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Re:Does DNA have the equivalent of IF-statements, WHILE loop... by visarga on Wednesday January 10, 2024 @04:31AM (#38938180)
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 transcription factors are inhibitory. [1]

These networks are similar to neural networks in that they process information through a series of interconnected nodes (genes and proteins, in the case of GRNs) that influence each other's activity. The activation or inhibition of one gene by a transcription factor can trigger a cascade of events, much like the way neurons activate each other in a neural networks.

[1] https://en.m.wikipedia.org/wiki/Gene_regulatory_network

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by Garlef on Wednesday January 10, 2024 @04:41AM (#38938268)
Before anyone jumps to esoteric conclusions:

This is more likely a result of neural networks being very general: General in the sense that they are able to approximate/model a lot of dynamic systems that allow operadic composition.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by fasterik on Wednesday January 10, 2024 @05:34AM (#38938652)
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?
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by gumballindie on Wednesday January 10, 2024 @05:39AM (#38938700)
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.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by fasterik on Wednesday January 10, 2024 @05:44AM (#38938738)
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.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by gumballindie on Wednesday January 10, 2024 @10:01AM (#38939602)
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 loop... by mewpmewp2 on Wednesday January 10, 2024 @11:35AM (#38940399)
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 loop... by gumballindie on Wednesday January 10, 2024 @11:43AM (#38940492)
> now have proof in terms of intelligence of ChatGPT

What.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by CamperBob2 on Wednesday January 10, 2024 @12:35PM (#38940986)
You are intelligent. But we could get an equally-intelligent reply out of ChatGPT. Ergo, it's also intelligent.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by gumballindie on Wednesday January 10, 2024 @01:07PM (#38941345)
Yeah no, that's bullshit. It's like saying my laptop emits sound, meaning it can sing.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by mensetmanusman on Wednesday January 10, 2024 @05:30PM (#38944336)
ChatGPT is a type of intelligence just like a dog or a bird is a type of intelligence.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by gumballindie on Wednesday January 10, 2024 @06:47PM (#38945292)
Yup, the world has gone mad. Flat earthers, anti-vaxxers, now ai intelligence believers.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by mensetmanusman on Wednesday January 10, 2024 @07:29PM (#38945676)
Not sure why saying artificial intelligence is a type of intelligence is controversial, it's in the name...

It's definitely not human intelligence if that's what you are wondering.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by mewpmewp2 on Wednesday January 10, 2024 @07:39PM (#38945759)
Hmm... What are you, an ATM machine believer?
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by gumballindie on Wednesday January 10, 2024 @08:05PM (#38946028)
Corporations tried selling us intelligent fridges for decades. It doesnt mean it was true. Nor does it mean a procedural text generator is intelligent. It performs well at emulating intelligence but it’s about as intelligent as a rock - it can be used intelligently but on its own it does nothing.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by guyomes on Wednesday January 10, 2024 @06:42AM (#38938969)
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 time of evolution, functions depending on a lot of parameters appear. Yet Biological Neural Circuits seem quite bad at approximating simple continuous functions such as the multiplication between two numbers.

Gene Neural Network and Biological Neural Circuit are quite impressive structures considering their size, materials, and energy constraints. However if you allow bigger size, more energy, and faster conducting materials, it should be possible to do have faster modeling tools.

Moreover, to better take into account non-linear functions, my two cents is that Perceptrons could be further enhanced using piecewise polynomial functions instead of piecewise linear functions [4,5].

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

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

[3]: https://en.wikipedia.org/wiki/Perceptron

[4]: https://doi.org/10.1109/TPAMI.2021.3058891

[5]: https://doi.org/10.1109/TPAMI.2022.3231971

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by mewpmewp2 on Wednesday January 10, 2024 @11:20AM (#38940255)
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 loop... by guyomes on Wednesday January 10, 2024 @04:31PM (#38943484)
> That seems like almost fundamental emergent idea that is behind all the intelligence in the World.

That is indeed quite nice, yet intelligence seems much more diverse in biological organisms and not always reduced to nodes and edge strengths. The nodes and edges are a way to store data and to modify it that seems particularly well adapted mechanisms based on electricity.

On the other hand, there exists other very different (and slower) biological intelligent mechanisms that are not based on electricity. For example, a tree is perfectly adapted to its environment, capable of taking energy from the sun, materials from the ground, transform it, and so on. Yet the intelligent mechanism that created trees is not based on neural networks as far as I understand it. In this mechanism, the data is stored in DNA, and DNA can be rewriten at each new generation. It is a completely different (and slower) approach.

Finally I agree that the emergence of fast intelligence through neural network is incredible, although for me the first impressive advance is the use of the electricity to speed up the information exchange. The arrangements in nodes and edges could follow naturally from the fact that the transmission of electric signals works better through 1D circuits. The second impressive advance is the way the networks are layered. This is critical and very difficult to have an arrangement of edges and nodes that can both be trained and inferred efficiently. Without the proper arrangement, a biological neural network or a computer circuit is much less intelligent.

