[inigojonesguy]

>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]

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.

[dekhn]

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.

[sooheon]

Rather than assert the negative, can you state some positive facts about one or the other that makes this point clear?

[throwanem]

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]

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]

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]

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.

[Turing_Machine]

Genomes are absolutely digital. GATC is no different from 1 and 0. It's just using a different base (pun intended).

Files on disks have end of file markers, just like the start and stop sequences in DNA. Operating systems have cron jobs (themselves digital) that control when other programs execute.

[sooheon]

> software is digital; genomes are not

False by definition: Digital data is "information represented as a string of discrete symbols each of which can take only one of a finite number of values"

https://en.wikipedia.org/wiki/Digital_data

[inigojonesguy]

I agree with you here but I get to a happy conclusion. The (self- or culturally imposed) constraint on computation to be semantically meaningful for humans does not apply for genomes. But this is already useful, because it means we at least have a hint about where to dig more in programming.

There is Theory of Computation and there is Theory of Programming. Your arguments apply to TOP but not to TOC.

https://pron.github.io/posts/what-we-talk-about-when-we-talk...

[only_as_i_fall]

This all seems like minor differences.

Plenty of software is neither written nor comprehensible I can assure you of that.

Like I don't think your necessarily wrong, but pointing out the literal differences between the two topics doesn't explain to me why the analogy is wrong and therefore doesn't support your argument.

It's like saying "I'm nothing like my mother; I don't even have long hair"

[techbio]

I think the environment is the confounding factor rather than programmer working life-span.

An OS is just so much simpler than dynamically constrained energetic replicators in an always and everywhere collapsing wave function.

[techbio]

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'.

[burning_hamster]

As a bioinformatician, I cannot wait to use this quote on someone.

[throwanem]

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]

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.)