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The best analogy to this field and the many, many problems it might run into is biotech. This is actually quite funny because in the early days the main analogy

The best analogy to this field and the many, many problems it might run into is biotech. This is actually quite funny because in the early days the main analogy to biotech was the computer / state-machine. For some background, biotech has undergone many booms and busts in the last half century; unlike the last tech bubble, these booms and busts have flown somewhat under the radar. In fact, Jurassic Park, written in 1990, is actually a book /about/ the late 80’s biotech bubble. There is a really fun part in the book where they are talking about making miniature dinosaurs that will only eat Ingen-brand dinosaur pet food (Ingen was the company behind Jurassic Park). Anyway, with biotech, the problem has been, again and again, the assumption that a system is radically simpler than it. Biology is so incredibly complicated that it puts the largest engineering book I have, a 1500 TCP/IP protocol book (No Starch) to shame. I mean at least we know how TCP/IP works. With biology, the manual might be closer to 900,000 pages and we only have 40% of the table of contents and maybe 800 pages (out of order) so far. BEST EXAMPLE: In the 70’s, once large portions of the genome started to be identified and linked to specific genes that were known to cause traits or diseases, it was widely assumed that creating/reading/updating/deleting genes on DNA would be relatively straightforward, particularly as more of the genome was uncovered. However, as was later discovered, many traits or diseases might be the result of 200+ genes that are also used elsewhere. Turn off just 1 gene for a disease, and 1). it won’t do anything because you didn’t turn off the other 199, and 2). oh wow that gene was actually used for something else and now you’ve lost the ability to form eyeballs / are born without anything in your eye sockets.

knight-of-lambd 9y ago
> Turn off just 1 gene for a disease, and 1). it won’t do anything because you didn’t turn off the other 199, and 2). oh wow that gene was actually used for something else and now you’ve lost the ability to form eyeballs / are born without anything in your eye sockets. Certainly not on the same scale, but this resonates with my experiences with legacy code. I think this similarity is more than superficial. Energetic systems evolve over time to become tangled, correlated messes, without some other force counteracting this tendency (ie. refactoring). I wonder if DNA has analogous mechanisms.
- PeterisP 9y ago
  Yeah, in some way it feels that there's essentially a huge software (reverse) engineering project. We have the technical ability to read all the code in our DNA, understand what small parts of it do (e.g. making a particular protein), and model some of the small scale behavior. And we've got a very, very, very large codebase of mishmash undocumented legacy homegrown code that sort of does what we want but in an unstable and occasionally buggy manner. And we've got a strong wish to fix some bugs (i.e. genetic diseases) and possibly add some features (e.g. longer quality lifespan, increased capabilities). So we'd like to reverse-engineer this system. The good part is that we only have to do it once and we can cooperate on it; the bad part is that the system is really complex and (more importantly) horribly interdependent; it actually implements pretty much all the practices that we know makes code unmaintainable. Anyway. The hypothesis I'm trying to make is that this seems to indicate that research on advanced methodologies and tools to analyze and understand large quantities of tangled (and possibly intentionally obfuscated) computer code; work techniques and algorithms for computer(machine learning?)-aided understanding and reverse engineering large quantities of code seem likely to eventually have practical applications in biotech. Yes, contemporary code behavior is quite far from protein interaction. That's ok - we're quite far from starting to properly reverse-engineer (in this context) biotech as well; with every decade, code (and its analysis) will become more complex and biotech more understood, eventually meeting. And when designing tools for analysis of very complicated systems, the tools will anyway have to be adapted not to the systems but to the analyzer, to the limitations of what structures the human researchers can understand and "keep in their head" and what needs to be automatically summarized/structured by tools.
  - mrep 9y ago
    > The good part is that we only have to do it once and we can cooperate on it; I'm not a biology person but I think everyone except identical twins has different DNA which makes the problem so much harder since "doing it once" only solves one person's problem when every variable (dna) can potentially interact with every other (n^n problem where n = 3,000,000,000 potential pairs which is an insane number, granted it almost certainly has some defined structure which reduces the potential differences but that will still be a huge number) . Also, you have the whole nature versus nurture problem which makes biology even harder.
rangibaby 9y ago
Civilization (II)’s “modern” techs are like a time capsule of the late 80s / early 90s. - Cure for Cancer is a wonder of the world and requires “genetic engineering” - You can build SDI lasers in every city, and they work. In 2018 the current state of the art is “it will probably shoot down an ICBM, maybe” - Fusion power and room temperature superconductor are basic research projects. The technology immediately preceding superconductor is ... plastics - SETI project is a wonder of the world and gives a huge boost to scientific research. The obvious choice now would be to change it for “the internet” but hindsight is 20/20
- Retra 9y ago
  Part of that is because Civ II is meant to model a large span of technologies over time using a fairly uniform mechanism. It would be infeasible to include the vast numbers of technological branches that have occurred in modern times while not making the game one that takes place mostly in modern times... So it only picks a few representative technologies so show you.
  - rangibaby 9y ago
    I understand that. My point was that the modern tech tree has many ...optimistic technologies that don't even exist now but were considered "close" or even already developed in that time period like advanced biotech (like the parent comment mentioned) or fusion power (cold fusion).
anonytrary 9y ago
So true about TCP/IP. Even rocket science is a joke compared to most biological systems. That said, even a set of rules as simple as TCP/IP can lead to complex, valuable systems (e.g. WWW). TCP/IP rules leading to the web is nothing compared to physical rules leading to biological life, true. Even in 2018, one could say that computers' potential has barely been tapped.
red75prime 9y ago
> many traits or diseases might be the result of 200+ genes that are also used elsewhere. What are examples of 200+ gene diseases? At this level of genetic sophistication it should probably be called a trait which causes disadvantages in some situations.
stinos 9y ago
the manual might be closer to 900,000 pages Knowing a thing or two about neurophysiology, this seems like a vast underestimation (since a biology book should also cover that, likely most complicated of all, topic). So vast I wouldn't even dare putting a number on it, because there is so much we don't know about the brain, it is hard to even estimate how much we don't know. (Which by the way also puts some AI claims regarding replication of brain functionality in a different light)
bewo001 9y ago
A genetic algorithm designed an FPGA logic that couldn't possible work under usual rules, but actually did and used less resources than any human design. As it turned out, the genetic algorithm exploited some analogue properties of the FPGA, which a human designer would never attempt to do. Genetics seem to favor efficient systems over understandable and easily extendable systems. Paper "Adrian Thompson, An Evolved Circuit, Intrinsic in Silicon, Entwined With Physics."

