5 ms·

As someone building software to design genetic tools, this is actually a pretty good overview. It's analogies are pretty solid, even if they are just analogies

As someone building software to design genetic tools, this is actually a pretty good overview. It's analogies are pretty solid, even if they are just analogies. It's a well-described snapshot of the early phase of education where this helps build a grand intuition and relations between disciplines. Just be careful to remember that they're just analogies, and in general can't be relied on to actually discover, invent, design or conclude. The fun part for everyone here is that the science has improved so far so quickly that at this point that we are starting to be able to improve, implement and otherwise make good on those coding-style capabilities. We can start to write, patch, update, and affect that code - and do so in intelligent and rational ways, rather than the screens set up in the past century. The next section I would add would be one that actually started to talk about the compiled programs - the protein's themselves. All that code, all those rules, all those heuristics are there to be run through an atomic 3D-printer to produce proteins. And in an ensemble, those proteins form a closed community within a cell, which then form communities in a tissue, which form in communities called an organism. Those compiled proteins actually do the work at the lowest levels but often get a bit of short shrift while we all stare at their source-code in amazement. The source is elegant, but the programs are even more amazing, in my humble opinion. Here are some 'profiles' of the kinds of economically and socially interesting programs we've started to make based on the above source-code. An 'app-store' of compiled apps if you will: https://serotiny.bio/notes/proteins/ https://serotiny.bio/notes/proteins/

westoncb 9y ago
> The source is elegant, but the programs are even more amazing, in my humble opinion. Makes me curious about the 'runtime' which makes their impressive execution possible—granting that the analogy has definite limitations and could be misleading. The aspect of a 'runtime' which I see carrying over is that once the 'source' is 'compiled' into proteins, something makes the interesting behavior of those proteins what it is. I think where the analogy could be misleading is that the architecture of programming language runtimes tends to be a single coherent system with definite separation from programs executing within; whereas in the case of proteins, a large part of what provides for their biologically interesting behavior is just their general chemical properties (which are sort of contained within the 'programs' themselves, rather than in a separate external system). But there are probably aspects of the environment into which the proteins are released that systematically influence their behavior in a way that could be abstracted and studied (at which point it might have some loose resemblance in role to language runtimes). Maybe?
- jfarlow 9y ago
  In that regard, the protein programs exist and interact with each other in a runtime environment/OS that is 'physics'. Which is cool. Especially, because those programs, when run together, along with all sorts of other small molecule/lipid/temperature conditions are sufficient to output, well, me.
  - westoncb 9y ago
    I was somewhat avoiding bringing that up just because, in theory, every physical 'system' in the universe just boils down to physics—and this question gets pretty close to the line between where it's useful to start talking about a higher-level system, versus thinking in terms of chemistry (and/or physics). So it could get confusing. If there is a higher level system analogous to a runtime-environment which could be abstracted from actual genetic machinery, I would bet the rules of its operation would still be at least partially in terms of chemical rules (in other words, you couldn't abstract over it entirely). My justification for it is that I think the system is split between the decentralized behavior of proteins and enzymes etc. just following the rules they always follow, combined with the external 'system' which sets up conditions constraining and otherwise directing the proteins. That second system could maybe be higher level, but it's still central to its operation that it interfaces with a 'raw' chemical system. (Just an idea of course—my confidence that it means anything is ~12%). Edit: another analogy to maybe clarify (or confuse) things. I see the proteins/enzymes etc. which I described as decentralized as operating like a cellular automaton (e.g. Conway's GoL), but then the 'external'/centralized system as like another layer of rules which sort of pushes around clusters of cells in the grid in various significant ways, while all those clusters are still locally just executing the simple automaton rules.
