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The library analogy seems really apt here. This article seems to argue that Nature has selected for genes (and by extension, perhaps whole genomes) that in som

The library analogy seems really apt here. This article seems to argue that Nature has selected for genes (and by extension, perhaps whole genomes) that in some sense are likely to benefit from small mutations. That means that even if two genomes lead to phenotypically identical organisms, the one whose genome is more robust to small changes (either by continuing to function the same way, or to have a different, but still useful function) is better. Is there a specific term for this? This implies that 'How likely is this particular organism to survive in this particular environment?' is not precisely the same as 'How well will this genome persist over evolutionary time as the environment changes?', but they seem to both go under the term 'fitness', even though one is more 'meta-' than the other. Similarly, software engineers do not simply search the space of programs for ones that give the exact desired output, but within the set of working programs that identical output, we also select for ones where small changes will lead to different but still-useful programs. We call these features 'maintainability' and 'readability', and we use 'libraries' to help do this. And just like we don't necessarily use the entirety of a library, it seems possible that large stretches of non-coding DNA are simply genes that aren't currently useful, but are kept around as raw material for future evolution. "It is not the strongest of the species that survives, nor the most intelligent; it is the one most adaptable to change."

mdda 10y ago
But also imagine that the algorithms you write had to work (perhaps slightly differently, but essentially the same) when hit with bit-flips in the code. How would one do that? Perhaps have multiple copies, or coding redundancy, or fix-up routines, or fall-back instructions. All the kind of stuff that mother nature already figured out. But that should be unsurprising, since without that robustness, the evolution thing would kill our progeny almost every time. Building the robustness is almost as important as building the functionality.
- smallnamespace 10y ago
  One could also view unit tests and static type checking as making a program more robust to incorrect programmer-directed changes.
  - mdda 10y ago
    You'd also need to robustify the compiler itself to bit-wise errors, and its output.
    - posterboy 10y ago
      > to robustify Did you mean to reinforce?
- j-g-faustus 10y ago
  > imagine that the algorithms you write had to work (perhaps slightly differently, but essentially the same) when hit with bit-flips in the code. How would one do that? Gray code [1] does it for integers: Any two consecutive values are one bit-flip apart. Instructions could perhaps be encoded similarly: Say an n-bit gray code represents an instruction. Each instruction has an n-bit ID, IDs are spread evenly over the space of n-bit values, and each instruction code resolves to the ID with the smallest Hamming distance [2]. Then most bitflips would yield essentially the same program, as long as the number of instructions is small compared to the number of n-bit values. Our CPUs wouldn't run that directly, but I think it should be possible to construct simple bytecode instruction sets where practically any permutation of bits gives a syntactically valid program, and where bit sequences with a small Hamming distance in most cases resolve to similar programs. [1] https://en.wikipedia.org/wiki/Gray_code https://en.wikipedia.org/wiki/Gray_code [2] https://en.wikipedia.org/wiki/Hamming_distance https://en.wikipedia.org/wiki/Hamming_distance
philipov 10y ago
> Is there a specific term for this? I think robustness is the specific term for that.
- posterboy 10y ago
  A quick search would confirm that mutational robustness is _a_ right term for this.
deleted 10y ago
[deleted]
onetimepadder 10y ago
"It is not the strongest of the species that survives, nor the most intelligent; it is the one most adaptable to change." Isn't this (from a very, very high perspective) the reason why thousands of years of power concentration / consolidation / empire-building endeavors went down the drain each and every time .. and the current attempt (where attempt is too weak of a word), regardless of the tools/strategies/technologies being used(yes _you_ are a part of it) is nothing more than a manifestation of the same power-hungry "elite" ape-brains steering the world counter-nature(from decentralization, competition etc) into its abyss? Everyone knows that a system that can't evolve is a dead system .. and not everyone but at least some people know that today's elite mindset with most of its "enlightened" ideas (some if its proverbial arms even using the same, cherry-picked nature-references as the one I'm picking on right now) - are conceptually the same regardless of the time period Sorry for this rant, I think our civilization won't survive if the world keeps its current direction(well, the parts that will make it .. and yes both species), decentralization, limiting the concentration of power whatever it takes .. that's the only way "current" as in the last 300-200 years give-or-take *"specie_s_" including moechtegern new species as ref. Edit: Grammar fixes
- smallnamespace 10y ago
  > decentralization, limiting the concentration of power whatever it takes .. that's the only way Unfortunately, successfully addressing global warming and over-use of resources is probably going to require more coercion and centralization. Even bilateral agreements must be backed by credible threats, like sanctions, or they won't work.
