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

464 点作者 ent101超过 1 年前

52 条评论

visarga超过 1 年前

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] <a href="https://en.m.wikipedia.org/wiki/Gene_regulatory_network" rel="nofollow">https://en.m.wikipedia.org/wiki/Gene_regulatory_network</a>

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Daub超过 1 年前

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 the result to be fundamental: changing the very nature of how computing is conceived of.

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robviren超过 1 年前

I always think of DNA a lot like programming over the course of millions of years. A strung together series of hackish, barely functioning, uncommented code with no documentation whatsoever. Any reason for why a snippet of code ended up being the way it is has been completely lost to time. All we know is that changing it is bad, certain chunks of code lead to certain behavior, and that the more we look at the code the code spaghetti like it appears.

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fjfaase超过 1 年前

The KMT2D gene [1] is one example of a gene that I know of that regulates the express of other genes. Defects to this gene often result in the people having the Kabuki Syndrome [2].If I remember correctly, Bert Hubert in his talk 'DNA: The Code of Life (SHA2017)' [3] gives an example of an IF-behaviour.[1] <a href="https://en.wikipedia.org/wiki/KMT2D" rel="nofollow">https://en.wikipedia.org/wiki/KMT2D</a>[2] <a href="https://en.wikipedia.org/wiki/Kabuki_syndrome" rel="nofollow">https://en.wikipedia.org/wiki/Kabuki_syndrome</a>[3] <a href="https://www.youtube.com/watch?v=EcGM_cNzQmE" rel="nofollow">https://www.youtube.com/watch?v=EcGM_cNzQmE</a>

nihzm超过 1 年前

Related to the first answer: Tim Blais on youtube has made a catchy "edutainment" song [1] on molecular machines based on A. Leigh's research (eg [2]) with some cool animations that show how electrochemical "switches" can encode a binary state, which one could (in principle) use to build logic gates.[1]: <a href="https://www.youtube.com/watch?v=ObvxPSQNMGc" rel="nofollow">https://www.youtube.com/watch?v=ObvxPSQNMGc</a>[2]: <a href="https://pubs.acs.org/doi/10.1021/acs.chemrev.5b00146" rel="nofollow">https://pubs.acs.org/doi/10.1021/acs.chemrev.5b00146</a>

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dawnofdusk超过 1 年前

An interesting question because all of this genetic encoding and expression is probabilistic at its very core (it has to be, otherwise there wouldn't be evolution), whereas it would be very bad if basic operations in a CPU had similar level of error rates.Interesting to me how the top comment has talked about constructing logic gates out of biological circuits. I wonder if anyone has done the opposite, i.e., write a probabilistic programming language whose operations are under the same amount of noise as a cell?

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photochemsyn超过 1 年前

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.

zubairq超过 1 年前

I’ve always wondered about DNA from a programming language point of view and always thought it was more like a data structure than a language

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martythemaniak超过 1 年前

I got into synthetic bio for a little while and ended up reading this intro textbook: <a href="https://www.amazon.ca/Introduction-Systems-Biology-Principles-Biological/dp/1584886420" rel="nofollow">https://www.amazon.ca/Introduction-Systems-Biology-Principle...</a>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"

rsingla超过 1 年前

For an individual interested in computational biology, or George church's course is excellent.From the description: "This course will assess the relationships among sequence, structure, and function in complex biological networks as well as progress in realistic modeling of quantitative, comprehensive, functional genomics analyses. Exercises will include algorithmic, statistical, database, and simulation approaches and practical applications to medicine, biotechnology, drug discovery, and genetic engineering."<a href="https://ocw.mit.edu/courses/hst-508-genomics-and-computational-biology-fall-2002/" rel="nofollow">https://ocw.mit.edu/courses/hst-508-genomics-and-computation...</a>

platz超过 1 年前

<pre><code> IF : Transcriptional activator; when present a gene will be transcribed. WHILE : Transcriptional repressor; gene will be transcribed until repressor is not present. </code></pre> 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."

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arketyp超过 1 年前

It's curious how DNA and enzymes are quite literally like a Turing machine tape and head.

