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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?

#71

    IF : Transcriptional activator; when present a gene will be transcribed.
    WHILE : Transcriptional repressor; gene will be transcribed until repressor is not present.
as stated, IF and WHILE are equivalent (the WHILE is some variation of a contrapositive of an IF)

secondly, it doesn't make sense that a "repressor" would cause transcription unless it is absent, since " A transcriptional repressor is a protein that regulates gene expression by inhibiting the initiation of transcription".

It is a repressor's PRESENCE that inhibits expression, not it's ABSENCE. Hence it would make more sense to say "Transcriptional repressor; gene will be transcribed until repressor is PRESENT."

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

#72
nope, chemistry/physics involved & dna processint doesn't work that way. (Msc Comp.sci&Bioinformatics / sw engineer here)

it's very much about physical environment and chemical reactions happening (all in parallel) and molecules with different sizes/shapes interacting in specific conditions not instructions for specific computer architecture being executed.

ps. i'm not saying its not possible, it's that it doesnt happen that way in living cells.

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

#74
post #62
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…

Is it not true that some of the confusion stems from the mistaken idea that DNA is computing/computable? One might make logic gates out of plumbing, but the plumbing at my house isn't some 0.1Hz computing device, it's indoor water so I can boil pasta, brush my teeth, and flush away smelly waste.

DNA's primary (though maybe not only) function is to act as a blueprint for constructing proteins. What little logic exists in it naturally has to do with conditionally expressing those only when it is advantageous to the organism. That's not necessarily the same thing as a logical if.

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

#75
post #62
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…

I don't think GP implied that you cannot simulate cell chemistry on a Turing complete machine to a reasonable accuracy given enough resources. I think the point was that you can't think of genes as logic gates.

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

#76

Earlier quoted context omitted.

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.

There are many such papers. However they need to be understood as extremely speculative, if not outright woo-woo, as there is currently no reason to believe that the brain is capable of maintaining any sort of even modestly-large-scale entanglement properties.

These papers, and people commenting on them, also often appear to believe that just finding that entanglement is happening would itself mean something; it's not hard to read them as basically saying "and we found the 'Here There Be Magic' in the brain!" They don't even seem to speculate as to what the entanglement and "quantum" would be doing. What visible difference would it make versus a non-"quantum" brain? How could we determine that the brain is using "quantum" to do something that could not otherwise be explained or is somehow irreducible to some otherwise-classical phenomenon? Not only do I not see answers, not only do I not even really see theories, I don't even see much recognition that the question exists.

We have quantum computers right now. They are small, but they are fully quantum. They don't do anything by virtue of their quantumness. They aren't sitting there being ambiently quantum. They have to be set up, then executed, then answers read out, and the way in which they deviate from non-quantum computers is actually perfectly mathematically characterizable. And it is not clear to me exactly how those differences are supposed to be useful to describing how a brain works even if functioning quantum computers can be found. Basically, the problem of how a brain works is so vast that the question of whether or not it has some sort of quantum computer in it sinks without a trace, and certainly without providing any sort of explanation at the present time.

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

#77

Earlier quoted context omitted.

Yes it was nature that figured out ai neural nets are efficient not humans implementing algorithms that found out that nature makes efficient use of neural nets. Aliens will first have to make contant and dully learn how to use neural nets to develop intelligence. A catch 22.

What I mean by aliens using neural nets is that we don't know what percent of evolved intelligent species would have neural nets as an integral part of their cognition like we do. And we don't know what alternative paths there are to the evolution of intelligence.

I think the way life is built on earth is the rule throughout the universe. For any type of organic “computation” there needs to be something similar to a neural net. Perhaps a different “implementation” but it should be largely the same.

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

#78
post #62
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…

you are limiting computation to discrete computation.

Biology is analog, which is a whole different ballgame compared Turing completeness. And extremely hard to replicate with digital paradigms

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

#79
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

This is a giant problem with software engineers, which makes us quite obnoxious.

We have mental models that work for understanding computers, and then go misapply that those models to everything else in the universe. Frequently that turns into arrogance, by insisting the right way to think anything is in computer-terms, and every other way of thinking is inferior and wrong. Then you get stuff like Engineer's Disease, where you get some software guy lecturing actual experts in other fields about how they're doing it all wrong, or declaring alien fields to be nonsense because they're different.

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

#80
IF lactose is present in the extracellular environment && IF glucose is NOT present in the extracellular environment:

Activate the lac operon and transcribe the genes for lactose uptake and metabolism, entering a while loop:

WHILE lactose is present: Keep transcribing those genes.

However, this is not the DNA acting alone, it's just a component in the cellular system. The cell (E. coli in this case) is always generating a minimal amount of lactose and other sugar transporters, which act as sensors in the cell membrane that trigger feedback loops (otherwise, how would the cell ever know lactose was present?). If glucose is present, E. coli uses it preferentially and downregulates other sugar uptake and metabolism genes. This is all fairly analog rather than digital, i.e. genes that are 'turned off' may still be transcribed at a very low level.

DNA is probably more comparable to RAM, and the CPU perhaps comparable to the transcriptome (DNA -> mRNA) and the ribosome (mRNA -> protein), and overall the cell is running something comparable to a parallel multi-process fetch-decode-execute cycle.

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