Ask HN: Can we think of DNA as Infrastructure as Code

I&#x27;ve both worked with infrastructure as code, Pulumi, and was a grad student researcher in bioinformatics for several years, and I&#x27;ve developed the following take:<p>Biology is messy, tangled, and sloppy system built over a billion years under evolutionary pressure. There&#x27;s no clear analogy to intelligently designed software, and anytime you make an analogy, like DNA == Source code, there&#x27;s a mechanism which would destroy it&#x27;s predictive power to explain biological phenomena. Like with DNA, computer software doesn&#x27;t create the machine it&#x27;s executed on, code is 1d, while DNA is definitely multi-dimensional, where it&#x27;s folding, epigentic modifications, and other modifications matter a lot.<p>All the interesting biology for complex animals happens during the first few stages of development. There&#x27;s no computational equivalent to this recursively constructive process. Additionally, biology has a single guiding principle through which we understand everything: evolution, and using computer analogies really diminish that.<p>Therefore, biology is biology. It&#x27;s not analogous to a Von Neuman architecture machine, or any other computing device we&#x27;ve created. The first principles are simple different.

Chromatin, not just DNA. Anyway, the &quot;code&quot; category is too simple to describe what is actually happening. There is a sort of nanoscale industrial cyber-bio-physical-chemical plant&#x2F;factory&#x2F;machinery&#x2F;complex within each cell. If you consider CS-stuff as an analogy, you might miss the &#x27;physical-chemical&#x27; aspect of it all. Like, you know, you would not call an autonomous android with embedded micro chemical facility just a computer or server. Yes it is also a computer, yes it runs some code, but it is moving, it is chemically very active, it has sort of initiative capabilities. cs analogies are way too barren.

You might be interested in reading some of Bert Hubert&#x27;s articles, specifically &quot;DNA seen through the eyes of a coder&quot;: <a href="https:&#x2F;&#x2F;berthub.eu&#x2F;articles&#x2F;posts&#x2F;amazing-dna&#x2F;" rel="nofollow noreferrer">https:&#x2F;&#x2F;berthub.eu&#x2F;articles&#x2F;posts&#x2F;amazing-dna&#x2F;</a>

There is no direct parallels. And guess what - the brain is not even a computer.<p>Everything this was just metaphors for non experts, irrelevant contexts and making money on pseudo science books.

Not as Infra as Code but you could think of it as another stack with its own architechture and programming language. Also runs on jelly instead of electronics.

What always surprised me is not DNA, but how other non-living things can exist at all without DNA. It makes sense to me that I have green eyes since that&#x27;s what my DNA says... but where is defined that a rock has a particular color or weight or texture?<p>Whenever I think of how planets move around a star, I always think &quot;Ok. So, I imagine that at some point the universe should know the distance between planet X and star Y, and also, probably, maybe, it should know their masses... but that data is nowhere defined (that we know). So, is the data computed &#x27;on the fly&#x27; every $minimal-unit-of-time?). Perhaps the universe doesn&#x27;t need to know distances nor masses, though.

Yes, but the computer that runs the code is the body that grows it, and each one is different.

Computation is everywhere. Read about CRISPR and tape based Turing machines.

We can if we&#x27;d like to but remember that it&#x27;s an analogy, no matter how useful, inspiring or beautiful the connections might be.<p>I don&#x27;t like this analogy too much because it collapses &quot;DNA&quot; into a singular thing that&#x27;s somehow related to classical computing, even though there&#x27;s no indication that DNA and the multiple layers of systems interacting with it are limited in the same ways as classical computers.<p>I prefer to think of the DNA as a medium for memory, one of many mediums for memory.<p>Memory is everywhere, whether or not anyone or anything remembers it.

A better analogy for DNA in computer science would be LLMs. Each organism&#x27;s DNA represents an experiment being performed in service of training a model. If that experiment manages to procreate, its successful mutations graduate into another round of experiments.<p>This has gone on for several billion years, resulting in a largely stable model within which experiment are continuing to be run.<p>As with LLMs, DNA doesn&#x27;t know anything about the data it is being trained on (&quot;Nature&quot;). And that model continues to change even as the experiments are run.<p>So DNA is a &quot;blockchain&quot; record of previous and current hypotheses on which traits enable an organism to live to viability. Some of these hypotheses are &quot;dead code,&quot; as the environment no longer contains the pressure which made them critical. Some of them are essential to viability. Some of them are experiments whose value has not yet been determined.<p>Assuming your question is whether IaC could learn from patterns in DNA, I think that&#x27;s a very interesting idea. Certainly we desire that every loadbalancer, database, and iam policy be capable of self-defense, and be the hardiest, most fit version of itself possible.<p>Where the analogy struggles is that people writing IaC are more in the business of designing &quot;natures&quot; than they are designing individual organisms which would survive a chaotic and hostile &quot;nature&quot; being enforced on them. And people who write IaC might be unhappy to hear that getting to a &quot;viable&quot; database would require launching several thousand databases in an environment and, after some period of changes, seeing which one is performing best so they can clone that &quot;best&quot; database configuration when new databases are needed.

