m.wikipedia.org/wiki/Riboswitch

Polymorphism?

Or spaghetti assembler code

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

#104

Post by cheschire »

AlbertCory wrote: post #98

PCR was partially inspired by loops in programming languages, according to Kary Mullis, who got the Nobel for its invention. (I heard him say it at Google, but I just checked YouTube and I don't think that particular visit is there. Maybe it's in other places?)

I had to check Kary Mullis's wikipedia page to figure out that PCR stood for polymerase chain reaction. While there, I got the distinct impression someone who disliked him was responsible for editing quite a lot of his article.

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

#106

Post by __s »

abhiyerra wrote: post #105
zubairq wrote: post #103

I’ve always wondered about DNA from a programming language point of view and always thought it was more like a data structure than a language

I’ve always thought Lisp is the closest approximation to DNA.

I guess you're thinking of functional lisp? SKI combinators except instead DNA is GCAT combinators

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

#107

Post by InSteady »

robviren wrote: post #51

I always think of DNA a lot like programming over the course of millions of years. A strung together series of hackish, barely functioning, uncommented code with no documentation whatsoever. Any reason for why a snippet of code ended up being the way it is has been completely lost to time. All we know is that changing it is bad, certain chunks of code lead to certain behavior, and that the more we look at the code th…

The ultimate spaghetti codebase.

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

#108

Post by breischl »

Daub wrote: post #63
marginalia_nu wrote: post #29

Earlier quoted context omitted.

A lot of how we conceive of computation today is based on observation of nature. It's the a logical conclusion to the study of logic, which is a line of inquiry that dates back to antiquity when sophistry was becoming a real institution and there was yet no real systematic way of determining if something was true other than whether it sounded true.

I'm not sure that nature and logic are related in the way you imply. A different question: Is not the atomic indivisible of computing no more that a simple switch? A binary? Is there an equivalent for this in the human mind/brain? I suspect not but would like to hear from someone who knows more.

>Is not the atomic indivisible of computing no more that a simple switch? A binary?

It is for the dominant computing paradigm currently in use, but that isn't a universal truth. As I understand it, we use binary logic primarily because it's more tractable for humans to think about and work with, not because it's the only option or even the best option in all cases. For instance there are plenty of analog computers in history, which are in some ways more closely related to biological "computers".

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

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

#109

Post by dekhn »

akira2501 wrote: post #2

My favorite thing about mtDNA is that two separate genes overlap using separate reading frames. The end of one gene is the same as the start of another, and they are laid out in the circular mitochondrial genome to take advantage of this fact. I've also read that DNA chromosomes can under go conformal changes in response to the environment it's in, making certain reading frames more or less likely to be transcribed,…

overlapping genes show up all over the place and I think they contribute to lots of errors in papers. During my postdoc I analyzed the results from a yeast gene survey where the authors ignored genes overlapping and misannotated genes, imputing their function when really it was the overlapping gene. This is where I started to learn that "if it's in Nature, it's probably wrong"
Post reply on HN