knight-of-lambd 9y ago

> Turn off just 1 gene for a disease, and 1). it won’t do anything because you didn’t turn off the other 199, and 2). oh wow that gene was actually used for something else and now you’ve lost the ability to form eyeballs / are born without anything in your eye sockets. Certainly not on the same scale, but this resonates with my experiences with legacy code. I think this similarity is more than superficial. Energetic systems evolve over time to become tangled, correlated messes, without some other force counteracting this tendency (ie. refactoring). I wonder if DNA has analogous mechanisms.

PeterisP 9y ago
Yeah, in some way it feels that there's essentially a huge software (reverse) engineering project. We have the technical ability to read all the code in our DNA, understand what small parts of it do (e.g. making a particular protein), and model some of the small scale behavior. And we've got a very, very, very large codebase of mishmash undocumented legacy homegrown code that sort of does what we want but in an unstable and occasionally buggy manner. And we've got a strong wish to fix some bugs (i.e. genetic diseases) and possibly add some features (e.g. longer quality lifespan, increased capabilities). So we'd like to reverse-engineer this system. The good part is that we only have to do it once and we can cooperate on it; the bad part is that the system is really complex and (more importantly) horribly interdependent; it actually implements pretty much all the practices that we know makes code unmaintainable. Anyway. The hypothesis I'm trying to make is that this seems to indicate that research on advanced methodologies and tools to analyze and understand large quantities of tangled (and possibly intentionally obfuscated) computer code; work techniques and algorithms for computer(machine learning?)-aided understanding and reverse engineering large quantities of code seem likely to eventually have practical applications in biotech. Yes, contemporary code behavior is quite far from protein interaction. That's ok - we're quite far from starting to properly reverse-engineer (in this context) biotech as well; with every decade, code (and its analysis) will become more complex and biotech more understood, eventually meeting. And when designing tools for analysis of very complicated systems, the tools will anyway have to be adapted not to the systems but to the analyzer, to the limitations of what structures the human researchers can understand and "keep in their head" and what needs to be automatically summarized/structured by tools.
- mrep 9y ago
  > The good part is that we only have to do it once and we can cooperate on it; I'm not a biology person but I think everyone except identical twins has different DNA which makes the problem so much harder since "doing it once" only solves one person's problem when every variable (dna) can potentially interact with every other (n^n problem where n = 3,000,000,000 potential pairs which is an insane number, granted it almost certainly has some defined structure which reduces the potential differences but that will still be a huge number) . Also, you have the whole nature versus nurture problem which makes biology even harder.

rangibaby 9y ago

Civilization (II)’s “modern” techs are like a time capsule of the late 80s / early 90s. - Cure for Cancer is a wonder of the world and requires “genetic engineering” - You can build SDI lasers in every city, and they work. In 2018 the current state of the art is “it will probably shoot down an ICBM, maybe” - Fusion power and room temperature superconductor are basic research projects. The technology immediately preceding superconductor is ... plastics - SETI project is a wonder of the world and gives a huge boost to scientific research. The obvious choice now would be to change it for “the internet” but hindsight is 20/20

Retra 9y ago
Part of that is because Civ II is meant to model a large span of technologies over time using a fairly uniform mechanism. It would be infeasible to include the vast numbers of technological branches that have occurred in modern times while not making the game one that takes place mostly in modern times... So it only picks a few representative technologies so show you.
- rangibaby 9y ago
  I understand that. My point was that the modern tech tree has many ...optimistic technologies that don't even exist now but were considered "close" or even already developed in that time period like advanced biotech (like the parent comment mentioned) or fusion power (cold fusion).

anonytrary 9y ago

So true about TCP/IP. Even rocket science is a joke compared to most biological systems. That said, even a set of rules as simple as TCP/IP can lead to complex, valuable systems (e.g. WWW). TCP/IP rules leading to the web is nothing compared to physical rules leading to biological life, true. Even in 2018, one could say that computers' potential has barely been tapped.

red75prime 9y ago

> many traits or diseases might be the result of 200+ genes that are also used elsewhere. What are examples of 200+ gene diseases? At this level of genetic sophistication it should probably be called a trait which causes disadvantages in some situations.

stinos 9y ago

the manual might be closer to 900,000 pages Knowing a thing or two about neurophysiology, this seems like a vast underestimation (since a biology book should also cover that, likely most complicated of all, topic). So vast I wouldn't even dare putting a number on it, because there is so much we don't know about the brain, it is hard to even estimate how much we don't know. (Which by the way also puts some AI claims regarding replication of brain functionality in a different light)

bewo001 9y ago

A genetic algorithm designed an FPGA logic that couldn't possible work under usual rules, but actually did and used less resources than any human design. As it turned out, the genetic algorithm exploited some analogue properties of the FPGA, which a human designer would never attempt to do. Genetics seem to favor efficient systems over understandable and easily extendable systems. Paper "Adrian Thompson, An Evolved Circuit, Intrinsic in Silicon, Entwined With Physics."