Finally in the future we could imagine intelligent mechanisms based on quantum mechanics for example. In this case, it would probably be vastly different from nodes and edges, due to the underlying physical constraints that are different in electricity and in quantum mechanics.

tldr: yes nodes and edges seem fundamental in fast intelligence based on electricity, but other very different intelligent mechanism exist in biological organisms, and other very different intelligent mechanisms could still be invented in the future.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by petsfed on Wednesday January 10, 2024 @12:50PM (#38941142)
Just a sidebar here, I think the urge to jump to esoteric conclusions is very strong because we are (rightly) trained to not expect that nature at large uses the same tools that we have developed. So its very validating (and also kind of unnerving) when we do find the suggestion that we're "right" at a more fundamental level.

Consider that the uncertainty relations in physics fall neatly out of Fourier Analysis, which could suggest that the universe also does Fourier Analysis to figure out where things are and how fast they're going. But really, its that classical interaction is a sort of mechanical Fourier transform.

I think that moment where it feels like we brush against the real clockwork of the universe has an eldritch, cosmic-horror quality to it, which is both addictive and maddening.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by namaria on Wednesday January 10, 2024 @04:43PM (#38943650)
Sure, nothing profound about trillion-strong fleets of self replicating nanobots controlled by chemical computers processing high dimension data about their environments with complex entanglements giving rise to specialized clusters of information processing neural masses, capable of then communicating with other similar entities, building knowledge about data processing and storage over millennia, starting with clay tablets and ending up with advanced machinery that can be used to create elaborate patterns of data flows that can help us peer through the universe, inside our bodies, understand in intricate detail everything that happens across billions of light years and over billions of years.

Nothing profound at all about any of that. Just very general structures.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by forceIsStr0ng on Wednesday January 10, 2024 @01:01PM (#38941270)
Yes this because DNA is a data structure not a physical force.

If DNA of some sequence, then interaction with electromagnetic fields, gravity, strong/weak nuclear force of xyz properties will probably result in mutation along path abc, a theory the speaker must provide replicable statistical analysis to back up or it goes in the bin.

IT obsession with data models has pushed IT workers into pseudoscience that ignores entropy, Lindy effects; structure is mutable. Physical forces are not. Data structures are not physical forces. They’re leaky mental models our biology garbage collects due to entropy and Lindy effects.

Anyway just the take of an EE who finds the obsession with software development bizarre, full of statistical mirages, hallucinated accomplishments.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by stultissimus on Wednesday January 10, 2024 @03:09PM (#38942478)
Synthetic biologist here. This is a good answer, but looking at man-made genetic programs can give us a simplified perspective. We've made significant progress engineering programs that enable human T cells to kill target (cancer) cells _conditionally_ based on their surface marker expression [1]. This is in contrast to conventional CAR-T cells which are already on the market (see Kymriah, etc.). A simple AND gate T cell circuit is currently being tested in humans [2].

Numerous strategies now exist to write cellular decision making programs using synthetic circuits. We are entering an era where we can write DNA programs and put them into people; I wonder how we can interest more CS-minded people in this kind of "synthetic biology as programming", especially as we move from proof of concept studies in bacteria to real trials in humans [2].

[1]: https://pubmed.ncbi.nlm.nih.gov/33243890/ [2]: https://arsenalbio.com/2023/05/16/arsenalbio-announces-prese...

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by FLT8 on Wednesday January 10, 2024 @04:04PM (#38943116)
Sounds exciting, but also a little scary.

I'm imagining a biological variant of eg. Verilog or VHDL, as this seems like the kind of domain where tools that allow for formal verification would be highly desirable.

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by stultissimus on Wednesday January 10, 2024 @04:48PM (#38943717)
This has actually been done for genetic circuits in E coli (bacteria) by Chris Voight's lab at MIT. Their platform is called Cello [1], and it enables interoperation between Verilog/HDL and genetic code. This kind of thing has not yet reached practical utility in human cell engineering, but companies like Asimov [2] are pushing hard in that direction

[1] https://www.cidarlab.org/cello

[2] https://www.asimov.com/

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by mcnnowak on Wednesday January 10, 2024 @03:26PM (#38942618)
Any tips or "get your foot in the door" advice on how someone currently in a CS career, but interested in biology could make this career transition? As a simple CS-minded person, I don't see any LeetCode for synthetic biology sites :)
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by stultissimus on Wednesday January 10, 2024 @04:52PM (#38943775)
Reading life science textbooks and substacks is a great way to get started (see [1], [2]).

Also, there is a major deficit of software engineering talent in biology research (probably because pro SWEs are too expensive for academic labs, and those labs are where much of the foundational research is done). If you have the bandwidth, part time / volunteer work with an academic lab in your area could be a great way in the door.

[1] https://centuryofbio.com/

[2] https://substack.com/profile/11154869-niko-mccarty

Re:Does DNA have the equivalent of IF-statements, WHILE loop... by visarga on Thursday January 11, 2024 @02:22AM (#38948889)
I was hoping someone who knows more that me to correct/expand my comment. Thanks
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by huytersd on Wednesday January 10, 2024 @03:29PM (#38942664)
So it sounds like event based architecture. You send out events in response to other events and the event sender is “regulated” by other events.
Re:Does DNA have the equivalent of IF-statements, WHILE loop... by samuell on Friday January 12, 2024 @07:24AM (#38967225)
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.