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Alpha3031超过 1 年前

Carroll is probably one of the better known researchers focusing on the evolution of cis-regulatory elements, non-coding sequences which regulate the expression of nearby genes. I would consider his 2005 book Endless Forms Most Beautiful to be a reasonable introduction. For something more less pop-sci I understand Davidson and Peter's (2015) Genomic Control Process has been fairly well received, as well. Though both are on the older side of things now, and admittedly I'm not too familiar with the current literature, they would probably be my recommendations. There are also non-gene regulatory elements of course.

lo_zamoyski超过 1 年前

The question is misleading because computation is not an objective phenomenon in nature (save in the minds of observers). You can interpret natural phenomena computationally, sure, and there may well be a way to do this with DNA (in fact, some have done that). But there's no computation "out there". Even the computer in front of you isn't objectively computing. It behaves in a way that corresponds with a computational interpretation, but nothing going on inside of it is a computation operation per se.

gameman144超过 1 年前

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.<a href="https://en.m.wikipedia.org/wiki/Riboswitch" rel="nofollow">https://en.m.wikipedia.org/wiki/Riboswitch</a>

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DoreenMichele超过 1 年前

IF-statements: An IF statement executes the code in a subsequent code block if some specific condition is met.Cell chemistry can impact production of the protein strings DNA codes for and can impact if they are even functional.Not a programmer, so maybe that's not a good analogy. But it's what came to mind as an amateur student of "Exactly how do my defective genes make my life a living hell?"

shpx超过 1 年前

What about length prefixed strings? There's obviously "byte" terminated strings (start and stop codons) but there's probably situations where it makes sense for biological systems to store the length (or likely reading different lengths produces different molecules, as a form of compression) at the beginning and count it out.

markzporter超过 1 年前

This set of slides provides a good rundown of some of the work done in DNA computing: <a href="https://cs.uwaterloo.ca/~lila/pdfs/Computing%20with%20DNA.pdf" rel="nofollow">https://cs.uwaterloo.ca/~lila/pdfs/Computing%20with%20DNA.pd...</a>Notably solving TSP using the mechanics of DNA. Very interesting!

hnthrowaway0328超过 1 年前

Judging from:>It is also to be noted that DNA is just a set of instructions and not really a fully functional entity (it is functional to some extent). However, even being just a code it is comparable to a HLL code that has to be compiled to execute its functions. See this post too.Maybe microcode?

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AlbertCory超过 1 年前

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?)

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drones超过 1 年前

With our archaic use of Von-Neumann architecture, bacteriophages must think so little of us.

gwern超过 1 年前

<a href="https://www.lesswrong.com/posts/bNXdnRTpSXk9p4zmi/book-review-design-principles-of-biological-circuits" rel="nofollow">https://www.lesswrong.com/posts/bNXdnRTpSXk9p4zmi/book-revie...</a>

wcoenen超过 1 年前

To get a glimpse of how cell "logic" works, I think clocks are a nice starting point.<a href="https://www.youtube.com/watch?v=nq7v1Z2SmdQ" rel="nofollow">https://www.youtube.com/watch?v=nq7v1Z2SmdQ</a>

marvinborner超过 1 年前

(Slightly) related: Chemlambda[1], simulating combinatory logic and lambda calculus with molecules.[1] <a href="https://chemlambda.github.io/index.html" rel="nofollow">https://chemlambda.github.io/index.html</a>

cariaso超过 1 年前

<a href="https://berthub.eu/articles/posts/amazing-dna/" rel="nofollow">https://berthub.eu/articles/posts/amazing-dna/</a>

kovacs_x超过 1 年前

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.

sojuz151超过 1 年前

Alternative splicing is another way of including IF statements. Depending on many conditions some parts of the RNA might be added/removed before the translation

kul_超过 1 年前

I misread this for some reason and I am now interested to know if DNS can be made to work dynamically this way instead of being just preconfigured static records?

feverzsj超过 1 年前

It's like reverse engineering alien technology.

Sparkyte超过 1 年前

That is an interesting thought. I take this with a grain of salt, one gram of DNA is supposedly 455 exabytes of data.

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JoBrad超过 1 年前

So in Biology everything is a global variable and side effects are the standard. Got it.

