4 ms·

DNA is code, we just don't have a compiler yet.

eli_gottlieb 11y ago
Phenotype = genotype + environment + reproductive phenotype (that is, the seed shell for a plant, egg for a bird, or the uterus for a mammal). Being able to rewrite the genotype doesn't give you total customization of the resulting phenotype.
- mylons 11y ago
  and this is just our current understanding, which is certainly going to shift as measurement becomes cheaper and more accurate. iterative science!
- ethbro 11y ago
  Wouldn't the reproductive phenotype in this case also be genetically controlled (albeit in the previous generation's)?
  - eli_gottlieb 11y ago
    Except that it's also subject to its own environmental influences, separately from those which impact the new individual after its birth.
- refurb 11y ago
  Exactly! Identical twins have the same DNA, but they don't have the same fingerprints. Why? Different environment in the womb. Could we tweak things like eye color? Sure. Things like intelligence? Much, much harder.
mylons 11y ago
this is overly simplistic
- udp 11y ago
  Simplistic, but a good way to think of the difference between genetic engineering and synthetic biology. Genetic engineering is like reverse engineering: poking around in an executable to change bits of the assembler and see what happens. Synthetic biology is attempting to build a top-down approach for genetic designs: specification, design, implementation, testing - and in that model, the DNA is the machine code and we are indeed trying to make a compiler.
  - jacquesm 11y ago
    Sure, but that still requires you to stay within the boundaries of what is expressible in the first place. Rakes, maybe. Bedframes: not so much.
    - udp 11y ago
      Yes, I'm not saying we're going to be able to grow bedframes. I just quite like the "DNA is code and we need a compiler" analogy.
      - jacquesm 11y ago
        If only it were that simple. We're very far away from understanding how a particular DNA string relates to phenotypes. All we've found to date is a bunch of configuration bits and maybe a general idea of how things might be related to each other but not much more than that. The gap in understanding between 'here are a bunch of bits that appear to do 'x'' and 'x' is vast, far larger than the gap between say being able to build a compiler to have an executable perform in a certain way. If anywhere that is where the real breakthrough will be, in being able to effectively map the chain of binary bits in a genome to a certain phenotype in a mature organism without any 'leftover bits'. Once you have that chain of causality mapped out in enough detail to clearly link all causes with their effects you can start engineering something to act in a way that is far outside what we normally find in nature. I'm not sure if I'm expressing myself clearly about all this, maybe someone more versed in the matter can chime in but the path between DNA and organism is a lot longer and less well understood than the path between a low level language program and the resulting output of that program. Just having a 'compiler' will not change much about that understanding, though once we have that compiler we may be able to advance our understanding by a more direct approach in modifying pieces of an existing genome to observe the effects in the organism. For sure it will speed things up. edit: if we did have that understanding it would be trivial to create a digital representation of a (simple) organism from it's sequenced DNA. The fact that we are nowhere near capable of doing this is a simple proof that merely being able to create a certain sequence of bits will not give us the capability to create organisms to order.
TeMPOraL 11y ago
DNA seems to be strongly compressed code that's also used as data. But we're not even sure if it encodes everything there is about an organism. Keep in mind that organisms aren't made in a single factory, they build child organisms, which then build further organisms, etc., creating a chain. You can imagine it as being a single runtime, accumulating state. It is possible that, e.g. replication machinery gets altered in such a way that it builds altered copies - the information about this alteration may had disappeared from DNA or never be there in the first place, and yet the alteration propagates. TL;DR: read "Reflections on Trusting Trust", the same phenomena applies to biology.
Excavator 11y ago
Define compiler? As I recall it Genome Compiler[1] allows you to define functions and then order the finished product. 1: http://www.genomecompiler.com/ http://www.genomecompiler.com/
bsima 11y ago
I think this was written just for you: http://xkcd.com/1605/ http://xkcd.com/1605/

Phenotype = genotype + environment + reproductive phenotype (that is, the seed shell for a plant, egg for a bird, or the uterus for a mammal). Being able to rewrite the genotype doesn't give you total customization of the resulting phenotype.

mylons 11y ago
and this is just our current understanding, which is certainly going to shift as measurement becomes cheaper and more accurate. iterative science!
ethbro 11y ago
Wouldn't the reproductive phenotype in this case also be genetically controlled (albeit in the previous generation's)?
- eli_gottlieb 11y ago
  Except that it's also subject to its own environmental influences, separately from those which impact the new individual after its birth.
refurb 11y ago
Exactly! Identical twins have the same DNA, but they don't have the same fingerprints. Why? Different environment in the womb. Could we tweak things like eye color? Sure. Things like intelligence? Much, much harder.

mylons 11y ago

this is overly simplistic

udp 11y ago
Simplistic, but a good way to think of the difference between genetic engineering and synthetic biology. Genetic engineering is like reverse engineering: poking around in an executable to change bits of the assembler and see what happens. Synthetic biology is attempting to build a top-down approach for genetic designs: specification, design, implementation, testing - and in that model, the DNA is the machine code and we are indeed trying to make a compiler.
- jacquesm 11y ago
  Sure, but that still requires you to stay within the boundaries of what is expressible in the first place. Rakes, maybe. Bedframes: not so much.
  - udp 11y ago
    Yes, I'm not saying we're going to be able to grow bedframes. I just quite like the "DNA is code and we need a compiler" analogy.
    - jacquesm 11y ago
      If only it were that simple. We're very far away from understanding how a particular DNA string relates to phenotypes. All we've found to date is a bunch of configuration bits and maybe a general idea of how things might be related to each other but not much more than that. The gap in understanding between 'here are a bunch of bits that appear to do 'x'' and 'x' is vast, far larger than the gap between say being able to build a compiler to have an executable perform in a certain way. If anywhere that is where the real breakthrough will be, in being able to effectively map the chain of binary bits in a genome to a certain phenotype in a mature organism without any 'leftover bits'. Once you have that chain of causality mapped out in enough detail to clearly link all causes with their effects you can start engineering something to act in a way that is far outside what we normally find in nature. I'm not sure if I'm expressing myself clearly about all this, maybe someone more versed in the matter can chime in but the path between DNA and organism is a lot longer and less well understood than the path between a low level language program and the resulting output of that program. Just having a 'compiler' will not change much about that understanding, though once we have that compiler we may be able to advance our understanding by a more direct approach in modifying pieces of an existing genome to observe the effects in the organism. For sure it will speed things up. edit: if we did have that understanding it would be trivial to create a digital representation of a (simple) organism from it's sequenced DNA. The fact that we are nowhere near capable of doing this is a simple proof that merely being able to create a certain sequence of bits will not give us the capability to create organisms to order.

TeMPOraL 11y ago

DNA seems to be strongly compressed code that's also used as data. But we're not even sure if it encodes everything there is about an organism. Keep in mind that organisms aren't made in a single factory, they build child organisms, which then build further organisms, etc., creating a chain. You can imagine it as being a single runtime, accumulating state. It is possible that, e.g. replication machinery gets altered in such a way that it builds altered copies - the information about this alteration may had disappeared from DNA or never be there in the first place, and yet the alteration propagates. TL;DR: read "Reflections on Trusting Trust", the same phenomena applies to biology.

Excavator 11y ago

Define compiler? As I recall it Genome Compiler[1] allows you to define functions and then order the finished product. 1: http://www.genomecompiler.com/ http://www.genomecompiler.com/

bsima 11y ago

I think this was written just for you: http://xkcd.com/1605/ http://xkcd.com/1605/