    - jfarlow 9y ago
      Very much. We've actually tried to capture some of those runtime variables within proteins and break down the programs into smaller compossible units. And start to keep track of which conditions are required for particular functionalities of which components. Life has already made a bunch for us to look at. Ultimately, in our hands, those properties are strongly linked to physical associations, locations within a cell, enzymatic capabilities, and i/o (light, heat, chemical concentrations, force, etc.). Then you start (re)building little i/o robots from reusable components for use by and within cells that are regulated by their location and associations (in a wet Brownian environment). All by coding using that same genetic source.
hyperpallium 9y ago
How is it that proteins are able to build structures, like microtubules, cell walls and bone?
- jfarlow 9y ago
  Proteins are 1-dimensional chains of 'lego-like' molecules that fold into atomically-precise 3D tools. There are ~20 types of legos that have properties that differ along a number of axis like hydrophobicity, charge, reactivity, size, flexibility, etc. And those 20, in combination, seem to be enough to build all of the tools life needs to interact with its environment. Most proteins are assemblies of a few hundred such 'legos' (again, of which there are 20 types). Those 3D structures then, because they're encoded in the 'tape-like' DNA, can actually themselves be modular, rearranged, and this chunk can be lopped off and plopped onto that chunk, or assembled with this chunk over here. When you string a 'firefly-shine' protein next to a 'in-the-nucleus' protein, the firefly-shine protein will now be physically connected to the 'in-the-nucleus' signal, so you get firefly-shine in the nucleus. Now encode all the things proteins can do: bind to things, enzymatically make things, go places, make structures, sense chemicals, light, force, electricity, other atoms, etc. - and you get little multi-part robots made of those various active 'chunks'. If you have a protein piece that itself assembles in a hexagonal-like shape, you could imagine assembling a number of them into a soccer ball - just as a virus does to protect its DNA. Or if there are small Brownian-aware 'ratchets' attached to stiff fiber-like proteins, you can get proteins that move or walk: https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=y-uuk4Pr2i8 The microtubule's they're walking over are themselves linear assemblies of proteins: https://www.youtube.com/watch?v=jGmz4xVP50M https://www.youtube.com/watch?v=jGmz4xVP50M Similarly, spider silk is protein: https://boltthreads.com/ https://boltthreads.com/ And leather is protein: http://provenance.bio/ http://provenance.bio/ Here are some more animations. The only thing wrong is how empty the space is. In real life, there is no empty space at all - it's jammed pack with other proteins and molecules: https://www.youtube.com/watch?v=FzcTgrxMzZk https://www.youtube.com/watch?v=FzcTgrxMzZk https://www.youtube.com/watch?v=VdmbpAo9JR4 https://www.youtube.com/watch?v=VdmbpAo9JR4 Bone is a mineral deposit, deposited by proteins within particular cells: https://en.wikipedia.org/wiki/Osteoblast#Osteogenesis https://en.wikipedia.org/wiki/Osteoblast#Osteogenesis Cell walls or lipid membranes are fats that are generated in the right concentration by proteins, and then allowed to self-assemble, creating well-controlled environmental compartments for sensitive proteins to remain functional.
mygo 9y ago
You made this? Awesome I ran into it a while back and thought it was really interesting. Does this mean you're tapped into the synthetic biology networks? Would love to chat about that, as its something I want to get into more due to my biology + programming background.
- jfarlow 9y ago
  We did, brother & I. We're trying to make useful the abstraction layer above DNA. We think there's much benefit to thinking and placing complexity at the protein level, and back-calculating the DNA, completely offloading the complexity of actually manufacturing DNA. I'd be happy to chat. Email is my first name at serotiny.bio -Justin
  - jfarlow 9y ago
    To be clear, I'm not the writer of the original post about DNA as code. I created Serotiny and our protien design software, and was providing my thoughts on the post given my background.