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nyxtom超过 1 年前

We are never going to move beyond this analogy are we? We seem to be stuck here :/

Rezhe超过 1 年前

Rather than programming languages it sounds like a nature language.

kirykl超过 1 年前

Maybe it does but in a higher dimensionality that we cannot see

bilsbie超过 1 年前

I feel like the only possible answer is “we don’t know”

sargstuff超过 1 年前

Programming languages typically operate in middle of one higher/ one lower order level of logic.DNA describes hyperbolic multi-level of logic.The lowest level programming language (assembly) is designed tomap/correspond/translate directly to hardware electronic bits.Where, cpu emulates version of turing machine on assembly instructions.And cpu/hardware is under control of OS ( post-pc boot strap ).---The mapping between hardware & assembler may static (compiled) orinterpreted in real-time into a sequence of boolean AND's and OR's.At the assembly programming language level, the programming language'TERMINAL' construct is 1:1 with hardware. Such abstractions typicallyconveyed using BNF and/or various calculi such epsilon and lambda.As one progresses through higher level programming lanugages, have towork one's way through more and more non-ternmal instructions (aka grammar)to get to just the TERMINAL value to access that 1:1 mapping to 'run'.---Given constraints on article length, going to reduce the bodies hyperbolic geometrydescriptions down to a simplified analytic geometric analogy via bodies largest organ -- the skin.Can look at the skin as mobious strip where, gi tract is internal side compliment of external skin.Organs can be views as klein bottle chained together & interact/influence each other (per flow throughklein bottle opening and/or perfusion of klein bottle surface.Scaling down the cline bottle to cell & simplfied 2d spread sheet -- side a, side b and how progress between a & b.The external/internal enzymes, dna, vitimins/minerals etc influence what happens on the spreadsheetvia dna bnf / 4 symbol autonoma system and/or L-system.internal function calls equivalent to specific inter-cel functions per triggered by cell resources.Obviously, organs/cells need 'external function calls/libraries' to work, which are not covered here.While loops / if loops defined by enzyme/protines/etc created by dna interpretations. akawhile enough protine a exist -> create enzyme b. IF enzyme asdf exists -> create protine 1234---So, dna can be viewed as a type of turing machine aka has if / while / etc.. forms of expression.the rest of the body is just a lambda calculi / epsion calculi / process calclui interpreter/executor.DNA as the ultimate hyperbolic turing paper tape version of the Zark king[0]The unbounded creaping feature creature take to the extreme over a few millenea.---[0] : <a href="https://manybutfinite.com/post/the-thing-king/" rel="nofollow">https://manybutfinite.com/post/the-thing-king/</a>

pockmockchock超过 1 年前

isn't mRNA, crisper, prime-editing doing exactly that?

dazhbog超过 1 年前

Ghidra plugin for DNA blobs, anyone?

__loam超过 1 年前

It does not.

thih9超过 1 年前

> 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.

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psyklic超过 1 年前

In grad school, I (briefly) researched synthetic DNA logic gates. Using these, you can build neural networks in DNA [1] and probabilistic switching circuits (my co-authored paper) [2].To do this, you design DNA strands that bind to each other in designated regions when mixed.To make a logic gate, you just make some bindings conditional on other bindings. To detect that the gate is closed, you make the final binding uncover a fluorophore, which is detectable by a machine. (This is all called a *displacement cascade*.)Using our techniques, the DNA bindings could not be undone. However, I imagine that a source of new DNA strands to replenish the old would effectively implement re-callable functions.[1] Neural nets in DNA: <a href="http://qianlab.caltech.edu/nature10262.pdf" rel="nofollow">http://qianlab.caltech.edu/nature10262.pdf</a>[2] Probabilistic switching circuits: <a href="https://www.pnas.org/doi/full/10.1073/pnas.1715926115" rel="nofollow">https://www.pnas.org/doi/full/10.1073/pnas.1715926115</a>

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koeng超过 1 年前

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 that way. Its fundamental abstraction is different (mostly one of massive interconnectedness). Engineering logic gates and the like, mostly, doesn’t actually allow you to build better genetic circuits.