  - onetimepadder 10y ago
    Over-use of resources is actually a direct consequence of the consolidated global corporate power (from planned obsolescence through destroyed local markets/industry(with all its micro and regional economic and social consequences) .. just so global corporation A can ship products that were originally manufactured and consumed/sold locally - at a huge human and environmental cost - across the planet and make profits. Not because a product is cheaper for the consumer, nor because its better, this is solely the consequence of various coercive techniques (military, economical). Patents(yes, Watt actually postponed the onset of the industrial revolution at least 2 decades .. one example out of many), licenses and concessions(both meant as economic terms), etc et Too complicated topic for this kind of discussion but that's one huge misconception/piece of economic propaganda you cited there that had to be addressed The other one - even more potent and dangerous - is the notion that global problems need global governments(or, more precisely a consolidated global power). This is actually a two-part-question, a) Why is our current civilization unable to solve global problems(education, healthcare, social welfare, environmental damage) - which is a complicated topic on its own; b) how can a decentralized global society with a mostly local scope solve global issues. This is a special question of sorts because if you answer the a) part you will with high certainty arrive at an answer to the b) question too. (and no, centralization of power is not the answer)
labster 10y ago
And just like in libraries, junk DNA provides all of the code cruft you could ever ask for. Some organisms that go for the agile approach are able to (and mostly required to) minimize the amount of cruft, but most organisms just pay the cost of copying entirely useless stuff.
- lohankin 10y ago
  Junk DNA is not junk at all. http://www.scientificamerican.com/article/hidden-treasures-in-junk-dna/ http://www.scientificamerican.com/article/hidden-treasures-i... (there are many other recent publications, please google it)
Cybiote 10y ago
This is an excellent post smallnamespace. The area of research you're looking for is known as evolvability, reading these wiki/wikibook [↓] links is a good start for the topic. Evolution seems to have figured out a way to build representations such that nearby steps in random directions are nearby in a semantic (can't think of a better word atm) sense. This should surprise you. Think about an expression tree like (+ (x y)), it's very different from (/ (x y)) despite differing in just 1 position. Or consider that 12 and 32780 differ by only a bit in their binary representation. We humans could really do with figuring out how evolution takes a seeming discrete problem and works out a way to build representations such that efficient search is possible even without explicit derivatives. It's also interesting that, evolution might have taken this to a meta level with brains. From http://www.fil.ion.ucl.ac.uk/~karl/The%20free-energy%20principle%20A%20unified%20brain%20theory.pdf#page=7 http://www.fil.ion.ucl.ac.uk/~karl/The%20free-energy%20princ... > The beauty of neural Darwinism is that it nests distinct selective processes within each other. In other words, it eschews a single unit of selection and exploits the notion of meta-selection (the selection of selective mechanisms; for example, see REF. 89). In this context, (neuronal) value confers evolutionary value (that is, adaptive fitness) by selecting neuronal groups that meditate adaptive stimulus–stimulus associations and stimulus–response links. The capacity of value to do this is assured by natural selection, in the sense that neuronal value systems are themselves subject to selective pressure. This theory, particularly value-dependent learning90, has deep connections with reinforcement learning and related approaches in engineering (see below) A bit of an aside but: If you're interested in AI, it's really worth looking at what the people studying the intersection of evolution and learning are saying, at animal intelligence and at human brain development. It's surprising to me how many people think the current approach to reinforcement learning is but a hop and a skip to full human like generality. [-] https://en.wikibooks.org/wiki/Structural_Biochemistry/Stability,_Mutation_and_Evolvability https://en.wikibooks.org/wiki/Structural_Biochemistry/Stabil... https://en.wikipedia.org/wiki/Evolvability https://en.wikipedia.org/wiki/Evolvability
- plushpuffin 10y ago
  There was a good article about this in the April 2004 issue of Scientific American (paywalled, unfortunately; the name of the article is "Evolution Encoded"). It's about how similar gene sequences result in similar proteins, so that mutations don't necessarily result in death. http://www.scientificamerican.com/article/evolution-encoded/ http://www.scientificamerican.com/article/evolution-encoded/
ehsanu1 10y ago
Is there a specific term for this? This implies that 'How likely is this particular organism to survive in this particular environment?' is not precisely the same as 'How well will this genome persist over evolutionary time as the environment changes?', but they seem to both go under the term 'fitness', even though one is more 'meta-' than the other. This isn't quite the same, but this is related: https://en.wikipedia.org/wiki/Gene-centered_view_of_evolution https://en.wikipedia.org/wiki/Gene-centered_view_of_evolutio...

