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

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

#61

Post by rogerkirkness »

sebastianconcpt wrote: post #56
koeng wrote: post #53

I’ve worked in a lab of one of the original folks working on genetic logic gates, and honestly, no they don’t really work very well at all. I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible, and you can drill down other information carrying systems to that level, and then use that knowledge to build reliable systems. Biology does not work…

I bet there is way more quantum phenomena reasons involved in why that system was selected for being less fragile and having better stability/survaibability for a wider range of cases. Thinking in classical compute terms there is like asking for robots that inevitably break without the slightest chance of self repair, much less do it at minimal effort.

Yeah I think there's a paper about how brains most likely represent some things with quantum states which may explain why we don't understand them yet.

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

#62

Post by titzer »

koeng wrote: post #53

I’ve worked in a lab of one of the original folks working on genetic logic gates, and honestly, no they don’t really work very well at all. I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible, and you can drill down other information carrying systems to that level, and then use that knowledge to build reliable systems. Biology does not work…

> I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible, and you can drill down other information carrying systems to that level, and then use that knowledge to build reliable systems.

It doesn't matter what Turing-complete model you have; they are all equivalent, even if exponentially slower than another. And no, binary logic is not the most abstracted version possible. Clearly lambda calculus is....ok, just kidding. You can build a universal computer out of just two stacks, out of subtract-and-jump-if-zero, and a lot of other things. (https://gwern.net/turing-complete)

I don't think computer scientists really think that binary logic is the only computation paradigm that makes sense, it just happens to be one that we can make extremely fast and extremely reliable realizations of using electronic circuits. It's been phenomenally successful.

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

#63

Post by Daub »

marginalia_nu wrote: post #29
Daub wrote: post #4

I teach a creativity and innovation course at my uni. There are many examples I share with my students of inventions which started life as observations of nature (e.g. Velcro came about from observing how burrs stick to the fur of the inventor's dog). My bones tell me that there are discoveries about computing waiting to be made from observing how things are done in nature, particularly in the human mind. I imagine t…

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.

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

#64

Post by Daub »

gilleain wrote: post #30
Daub wrote: post #4

I teach a creativity and innovation course at my uni. There are many examples I share with my students of inventions which started life as observations of nature (e.g. Velcro came about from observing how burrs stick to the fur of the inventor's dog). My bones tell me that there are discoveries about computing waiting to be made from observing how things are done in nature, particularly in the human mind. I imagine t…

I recommend this book a lot, but 'Cats’ Paws and Catapults: Mechanical Worlds of Nature and People' ( https://www.goodreads.com/book/show/223609.Cats_Paws_and_Cat... ) is a great look at how biology inspires human design. One idea that is important (IIRC from this book) is that many examples are really inspiration, and not direct copying of design. Biology works very differently to human machines, with very different…

A great reference. Many thanks.

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

#65

Post by martythemaniak »

I got into synthetic bio for a little while and ended up reading this intro textbook: https://www.amazon.ca/Introduction-Systems-Biology-Principle...

If you've taken "Systems Engineering" or "Control Systems" type classes where you learn about oscillators and other high-level control systems work across a variety of engineering disciplines, this is a great into to how these systems are "implemented" and work inside of cells. It's not "IF" and "WHILE" loops, but more like "How are logical circuits such as e.coli path finding algorithms implemented in RNA"

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

#67

Post by [deleted] »

koeng wrote: post #53

I’ve worked in a lab of one of the original folks working on genetic logic gates, and honestly, no they don’t really work very well at all. I think a lot of computer scientists assume that their model of the world (binary logic) is the most abstracted version possible, and you can drill down other information carrying systems to that level, and then use that knowledge to build reliable systems. Biology does not work…

[deleted]

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

#69

Post by thih9 »

curiousParty wrote: post #36
thih9 wrote: post #9

> There are no equivalents of function calls. All events happen is the same space and there is always a likelihood of interference. Proof that code with all functions inlined, with only global variables, with bugs and happy accidents all over the place, eventually gains sentience and becomes self aware.

This isn't proof. Its wishful thinking. We don't yet understand the data structure of DNA fully, we don't know how a chemical storage system that is inherantly inert and relies on nanomachines (that it itself is responsible for providing the code for creating) to be useful even exists, let alone how it was made. How many happy accidents would it take to create cloudflare? This is overwhelmingly more complex than clou…

Looks like we understand it enough to say it's all a big ball of mud[1], at least based on that SO comment. Or are you saying that the comment is wrong? And yes, the effect is more complex than cloudflare. Then again, it is a ~6Gb (~0.85GB) executable blob[2]; this doesn't include the training sets and it took a bit to get there. Who knows, if cloudflare spent 4.5 billion years and a whole planet of resources on their next version, the result might have exquisite UX too (plus an ability to write tangental HN comments, and many more).

[1]: https://en.wikipedia.org/wiki/Anti-pattern#Big_ball_of_mud

[2]: "In humans, the total female diploid nuclear genome per cell extends for 6.37 Gigabase pairs (Gbp)", https://en.wikipedia.org/wiki/DNA#Amount

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

#70

Post by johnnyb_61820 »

DNA is a lot more like an FPGA than a traditional programming language. Basically, everything is wrapped in a while(true) that has conditionals as to whether or not it engages. Promoter sequences are the condition statements, and transcription factors are very similar to variable states, where the concentration of the transcription factor is essentially its value.
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