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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?

#91

Post by herval »

scrozier wrote: post #89

In middle age, I (a computer science grad and working programmer) went to graduate school for molecular biology. In the early days of studying biological systems, I was struck by how much they were like computer code, or at least logic constructs. I remember to this day the moment I realized that my orderly world of 0s and 1s was being saturated and methylated and energized in ways that were utterly unpredictable by…

Stephen Wolfram's theory is that everything is a massively parallel computation. Pretty fascinating stuff

https://writings.stephenwolfram.com/2020/04/finally-we-may-h...

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

#92

Post by mewpmewp2 »

guyomes wrote: post #49
fasterik wrote: post #39

Earlier quoted context omitted.

It's still an interesting fact that evolution seems to have figured out that neural networks are good at approximating arbitrary continuous functions. We could ask whether intelligent alien species are likely to use neural nets. In other words, are neural nets universal in some sense, or are they contingent to how life evolved on Earth?

From what I understand, Gene Regulatory Network [1] works very differently from Biological Neural Circuits [2]. Finally, Perceptron used in computers [3] is based on arithmetic operations and is again different from any of those two biological mechanisms. However, perceptron appears to be a good tool to model functions that depends on a large number of parameters. What we may infer from that is that after a lot of ti…

To me it seems like the fundamental idea is still the same. You have nodes that are connected to each other with strengths that can change according to feedback and complicated logic emerges from that.

That seems like almost fundamental emergent idea that is behind all the intelligence in the World.

It seems to allow for intelligence to occur, without this type of concept everything would just be random and chaotic.

The point is, how amazing it is that complicated behaviour can arise from this simple idea.

At this point it seems, that neural networks should really be taught at schools as soon as possible.

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

#93

Post by zelphirkalt »

herval wrote: post #91
scrozier wrote: post #89

In middle age, I (a computer science grad and working programmer) went to graduate school for molecular biology. In the early days of studying biological systems, I was struck by how much they were like computer code, or at least logic constructs. I remember to this day the moment I realized that my orderly world of 0s and 1s was being saturated and methylated and energized in ways that were utterly unpredictable by…

Stephen Wolfram's theory is that everything is a massively parallel computation. Pretty fascinating stuff https://writings.stephenwolfram.com/2020/04/finally-we-may-h...

Does he define computation? I am asking because just about everything could be seen as some form of computation, given no definition, duh.

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

#94

Post by 6177c40f »

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,…

I think you'll find some of the tricks that (mostly) viruses use to be interesting. Take a look at ribosomal frameshifting [1], where the viral RNA has a special structure such that at a certain point during translation in the ribosome it will skip back 1 nucleotide (a -1 frameshift; -2 and +1 frameshifts have been observed as well, more rarely), thus changing the whole reading frame.

Viruses use this to encode multiple protein products in a single strand of RNA, a sort of compression. But that's not all. Say that the amount of "0-frame" protein to "-1-frame" protein needs to be at a ratio of 20:1; then if the frameshift occurs with a probability of about 5% (i.e. 5% of the time that the viral RNA is translated), these protein products will then be produced in just the right ratio (this isn't a made up example either, see [2]). So not only does this trick allow for the RNA to be compressed, it also regulates protein expression. All with just one strand of RNA.

[1] https://en.wikipedia.org/wiki/Ribosomal_frameshift

[2] https://en.wikipedia.org/wiki/HIV_ribosomal_frameshift_signa...

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

#95

Post by gameman144 »

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

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

#96

Post by mewpmewp2 »

gumballindie wrote: post #77
fasterik wrote: post #43

Earlier quoted context omitted.

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.

Yeah, the amazing thing though is how such a simple concept can emerge into a very complex behaviour and intelligence.

And the fact that we know that and now have proof in terms of intelligence of ChatGPT, is to me pretty clear that achieving AGI is possible if you crack the way to structure your neural network.

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

#97

Post by pelagicAustral »

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?

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

#98

Post by AlbertCory »

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?)

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

#99

Post by 6177c40f »

One thing I've learned studying biology is that, while there are many decent anologies to computers, biology is really operating on a very different paradigm to the sort of programming most of us are used to.

Biology is based on "primitives" like feedback loops. For example, there are many cases where a protein that gets produced at the end of a signaling chain then goes on to stop or otherwise downregulate its own production (a negative feedback loop, positive feedback loops also exist).

Another fact that biology relies on is that increasing concentration of some molecule is essentially equivalent to increasing probability of some reaction occuring. In a negative feedback loop, for example, as the concentration of the end product increases, the probability of the reaction that that product takes part in that inhibits its own production increases. Systems then evolve such that the maximum amount of inhibition is most likely to occur when the end product is at just the right concentration.

I've often thought about making a programming language that simulates this paradigm to some extent; a probabilistic programming language where logic was implemented as feedback loops.

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

#100

Post by gumballindie »

mewpmewp2 wrote: post #96
gumballindie wrote: post #77

Earlier quoted context omitted.

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.

Yeah, the amazing thing though is how such a simple concept can emerge into a very complex behaviour and intelligence. And the fact that we know that and now have proof in terms of intelligence of ChatGPT, is to me pretty clear that achieving AGI is possible if you crack the way to structure your neural network.

> now have proof in terms of intelligence of ChatGPT

What.

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