mdda 10y ago

But also imagine that the algorithms you write had to work (perhaps slightly differently, but essentially the same) when hit with bit-flips in the code. How would one do that? Perhaps have multiple copies, or coding redundancy, or fix-up routines, or fall-back instructions. All the kind of stuff that mother nature already figured out. But that should be unsurprising, since without that robustness, the evolution thing would kill our progeny almost every time. Building the robustness is almost as important as building the functionality.

smallnamespace 10y ago
One could also view unit tests and static type checking as making a program more robust to incorrect programmer-directed changes.
- mdda 10y ago
  You'd also need to robustify the compiler itself to bit-wise errors, and its output.
  - posterboy 10y ago
    > to robustify Did you mean to reinforce?
j-g-faustus 10y ago
> imagine that the algorithms you write had to work (perhaps slightly differently, but essentially the same) when hit with bit-flips in the code. How would one do that? Gray code [1] does it for integers: Any two consecutive values are one bit-flip apart. Instructions could perhaps be encoded similarly: Say an n-bit gray code represents an instruction. Each instruction has an n-bit ID, IDs are spread evenly over the space of n-bit values, and each instruction code resolves to the ID with the smallest Hamming distance [2]. Then most bitflips would yield essentially the same program, as long as the number of instructions is small compared to the number of n-bit values. Our CPUs wouldn't run that directly, but I think it should be possible to construct simple bytecode instruction sets where practically any permutation of bits gives a syntactically valid program, and where bit sequences with a small Hamming distance in most cases resolve to similar programs. [1] https://en.wikipedia.org/wiki/Gray_code https://en.wikipedia.org/wiki/Gray_code [2] https://en.wikipedia.org/wiki/Hamming_distance https://en.wikipedia.org/wiki/Hamming_distance

philipov 10y ago

> Is there a specific term for this? I think robustness is the specific term for that.

posterboy 10y ago
A quick search would confirm that mutational robustness is _a_ right term for this.

deleted 10y ago

[deleted]

onetimepadder 10y ago

"It is not the strongest of the species that survives, nor the most intelligent; it is the one most adaptable to change." Isn't this (from a very, very high perspective) the reason why thousands of years of power concentration / consolidation / empire-building endeavors went down the drain each and every time .. and the current attempt (where attempt is too weak of a word), regardless of the tools/strategies/technologies being used(yes _you_ are a part of it) is nothing more than a manifestation of the same power-hungry "elite" ape-brains steering the world counter-nature(from decentralization, competition etc) into its abyss? Everyone knows that a system that can't evolve is a dead system .. and not everyone but at least some people know that today's elite mindset with most of its "enlightened" ideas (some if its proverbial arms even using the same, cherry-picked nature-references as the one I'm picking on right now) - are conceptually the same regardless of the time period Sorry for this rant, I think our civilization won't survive if the world keeps its current direction(well, the parts that will make it .. and yes both species), decentralization, limiting the concentration of power whatever it takes .. that's the only way "current" as in the last 300-200 years give-or-take *"specie_s_" including moechtegern new species as ref. Edit: Grammar fixes

