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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?

#161

Post by roughly »

munificent wrote: post #133
roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

The I think about it is like this: Code is read and maintained by humans, so it is under selection pressure to be comprehensible by human minds. Reality has no such constraint. If the biological processes of some animal lead to inscrutable irreducibly complex "spaghetti code" but the animal is slightly more likely to produce offspring... the complexity wins. The natural world doesn't care whether or not we can unders…

The evolutionary pressure is a root here, but the problem isn't readability, it's the lack of abstraction.

The central dogma is DNA -> RNA -> protein, except that: 1. RNA can fold into a functional molecule 2. RNA can be spliced differently to make several different proteins 3. RNA can bind with proteins to create other functional units 4. The availability of amino acids and TRNA units within the cell affects the speed at which a protein is translated from RNA, which can affect its structure, which affects its function 5. The codon language is not guaranteed identical between organisms, which means the same RNA sequence can encode for different amino acid sequences in different organisms

And that's just in the transcription/translation machinery. That's what I mean when I say there's no abstraction: biology is a physical system, which means molecular & atomic interactions influence every level of every process.

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

#162

Post by stultissimus »

visarga wrote: post #20

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 tr…

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 loops, or function calls?

#163

Post by bossyTeacher »

BenjiWiebe wrote: post #156
bossyTeacher wrote: post #151

Earlier quoted context omitted.

Does it? A button is not equivalent to an input anymore than pulling down a level that initiates a process that culminates in the lighting of a candle.

You put pizzas in and get pizzas out.

Just because you placed an object x inside an object y does not make y a computer -_- Computing is about data

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

#164

Post by roughly »

sjducb wrote: post #134
roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

As a biologist who moved into software engineering I love working with actual machines. You can think of a design, build it and have it work as you expect. You can’t do that in biology. The reason is that we “understand” how computers work. Our understanding of biology is nowhere near that level. A high percentage of established knowledge is wrong or so incomplete that it’s not useful for designing new systems. This…

I think another reason is that biological systems are _fantastically_ complicated - for example, we're finding that the spatial distribution of molecules within the cell affect enzymatic processes in ways that may have implications for alzheimer's and dementia. For another, there's various bacterial communities where, if you want to trace the enzymatic pathway for a particular product, you're jumping between species in the community, and not just once - that particular product is the result of multiple distinct enzymatic pathways in multiple different organisms (and whatever else exists in the environment outside the cell).

I've been a software engineer for 20 years now, I don't underestimate the complexity of computer systems or software - I think the number of people in the world who could really accurately describe every part of every system involved in showing you this note to you is maybe ten - but we've got nothing on biological systems.

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

#165

Post by willy_k »

withinboredom wrote: post #34
tralarpa wrote: post #13

Earlier quoted context omitted.

> whereas it would be very bad if basic operations in a CPU had similar level of error rates Evolution is about mutations when the executable file is copied.

That isn't how evolution works (or at least it is a gross generalization that is borderline wrong). You own cells mutate over your lifetime and the mutations may trigger genetic features across your entire body. Sometimes, these mutations cause errors that we call cancer, but not always. Evolution is when a certain genetic feature provides better fitness (which doesn't necessarily have to come from a mutation), and t…

So evolution is copying the state of a running executable (one that’s poorly memory managed and dependent on external variables) instead of the file itself, and evolution favors favors the copies that survive and maybe even run faster or are otherwise better.

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

#166

Post by __loam »

bossyTeacher wrote: post #163
BenjiWiebe wrote: post #156

Earlier quoted context omitted.

You put pizzas in and get pizzas out.

Just because you placed an object x inside an object y does not make y a computer -_- Computing is about data

We're using the definition you gave.

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

#167

Post by bossyTeacher »

__loam wrote: post #166
bossyTeacher wrote: post #163

Earlier quoted context omitted.

Just because you placed an object x inside an object y does not make y a computer -_- Computing is about data

We're using the definition you gave.

I said input though not "anything"

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

#168

Post by afhfah834 »

sjducb wrote: post #134
roughly wrote: post #129

Something to be aware of as a computer person coming into biology: Biology only _looks_ like it has logical constructs, abstraction layers, and general computational frameworks. When you start working with it, you'll find everything is messier than you expected and everything interacts with everything at every level. There are no abstractions, there are no actual boundaries, and your outputs are subject to evolutiona…

As a biologist who moved into software engineering I love working with actual machines. You can think of a design, build it and have it work as you expect. You can’t do that in biology. The reason is that we “understand” how computers work. Our understanding of biology is nowhere near that level. A high percentage of established knowledge is wrong or so incomplete that it’s not useful for designing new systems. This…

[dead]

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

#169

Post by mcnnowak »

stultissimus wrote: post #162
visarga wrote: post #20

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 tr…

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…

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 loops, or function calls?

#170

Post by huytersd »

visarga wrote: post #20

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 tr…

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.
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