5 ms·

I think what you’re describing here is called “epigenetics,” or how different genes are expressed or not expressed due to environmental and other outside factor

by shijie 7y ago

I think what you’re describing here is called “epigenetics,” or how different genes are expressed or not expressed due to environmental and other outside factors such as stress, etc...

rolph 7y ago
the big deal about epigenetics is that those [methylation and histone binding] are modifications that dont alter the sequence of the DNA but are also inherited by subsequent generations. https://www.thieme-connect.de/products/ejournals/abstract/10.1055/s-0029-1237423 https://www.thieme-connect.de/products/ejournals/abstract/10... https://sci-hub.se/10.1038/542406a https://sci-hub.se/10.1038/542406a
ryankemper 7y ago
For those that aren't familiar, this principle is known as gene expression: https://en.wikipedia.org/wiki/Gene_expression https://en.wikipedia.org/wiki/Gene_expression To make an analogy to software, a common pattern is to have a monolithic repo with many different "personalities" (codepaths / configurations) that utilize different subsets of the monolith. DNA seems to work under a similar principle, a given cell will preferentially transcribe parts of the DNA based on epigenetic factors.
enchiridion 7y ago
Maybe in a way. I think they are driving at an orthogonal argument. The DNA is more or less useless without cells. It seems like the machinery of the cell carries information about the whole of the organism in an abstract sense.
01100011 7y ago
I think the analogy would be something like: DNA is the code. Epigenetics are config options which can be saved to a file and passed on. The cell is the machine which interprets the DNA + config options. So there are three pieces, and I don't think OP was talking about epigenetics.
TeMPOraL 7y ago
What GP is talking about is that information is never fully contained in a medium; it's encoded in the tuple (the medium, what reads the medium). E.g. take a JPG file. The picture in that file isn't fully contained in the bits that file consists of. Some of the information is contained in the JPG specification (and through it, in the JPG decoding library). You need both to get at the picture. Meanwhile, with a different decoding program, the same file can represent a piece of music. Or a text document. "Gödel, Escher, Bach" goes into a detailed discussion about this. On top of that, GP is talking about hardware that builds its own copies, possibly imperfect copies. That implies a lot of information relevant to the organism may not be directly visible in the DNA - it may sit within the replication machinery, and evolve there. It's kind of similar to the difference between machine code and microcode + actual traces in silicon. A famous Turing Award Lecture by Ken Thompson, "Reflections on Trusting Trust", provides another example[0]. Consider a C compiler. How do you build one? From its C source code, using a different C compiler. Now imagine a malicious C compiler that a) injects a trojan into the compiled binary whenever it compiles, say, "login" program, and b) injects a trojan into the binary whenever it compiles another C compiler; that second trojan contains the code for injecting a) and b). You use that compiler to recompile the original C compiler, install it in a system - and from now on, not only "login" will be bugged, but you can't get a non-malicious compiler by recompiling the original one from source; the source contains no traces of the trojans, but they are there, in the binary of the compiler you're using, and they self-replicate. This is what I believe happens with life. -- [0] - https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_ReflectionsonTrustingTrust.pdf https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_Ref...
- dehrmann 7y ago
  > On top of that, GP is talking about hardware that builds its own copies, possibly imperfect copies. That implies a lot of information relevant to the organism may not be directly visible in the DNA - it may sit within the replication machinery, and evolve there. GGP here. This ^, and yes, not epigenetics.

by shijie 7y ago

I think what you’re describing here is called “epigenetics,” or how different genes are expressed or not expressed due to environmental and other outside factors such as stress, etc...

rolph 7y ago

the big deal about epigenetics is that those [methylation and histone binding] are modifications that dont alter the sequence of the DNA but are also inherited by subsequent generations. https://www.thieme-connect.de/products/ejournals/abstract/10.1055/s-0029-1237423 https://www.thieme-connect.de/products/ejournals/abstract/10... https://sci-hub.se/10.1038/542406a https://sci-hub.se/10.1038/542406a

ryankemper 7y ago

For those that aren't familiar, this principle is known as gene expression: https://en.wikipedia.org/wiki/Gene_expression https://en.wikipedia.org/wiki/Gene_expression To make an analogy to software, a common pattern is to have a monolithic repo with many different "personalities" (codepaths / configurations) that utilize different subsets of the monolith. DNA seems to work under a similar principle, a given cell will preferentially transcribe parts of the DNA based on epigenetic factors.

enchiridion 7y ago

Maybe in a way. I think they are driving at an orthogonal argument. The DNA is more or less useless without cells. It seems like the machinery of the cell carries information about the whole of the organism in an abstract sense.

01100011 7y ago

I think the analogy would be something like: DNA is the code. Epigenetics are config options which can be saved to a file and passed on. The cell is the machine which interprets the DNA + config options. So there are three pieces, and I don't think OP was talking about epigenetics.

TeMPOraL 7y ago

What GP is talking about is that information is never fully contained in a medium; it's encoded in the tuple (the medium, what reads the medium). E.g. take a JPG file. The picture in that file isn't fully contained in the bits that file consists of. Some of the information is contained in the JPG specification (and through it, in the JPG decoding library). You need both to get at the picture. Meanwhile, with a different decoding program, the same file can represent a piece of music. Or a text document. "Gödel, Escher, Bach" goes into a detailed discussion about this. On top of that, GP is talking about hardware that builds its own copies, possibly imperfect copies. That implies a lot of information relevant to the organism may not be directly visible in the DNA - it may sit within the replication machinery, and evolve there. It's kind of similar to the difference between machine code and microcode + actual traces in silicon. A famous Turing Award Lecture by Ken Thompson, "Reflections on Trusting Trust", provides another example[0]. Consider a C compiler. How do you build one? From its C source code, using a different C compiler. Now imagine a malicious C compiler that a) injects a trojan into the compiled binary whenever it compiles, say, "login" program, and b) injects a trojan into the binary whenever it compiles another C compiler; that second trojan contains the code for injecting a) and b). You use that compiler to recompile the original C compiler, install it in a system - and from now on, not only "login" will be bugged, but you can't get a non-malicious compiler by recompiling the original one from source; the source contains no traces of the trojans, but they are there, in the binary of the compiler you're using, and they self-replicate. This is what I believe happens with life. -- [0] - https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_ReflectionsonTrustingTrust.pdf https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_Ref...

dehrmann 7y ago
> On top of that, GP is talking about hardware that builds its own copies, possibly imperfect copies. That implies a lot of information relevant to the organism may not be directly visible in the DNA - it may sit within the replication machinery, and evolve there. GGP here. This ^, and yes, not epigenetics.