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I love thinking about life as computation. Cells are computers, enzymes are functions, ribosomes are compilers, nucleic acids are source code... Enzymes in par

I love thinking about life as computation. Cells are computers, enzymes are functions, ribosomes are compilers, nucleic acids are source code... Enzymes in particular are a lot like unix pipelines. An enzyme catalyzes its substrate's conversion into its product which is the substrate of another enzyme. When cells ingest glucose, it flows through the glycolysis metabolic pathway until it becomes pyruvate, and may be reduced even further depending on available resources. It's a huge pipeline of enzymes. They just kinda float around within the cell and randomly perform their tasks when their substrates chemically interact with them. No explicit program exists, it emerges from the system within the cell. Cell - Computer Enzyme - Function / Process / Filter Substrate - Data Product - Data Metabolic pathway - Program / Script I've been playing in my mind with an idea for an esoteric programming language modeled around enzymes. The program defines a set of enzymes which are functions that match on the structure of data, automatically apply themselves to them and produce a modified version of the input which may in turn match against other enzymes. The resulting program metabolizes input by looping over the set of enzymes and continuously matching and applying them until the data is reduced to its final form. If no enzymes match, the output is the unmodified input.

heavyset_go 1y ago
I think the issue with this way of thinking is that humans think in abstractions. Abstractions don't really exist, they're a product of the human mind, but then we apply them to nature. Calling DNA code, comparing NNs and the brain, etc. But those abstractions fall apart when you look a little too deeply at what actually happens in nature. Is DNA code? Or is it more like a machine? Is it neither, or is it something embedded in such a complex space that our simple abstractions can't capture the full nature of its being? When you look at the nature of DNA, it does more than simply act as code. It can edit and self-modify, self-assemble, self-replicate, it can turn genes on and off, it can perform what can be argued as computations itself. If you limit yourself to thinking of it as code, you might miss crucial ways it exists/performs in real life.
- matheusmoreira 1y ago
  > When you look at the nature of DNA, it does more than simply act as code. > It can edit and self-modify, self-assemble, self-replicate, it can turn genes on and off Unless my knowledge of biology is very outdated or incomplete, all of those things you cited are done to DNA. They don't happen spontaneously. DNA doesn't self-replicate, a whole bunch of enzymes come and actively copy it. Genes don't spontaneously turn on and off, some enzyme comes and attaches or removes a methyl group. DNA doesn't self-assemble, it is actively coiled around histones to form nucleosomes. Bacteria have a huge variety of enzymes for manipulating native and foreign DNA, they have their own CRISPR mechanisms.
  - zmgsabst 1y ago
    I think RNA (in particular, ribozymes) does those things. But DNA is effectively separation of concerns: RNA systems evolved to RNA mediated systems with DNA as more inert and reliable storage and enzymes as more effective catalysts. Or so the RNA world hypothesis goes.
    - matheusmoreira 1y ago
      > ribozymes I learned something new today! Thank you. It's impressive that RNA of all things can be folded in such a way that it also acts like an enzyme.
  - heavyset_go 1y ago
    I'm thinking more of early RNA and DNA life, where ideas like the RNA-world might have happened and applied. RNA can assemble, replicate, and catalyze to form deoxynucleosides in a proto-DNA, without "outside" work needing to happen from enzymes/proteins/etc. Similarly, RNA and DNA "machines" could have existed before cellular life, in which genetic material self-assembled, transferred genes horizontally/vertically, etc, blurring the lines between genes as "code" and something else.
  - dillydogg 1y ago
    There are deoxyribozymes though are far less common than ribozymes. DNA aptamers may also meet your definition of reactions involving DNA but not acting upon DNA.
AfterHIA 1y ago
You're one of those cats that provides a subtle reminder that Dr. Alan Kay (invented the tablet/Xerox ALTO interface) was first a biologist. Thank you for the enlightened smalltalk! (;3)
minkowski 1y ago
Have a look at the join calculus and the "chemical abstract machine" as implemented in JoCaml, e.g., https://sites.google.com/site/winitzki/tutorial-on-join-calculus-and-its-implementation-in-ocaml-jocaml https://sites.google.com/site/winitzki/tutorial-on-join-calc...
dluan 1y ago
You might be interested in Tinkercell, though at this point it may be somewhat outdated and old. There are lots of other more granular systems biology/chemical reaction network software tools, the most ambitious is probably OpenWorm which is still active. Just keep in mind though that you have to think of cells as very slow, but massively parallel computers.
discarded1023 1y ago
Luca Cardelli worked on this stuff a while back [1]. Perhaps "systems biology" [2] might provide an entry to the literature. [1] https://en.wikipedia.org/wiki/Luca_Cardelli https://en.wikipedia.org/wiki/Luca_Cardelli [2] https://en.wikipedia.org/wiki/Systems_biology https://en.wikipedia.org/wiki/Systems_biology
alberth 1y ago
You could also think about life as a "Factory" (instead of a computer) too: HUMAN FACTORY COMPUTER ----- ------- -------- Cell Factory Computer Enzyme Worker Functions Ribosome Assembler Compiler Acids Blue Print Source Code The difficulty with this type of analogy is so many things need these various capabilities that it's not unique to a computer, or a factory or even a human.