smallnamespace 10y ago
> decentralization, limiting the concentration of power whatever it takes .. that's the only way Unfortunately, successfully addressing global warming and over-use of resources is probably going to require more coercion and centralization. Even bilateral agreements must be backed by credible threats, like sanctions, or they won't work.
- onetimepadder 10y ago
  Over-use of resources is actually a direct consequence of the consolidated global corporate power (from planned obsolescence through destroyed local markets/industry(with all its micro and regional economic and social consequences) .. just so global corporation A can ship products that were originally manufactured and consumed/sold locally - at a huge human and environmental cost - across the planet and make profits. Not because a product is cheaper for the consumer, nor because its better, this is solely the consequence of various coercive techniques (military, economical). Patents(yes, Watt actually postponed the onset of the industrial revolution at least 2 decades .. one example out of many), licenses and concessions(both meant as economic terms), etc et Too complicated topic for this kind of discussion but that's one huge misconception/piece of economic propaganda you cited there that had to be addressed The other one - even more potent and dangerous - is the notion that global problems need global governments(or, more precisely a consolidated global power). This is actually a two-part-question, a) Why is our current civilization unable to solve global problems(education, healthcare, social welfare, environmental damage) - which is a complicated topic on its own; b) how can a decentralized global society with a mostly local scope solve global issues. This is a special question of sorts because if you answer the a) part you will with high certainty arrive at an answer to the b) question too. (and no, centralization of power is not the answer)

labster 10y ago

And just like in libraries, junk DNA provides all of the code cruft you could ever ask for. Some organisms that go for the agile approach are able to (and mostly required to) minimize the amount of cruft, but most organisms just pay the cost of copying entirely useless stuff.

lohankin 10y ago
Junk DNA is not junk at all. http://www.scientificamerican.com/article/hidden-treasures-in-junk-dna/ http://www.scientificamerican.com/article/hidden-treasures-i... (there are many other recent publications, please google it)

Cybiote 10y ago

This is an excellent post smallnamespace. The area of research you're looking for is known as evolvability, reading these wiki/wikibook [↓] links is a good start for the topic. Evolution seems to have figured out a way to build representations such that nearby steps in random directions are nearby in a semantic (can't think of a better word atm) sense. This should surprise you. Think about an expression tree like (+ (x y)), it's very different from (/ (x y)) despite differing in just 1 position. Or consider that 12 and 32780 differ by only a bit in their binary representation. We humans could really do with figuring out how evolution takes a seeming discrete problem and works out a way to build representations such that efficient search is possible even without explicit derivatives. It's also interesting that, evolution might have taken this to a meta level with brains. From http://www.fil.ion.ucl.ac.uk/~karl/The%20free-energy%20principle%20A%20unified%20brain%20theory.pdf#page=7 http://www.fil.ion.ucl.ac.uk/~karl/The%20free-energy%20princ... > The beauty of neural Darwinism is that it nests distinct selective processes within each other. In other words, it eschews a single unit of selection and exploits the notion of meta-selection (the selection of selective mechanisms; for example, see REF. 89). In this context, (neuronal) value confers evolutionary value (that is, adaptive fitness) by selecting neuronal groups that meditate adaptive stimulus–stimulus associations and stimulus–response links. The capacity of value to do this is assured by natural selection, in the sense that neuronal value systems are themselves subject to selective pressure. This theory, particularly value-dependent learning90, has deep connections with reinforcement learning and related approaches in engineering (see below) A bit of an aside but: If you're interested in AI, it's really worth looking at what the people studying the intersection of evolution and learning are saying, at animal intelligence and at human brain development. It's surprising to me how many people think the current approach to reinforcement learning is but a hop and a skip to full human like generality. [-] https://en.wikibooks.org/wiki/Structural_Biochemistry/Stability,_Mutation_and_Evolvability https://en.wikibooks.org/wiki/Structural_Biochemistry/Stabil... https://en.wikipedia.org/wiki/Evolvability https://en.wikipedia.org/wiki/Evolvability

plushpuffin 10y ago
There was a good article about this in the April 2004 issue of Scientific American (paywalled, unfortunately; the name of the article is "Evolution Encoded"). It's about how similar gene sequences result in similar proteins, so that mutations don't necessarily result in death. http://www.scientificamerican.com/article/evolution-encoded/ http://www.scientificamerican.com/article/evolution-encoded/

ehsanu1 10y ago

Is there a specific term for this? This implies that 'How likely is this particular organism to survive in this particular environment?' is not precisely the same as 'How well will this genome persist over evolutionary time as the environment changes?', but they seem to both go under the term 'fitness', even though one is more 'meta-' than the other. This isn't quite the same, but this is related: https://en.wikipedia.org/wiki/Gene-centered_view_of_evolution https://en.wikipedia.org/wiki/Gene-centered_view_of_evolutio...