5 ms·

>Don't try to think about genomics in programming terms. At some point, some Newton person will figure it. It always happen. As for now, it might be interesti

>Don't try to think about genomics in programming terms. At some point, some Newton person will figure it. It always happen. As for now, it might be interesting to understand why exactly the analogy between genomics and programming fails. It might bring interesting insights into both fields. So why not try to think about?

throwanem 5y ago
Because the only way to imagine a useful comparison between these fields can be made is to be profoundly ignorant of at least one of them.
- burning_hamster 5y ago
  As a bioinformatician, I cannot wait to use this quote on someone.
  - throwanem 5y ago
    As an enthusiastically former staff engineer at a bioinformatics institute, I'm happy to have been of help! Please feel free to do so without attribution; if nothing else, it'd be a shame at this late date to have my opinions of the caste system in academia disturbed by the novel experience of receiving credit for my contributions to the work of people with letters after their names. :D
    - airhead969 5y ago
      Department chairs > PIs >~ profs > visiting profs > assistant profs >~ visiting asst profs > postdocs > grad students > employees > undergrads > high-school interns Dedicated grant-writing staff are gold, literally and figuratively. (I worked at a biomedical informatics shop.)
- sooheon 5y ago
  Rather than assert the negative, can you state some positive facts about one or the other that makes this point clear?
  - throwanem 5y ago
    Software changes over spans of minutes to decades; genomes change over spans of millions of years. Software is written; genomes are not. The complexity of software is constrained by programmers' ability to comprehend it; the complexity of genomes is not. The environment in which software functions is determined by humans; the environment in which genomes function is not.
    - sooheon 5y ago
      Those are trivial surface level differences relative to the central idea of encoding, storing, replicating, editing digital information, which interfaces with other digital and analog systems.
      - throwanem 5y ago
        Not that there's much point to saying so, since you appear to be here for no other reason than to assert that my argument is false because you would prefer it be so, but here's another: software is digital; genomes are not.
        staticassertion 5y ago
        FWIW all of these differences still feel extremely surface level. I'm no expert but I certainly am, so far, aware of everything you've said with regards to how they differ - I'm kinda hoping for more, given the strong assertion you made that one can not relate the two without being fundamentally ignorant of either topic. I also think it's somewhat ironic that you're accusing them of only being here to say "you're wrong" but that's what you've done in this thread? I only bring this up because I think we're all after the same thing here - to understand an incredibly interesting topic. I suspect most of us are really here to learn and discuss. You seem like you have a background in the area, I'm sure we would all benefit from learning about the differences. If it's the case that the similar is that DNA and code both encode information, and the differences are based on how they do so, it's hard to see why you think they can't be related at all. You've been relating the two.
- techbio 5y ago
  I love this. It's a little black and white, but the comparison is as between video game worlds and the real world. Only enough to fool the willing eye. I use a variation of this form as 'persons whos science and religions conflict don't know enough about either one'.
- dekhn 5y ago
  I'm profoundly ignorant in neither (PhD in biophysics, software engineer for 20 years). Genomics and programming analogies are cool, but the most important thing is that understanding that molecular structures can encode information in a replicable way, and the discovery of application of entropy to data storage and transmission, demonstrates that information is a universal concept, that the genome is a data storage system, and the enzymes that operate it are operating on information, in a computational way. To me that's a pretty useful comparison.

throwanem 5y ago

Because the only way to imagine a useful comparison between these fields can be made is to be profoundly ignorant of at least one of them.

burning_hamster 5y ago
As a bioinformatician, I cannot wait to use this quote on someone.
- throwanem 5y ago
  As an enthusiastically former staff engineer at a bioinformatics institute, I'm happy to have been of help! Please feel free to do so without attribution; if nothing else, it'd be a shame at this late date to have my opinions of the caste system in academia disturbed by the novel experience of receiving credit for my contributions to the work of people with letters after their names. :D
  - airhead969 5y ago
    Department chairs > PIs >~ profs > visiting profs > assistant profs >~ visiting asst profs > postdocs > grad students > employees > undergrads > high-school interns Dedicated grant-writing staff are gold, literally and figuratively. (I worked at a biomedical informatics shop.)
sooheon 5y ago
Rather than assert the negative, can you state some positive facts about one or the other that makes this point clear?
- throwanem 5y ago
  Software changes over spans of minutes to decades; genomes change over spans of millions of years. Software is written; genomes are not. The complexity of software is constrained by programmers' ability to comprehend it; the complexity of genomes is not. The environment in which software functions is determined by humans; the environment in which genomes function is not.
  - sooheon 5y ago
    Those are trivial surface level differences relative to the central idea of encoding, storing, replicating, editing digital information, which interfaces with other digital and analog systems.
    - throwanem 5y ago
      Not that there's much point to saying so, since you appear to be here for no other reason than to assert that my argument is false because you would prefer it be so, but here's another: software is digital; genomes are not.
      - staticassertion 5y ago
        FWIW all of these differences still feel extremely surface level. I'm no expert but I certainly am, so far, aware of everything you've said with regards to how they differ - I'm kinda hoping for more, given the strong assertion you made that one can not relate the two without being fundamentally ignorant of either topic. I also think it's somewhat ironic that you're accusing them of only being here to say "you're wrong" but that's what you've done in this thread? I only bring this up because I think we're all after the same thing here - to understand an incredibly interesting topic. I suspect most of us are really here to learn and discuss. You seem like you have a background in the area, I'm sure we would all benefit from learning about the differences. If it's the case that the similar is that DNA and code both encode information, and the differences are based on how they do so, it's hard to see why you think they can't be related at all. You've been relating the two.
techbio 5y ago
I love this. It's a little black and white, but the comparison is as between video game worlds and the real world. Only enough to fool the willing eye. I use a variation of this form as 'persons whos science and religions conflict don't know enough about either one'.
dekhn 5y ago
I'm profoundly ignorant in neither (PhD in biophysics, software engineer for 20 years). Genomics and programming analogies are cool, but the most important thing is that understanding that molecular structures can encode information in a replicable way, and the discovery of application of entropy to data storage and transmission, demonstrates that information is a universal concept, that the genome is a data storage system, and the enzymes that operate it are operating on information, in a computational way. To me that's a pretty useful comparison.