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subroutine超过 1 年前

All the various logic gates have been observed in (DNA) gene expression studies - both naturally occurring and bioengineered tools. In particular there are tons of bioengineered tools for inducible gene expression that have all manner of gating mechanisms for precise temporal control of expression (triggered by behavior, environment, drug, elapsed time, etc.).Reading...<a href="https://en.wikipedia.org/wiki/Cre-Lox_recombination?wprov=sfti1" rel="nofollow">https://en.wikipedia.org/wiki/Cre-Lox_recombination?wprov=sf...</a><a href="https://en.wikipedia.org/wiki/Receptor_activated_solely_by_a_synthetic_ligand?wprov=sfti1" rel="nofollow">https://en.wikipedia.org/wiki/Receptor_activated_solely_by_a...</a><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802553/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2802553/</a><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772104/" rel="nofollow">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772104/</a>

akira2501超过 1 年前

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, which makes DNA something like an environmentally sensitive memory subsystem for RNA.Which I've always wondered if this mechanism is involved in how the homeobox genes work to alter genetic express across the "floor plan" of the body.Anyways, I guess all this means, to whatever extent you might be able to identify programming "constructs" within the system, the overall effects are going to be dominated by noise and emergent behaviors, and the overall mode of the system is one of "feedback control loops."

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i000超过 1 年前

To give a concrete examples1. The HOXD gene cluster adopts a mutually exclusive conformation. IF it "folds" to the left if results in the formation of digit bones ELIF it folds to the right of arm bones ELSE no bones etc. (very very roughly speaking): <a href="https://www.science.org/doi/10.1126/science.1234167" rel="nofollow">https://www.science.org/doi/10.1126/science.1234167</a>2. Another example are olefactory receptors, each olefactory sensory neuron (the cell that "smells") chooses to activate one out of a long array of possible receptors each specific to some smells. So somehow, somewhere a XOR logical operation is "computed" to "pick" <a href="https://europepmc.org/article/pmc/4882762" rel="nofollow">https://europepmc.org/article/pmc/4882762</a>

roughly超过 1 年前

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 evolutionary pressures even when sitting in a flask. Many an engineer has washed aground on the rocky shores of biological indeterminism - it's not a machine, no matter how much it kind of looks like one when you squint at it.

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6177c40f超过 1 年前

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.

corethree超过 1 年前

It's more like a 3d printer. But that 3d printer can print a computer which in turn has while loops, function calls and if statements.

dekhn超过 1 年前

Yes, DNA has rough equivalents to condition logic and loops, although not in a way that is as engineerable as a digital computer with a stack. The op-amp (which is a transistor that uses feedback, typically to amplify) is the one element that has a close analogy (hah) in biology (feedback systems based on transcription-controlling regulatory proteins).The other really cool example taht came up early in my education is the yeast mating switch. Yeast (s. cerevisiae) can be one of two "genders" and can only mate with the opposite gender. Yeast can change their gender: they keep two copies (alternates) of a single gene, and "cut/paste" one of the alternates into a different "currently active gender" location (<a href="https://en.wikipedia.org/wiki/Gene_conversion" rel="nofollow">https://en.wikipedia.org/wiki/Gene_conversion</a> is the general process, <a href="https://en.wikipedia.org/wiki/Mating_of_yeast#Mechanics_of_the_mating_type_switch" rel="nofollow">https://en.wikipedia.org/wiki/Mating_of_yeast#Mechanics_of_t...</a> is the mechanical process in yeast). It has some similarity to a flip flop.So I think the right level to think at is not the abstraction of computer programming languages, but circuit elements. Which is what makes these brilliant articles so much fun: <a href="https://www.cell.com/cancer-cell/pdf/S1535-6108(02)00133-2.pdf" rel="nofollow">https://www.cell.com/cancer-cell/pdf/S1535-6108(02)00133-2.p...</a> and <a href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005268" rel="nofollow">https://journals.plos.org/ploscompbiol/article?id=10.1371/jo...</a>To cut to the chase, engineering biology is a major pain due to the long evolutionary history of biological mechanisms, which makes them somewhat esoteric and abstruse. there is so much that can be said, but over tme, I've found that expounding on this is not very helpful.

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scrozier超过 1 年前

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 (the current state of) simple logic constructs. And that's the day I learned why we still have "wet" labs, to actually test things empirically, rather than vainly try to predict them computationally. :-)

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johnnyb_61820超过 1 年前

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.

bmartin13超过 1 年前

I'm pretty sure something this complex came from a higher order being. That whole order from chaos argument is not holding water for me with this degree of complexity.

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