westoncb 9y ago

> The source is elegant, but the programs are even more amazing, in my humble opinion. Makes me curious about the 'runtime' which makes their impressive execution possible—granting that the analogy has definite limitations and could be misleading. The aspect of a 'runtime' which I see carrying over is that once the 'source' is 'compiled' into proteins, something makes the interesting behavior of those proteins what it is. I think where the analogy could be misleading is that the architecture of programming language runtimes tends to be a single coherent system with definite separation from programs executing within; whereas in the case of proteins, a large part of what provides for their biologically interesting behavior is just their general chemical properties (which are sort of contained within the 'programs' themselves, rather than in a separate external system). But there are probably aspects of the environment into which the proteins are released that systematically influence their behavior in a way that could be abstracted and studied (at which point it might have some loose resemblance in role to language runtimes). Maybe?

jfarlow 9y ago
In that regard, the protein programs exist and interact with each other in a runtime environment/OS that is 'physics'. Which is cool. Especially, because those programs, when run together, along with all sorts of other small molecule/lipid/temperature conditions are sufficient to output, well, me.
- westoncb 9y ago
  I was somewhat avoiding bringing that up just because, in theory, every physical 'system' in the universe just boils down to physics—and this question gets pretty close to the line between where it's useful to start talking about a higher-level system, versus thinking in terms of chemistry (and/or physics). So it could get confusing. If there is a higher level system analogous to a runtime-environment which could be abstracted from actual genetic machinery, I would bet the rules of its operation would still be at least partially in terms of chemical rules (in other words, you couldn't abstract over it entirely). My justification for it is that I think the system is split between the decentralized behavior of proteins and enzymes etc. just following the rules they always follow, combined with the external 'system' which sets up conditions constraining and otherwise directing the proteins. That second system could maybe be higher level, but it's still central to its operation that it interfaces with a 'raw' chemical system. (Just an idea of course—my confidence that it means anything is ~12%). Edit: another analogy to maybe clarify (or confuse) things. I see the proteins/enzymes etc. which I described as decentralized as operating like a cellular automaton (e.g. Conway's GoL), but then the 'external'/centralized system as like another layer of rules which sort of pushes around clusters of cells in the grid in various significant ways, while all those clusters are still locally just executing the simple automaton rules.
  - jfarlow 9y ago
    Very much. We've actually tried to capture some of those runtime variables within proteins and break down the programs into smaller compossible units. And start to keep track of which conditions are required for particular functionalities of which components. Life has already made a bunch for us to look at. Ultimately, in our hands, those properties are strongly linked to physical associations, locations within a cell, enzymatic capabilities, and i/o (light, heat, chemical concentrations, force, etc.). Then you start (re)building little i/o robots from reusable components for use by and within cells that are regulated by their location and associations (in a wet Brownian environment). All by coding using that same genetic source.

hyperpallium 9y ago

How is it that proteins are able to build structures, like microtubules, cell walls and bone?

jfarlow 9y ago
Proteins are 1-dimensional chains of 'lego-like' molecules that fold into atomically-precise 3D tools. There are ~20 types of legos that have properties that differ along a number of axis like hydrophobicity, charge, reactivity, size, flexibility, etc. And those 20, in combination, seem to be enough to build all of the tools life needs to interact with its environment. Most proteins are assemblies of a few hundred such 'legos' (again, of which there are 20 types). Those 3D structures then, because they're encoded in the 'tape-like' DNA, can actually themselves be modular, rearranged, and this chunk can be lopped off and plopped onto that chunk, or assembled with this chunk over here. When you string a 'firefly-shine' protein next to a 'in-the-nucleus' protein, the firefly-shine protein will now be physically connected to the 'in-the-nucleus' signal, so you get firefly-shine in the nucleus. Now encode all the things proteins can do: bind to things, enzymatically make things, go places, make structures, sense chemicals, light, force, electricity, other atoms, etc. - and you get little multi-part robots made of those various active 'chunks'. If you have a protein piece that itself assembles in a hexagonal-like shape, you could imagine assembling a number of them into a soccer ball - just as a virus does to protect its DNA. Or if there are small Brownian-aware 'ratchets' attached to stiff fiber-like proteins, you can get proteins that move or walk: https://www.youtube.com/watch?v=y-uuk4Pr2i8 https://www.youtube.com/watch?v=y-uuk4Pr2i8 The microtubule's they're walking over are themselves linear assemblies of proteins: https://www.youtube.com/watch?v=jGmz4xVP50M https://www.youtube.com/watch?v=jGmz4xVP50M Similarly, spider silk is protein: https://boltthreads.com/ https://boltthreads.com/ And leather is protein: http://provenance.bio/ http://provenance.bio/ Here are some more animations. The only thing wrong is how empty the space is. In real life, there is no empty space at all - it's jammed pack with other proteins and molecules: https://www.youtube.com/watch?v=FzcTgrxMzZk https://www.youtube.com/watch?v=FzcTgrxMzZk https://www.youtube.com/watch?v=VdmbpAo9JR4 https://www.youtube.com/watch?v=VdmbpAo9JR4 Bone is a mineral deposit, deposited by proteins within particular cells: https://en.wikipedia.org/wiki/Osteoblast#Osteogenesis https://en.wikipedia.org/wiki/Osteoblast#Osteogenesis Cell walls or lipid membranes are fats that are generated in the right concentration by proteins, and then allowed to self-assemble, creating well-controlled environmental compartments for sensitive proteins to remain functional.

mygo 9y ago

You made this? Awesome I ran into it a while back and thought it was really interesting. Does this mean you're tapped into the synthetic biology networks? Would love to chat about that, as its something I want to get into more due to my biology + programming background.

jfarlow 9y ago
We did, brother & I. We're trying to make useful the abstraction layer above DNA. We think there's much benefit to thinking and placing complexity at the protein level, and back-calculating the DNA, completely offloading the complexity of actually manufacturing DNA. I'd be happy to chat. Email is my first name at serotiny.bio -Justin
- jfarlow 9y ago
  To be clear, I'm not the writer of the original post about DNA as code. I created Serotiny and our protien design software, and was providing my thoughts on the post given my background.