heavyset_go 1y ago

I think the issue with this way of thinking is that humans think in abstractions. Abstractions don't really exist, they're a product of the human mind, but then we apply them to nature. Calling DNA code, comparing NNs and the brain, etc. But those abstractions fall apart when you look a little too deeply at what actually happens in nature. Is DNA code? Or is it more like a machine? Is it neither, or is it something embedded in such a complex space that our simple abstractions can't capture the full nature of its being? When you look at the nature of DNA, it does more than simply act as code. It can edit and self-modify, self-assemble, self-replicate, it can turn genes on and off, it can perform what can be argued as computations itself. If you limit yourself to thinking of it as code, you might miss crucial ways it exists/performs in real life.

matheusmoreira 1y ago
> When you look at the nature of DNA, it does more than simply act as code. > It can edit and self-modify, self-assemble, self-replicate, it can turn genes on and off Unless my knowledge of biology is very outdated or incomplete, all of those things you cited are done to DNA. They don't happen spontaneously. DNA doesn't self-replicate, a whole bunch of enzymes come and actively copy it. Genes don't spontaneously turn on and off, some enzyme comes and attaches or removes a methyl group. DNA doesn't self-assemble, it is actively coiled around histones to form nucleosomes. Bacteria have a huge variety of enzymes for manipulating native and foreign DNA, they have their own CRISPR mechanisms.
- zmgsabst 1y ago
  I think RNA (in particular, ribozymes) does those things. But DNA is effectively separation of concerns: RNA systems evolved to RNA mediated systems with DNA as more inert and reliable storage and enzymes as more effective catalysts. Or so the RNA world hypothesis goes.
  - matheusmoreira 1y ago
    > ribozymes I learned something new today! Thank you. It's impressive that RNA of all things can be folded in such a way that it also acts like an enzyme.
- heavyset_go 1y ago
  I'm thinking more of early RNA and DNA life, where ideas like the RNA-world might have happened and applied. RNA can assemble, replicate, and catalyze to form deoxynucleosides in a proto-DNA, without "outside" work needing to happen from enzymes/proteins/etc. Similarly, RNA and DNA "machines" could have existed before cellular life, in which genetic material self-assembled, transferred genes horizontally/vertically, etc, blurring the lines between genes as "code" and something else.
- dillydogg 1y ago
  There are deoxyribozymes though are far less common than ribozymes. DNA aptamers may also meet your definition of reactions involving DNA but not acting upon DNA.

AfterHIA 1y ago

You're one of those cats that provides a subtle reminder that Dr. Alan Kay (invented the tablet/Xerox ALTO interface) was first a biologist. Thank you for the enlightened smalltalk! (;3)

minkowski 1y ago

Have a look at the join calculus and the "chemical abstract machine" as implemented in JoCaml, e.g., https://sites.google.com/site/winitzki/tutorial-on-join-calculus-and-its-implementation-in-ocaml-jocaml https://sites.google.com/site/winitzki/tutorial-on-join-calc...

dluan 1y ago

You might be interested in Tinkercell, though at this point it may be somewhat outdated and old. There are lots of other more granular systems biology/chemical reaction network software tools, the most ambitious is probably OpenWorm which is still active. Just keep in mind though that you have to think of cells as very slow, but massively parallel computers.

discarded1023 1y ago

Luca Cardelli worked on this stuff a while back [1]. Perhaps "systems biology" [2] might provide an entry to the literature. [1] https://en.wikipedia.org/wiki/Luca_Cardelli https://en.wikipedia.org/wiki/Luca_Cardelli [2] https://en.wikipedia.org/wiki/Systems_biology https://en.wikipedia.org/wiki/Systems_biology

alberth 1y ago

You could also think about life as a "Factory" (instead of a computer) too: HUMAN FACTORY COMPUTER ----- ------- -------- Cell Factory Computer Enzyme Worker Functions Ribosome Assembler Compiler Acids Blue Print Source Code The difficulty with this type of analogy is so many things need these various capabilities that it's not unique to a computer, or a factory or even a human.