You could, but DNA is a terrible &quot;language.&quot; It&#x27;s unreliable , degrades over time, accumulates and perpetuates errors, and if you use instructions in an order the compiler doesn&#x27;t like, you&#x27;ll get origami (loops, hairpins) instead of a program.

Unfortunately, the world didn&#x27;t need a first Gödel, Escher, Bach pseudoscientific conspiracy theory pin board that falls in love with the idea of beautiful ideas over the nuances of reality and the incomparable contrasts of entirely different things.

I learned about DNA transcription and translation while learning about mRNA vaccines in 2020. Here&#x27;s how I explained the process to myself:<p>1) DNA = source code on disk<p>2) RNA polymerase = disk read head<p>3) RNA = source code &#x2F; functions loaded to memory<p>4) Ribosome = JIT compiler<p>5) Proteins = small, single purpose executables (like unix commands)<p>6) Proteins once outside the cell = execution<p>If you think of the body as the hardware, then yes, there is some merit to thinking of DNA as infrastructure as code, operating system <i>and</i> application software.

I think Michael Levin would disagree:<p><a href="https:&#x2F;&#x2F;www.youtube.com&#x2F;watch?v=p3lsYlod5OU">https:&#x2F;&#x2F;www.youtube.com&#x2F;watch?v=p3lsYlod5OU</a>

Sure. <a href="https:&#x2F;&#x2F;youtu.be&#x2F;kbJxl7HU480" rel="nofollow noreferrer">https:&#x2F;&#x2F;youtu.be&#x2F;kbJxl7HU480</a>

genetic algorithms were stolen by the latter from the former

definitely not, go and look up epigenetics

DNA is a form of code, but it doesn&#x27;t encode programs. Instead, like an STL or STEP file it encodes HARDWARE designs.<p>While you could think of it as encoding infrastructure AND code (as in IaS) you&#x27;d need to go beyond that to include the hardware for computing AND physical function (like a whole car + computer) in that conception, which is not what IaS means.<p>The hardware side of DNA is easy to overlook since we don&#x27;t yet have the necessesary (CAD) design tools to easily understand the shape and mechanics of proteins just from reading a DNA sequence like we do for macroscale 3D models. But there are hard technological reasons for this.<p>DNA encodes information, but instead of binary organized into 8-64 bit bytes (10010110) it uses four base pairs (ATCG) organized into 3 letter codons, each of which represents one amino acid.<p>The cell assembles chains of amino acids which are then placed in an &quot;oven&quot; where the string of molecules folds back on itself to assemble a complicated and functional 3D shape.<p>When we say complicated, we really do mean complicated. Even the fastest modern super computers are unable to determine the shape of these protein based only on the DNA sequence input. Further, we are unable to simulate the way that a folded protein will interact with other molecules reliably.<p>Fortunately these kinds of problem will someday be easily solved by quantum computers, but for now we are stuck with approximations of questionable accuracy.<p>But there are very computer code-like elements to how cells work. Unfortunately it is all spaghetti code. One section of DNA often codes for proteins which bind to one or more other sections of DNA either increasing or decreasing the activity production of the proteins from those locations.<p>Additionally, some DNA sections code not for protein but RNA strings which are used mechanically by themselves or as part of proteins like CRISPER. RNA is always created as an intermediate step between DNA and Protein, but in this case it is used directly as fRNA (functional RNA). RNA can even fold on itself and act similar to proteins though it is much more fragile.<p>The many interactions between protein, DNA and RNA perform a kind of computation but it is very obfuscated.<p>The following are generalized interactions that take place in a cell (perhaps analogous to machine instructions) written in a kind of pseudocode, to help illustrate the recursive functions involved.<p>DNA + Protein = RNA;<p>RNA + Protein = Protein;<p>Protein = Protein++;<p>Protein = Protein--;<p>Protein = RNA++;<p>Protein = RNA--;<p>RNA = RNA++;<p>RNA = RNA-+;<p>RNA = Protein++;<p>RNA = Protein--;<p>Protein + RNA = DNA;<p>Any protein or fRNA can have multiple functions in a cell and affect the production other proteins and fRNAs by interacting with DNA or RNA or with other Proteins involved in the production chain. In addition to this, proteins and fRNA also physically move around other proteins and molecules and make up the structure and machinery of a cell.<p>Untangling it all is close to impossible currently. There is several billion years worth of tech debt and zero documentation.