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If you’re interested, much of what you’re asking about is actually known: (some) DNA sequences map directly to protein sequences. Because DNA has a 4 letter alp

If you’re interested, much of what you’re asking about is actually known: (some) DNA sequences map directly to protein sequences. Because DNA has a 4 letter alphabet (G, C, T, A), it takes three to map to one of the 2x different amino acids that make up proteins. Proteins, in turn, are the “machines” that work in cells. DNA also contains regulatory segments, errors, “dead” code left over (and carried through generations) long after it stopped being transcribed, DNA once inserted by viruses (both active and inactive) etc etc... If you want an analogy with computer code: it’s most like a spaghetti-code hair ball of assembly coding it’s own compiler, IDE, vim, a few games, and a neural network ten magnitudes the size of anything tensorflow can do. It does it all on hardware that works only probabilistically. And it is constantly starved for resources, leading to hacks such as DNA sequences that code for two completely different functioning proteins depending on reading it either forward or backward, or starting to read at an offset (what’s called a “reading frame”). There’s a thick book on molecular biology by Alberts et al. It’s the most phantastic deep dive into this, any many other, insanities. I believe Larry Page used to recommend it to all new googlers.

entee 9y ago
MBOC is the book you're looking for by Alberts: https://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts/dp/0815344325/ref=sr_1_2?ie=UTF8&qid=1519168605&sr=8-2&keywords=molecular+biology+of+the+cell https://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts/... It's standard reading at the very least as intro grad/senior undergrad student in the biosciences. Great book, well written, well curated. Parent commenter is correct, DNA->function is massively complicated. The main wiki article to start with is: https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology https://en.wikipedia.org/wiki/Central_dogma_of_molecular_bio... As the article notes, there are endless exceptions and edge cases. It links to various examples of those.
madhadron 9y ago
I've stopped recommending Alberts. It's a great cartoon guide to a mythical average eukaryotic cell, but it abstracts much farther than the data can bear and leaves the reader without the intellectual tools to work with the material in it. And so you get computer scientists thinking about assembly language and compiling and physicists building little stochastic models of state transitions without knowing the biological considerations that lead those efforts astray. Not that I have a book to recommend instead...
- entee 9y ago
  I disagree, it's a decent overview that introduces the major concepts and how they work. It's not intended to be at the cutting edge or to provide all caveats. By definition all textbooks in biochemistry, biology and the like are out of date by the time they go to press. The average MBOC provides is enough of a basic understanding of molecular biology to move on to more advanced work including papers that start to get into the nitty gritty details. Note that many people haven't been even exposed to the basics!
  - madhadron 9y ago
    I'm not worried about it being out of date. I worry about the misconceptions it leaves in the minds of those who learn from it. They can parrot the words, but the mental models that result from studying it regularly lead people astray. At least, that's my anecdotal observation from as a research biologist.
- collyw 9y ago
  Wow that's a blast from the past. I started a Molecular Biology undergrad in 1992 and that was one of the books we had to buy. Mr Alberts must be doing alight if that is a course text on many courses for so many years.
AllegedAlec 9y ago
> If you want an analogy with computer code: it’s most like a spaghetti-code hair ball of assembly coding it’s own compiler, IDE, vim, a few games, and a neural network ten magnitudes the size of anything tensorflow can do. It does it all on hardware that works only probabilistically. And it is constantly starved for resources, leading to hacks such as DNA sequences that code for two completely different functioning proteins depending on reading it either forward or backward, or starting to read at an offset (what’s called a “reading frame”). Not only that, but it's also (quite literally) radiation hardened: the genome has evolved to a state where most changes to the DNA do very little. Or, if the environment is changing frequently, it'll have evolved to a place in the genome space where it has a higher chance to obtain more beneficial mutations (for more info on this sort of stuff, look up articles by Hogeweg, Colizzi or Crombach). As a computational biologist, I can tell you that evolution works in many ways, but most likely not in the way you'd expect it to.

entee 9y ago

MBOC is the book you're looking for by Alberts: https://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts/dp/0815344325/ref=sr_1_2?ie=UTF8&qid=1519168605&sr=8-2&keywords=molecular+biology+of+the+cell https://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts/... It's standard reading at the very least as intro grad/senior undergrad student in the biosciences. Great book, well written, well curated. Parent commenter is correct, DNA->function is massively complicated. The main wiki article to start with is: https://en.wikipedia.org/wiki/Central_dogma_of_molecular_biology https://en.wikipedia.org/wiki/Central_dogma_of_molecular_bio... As the article notes, there are endless exceptions and edge cases. It links to various examples of those.

madhadron 9y ago

I've stopped recommending Alberts. It's a great cartoon guide to a mythical average eukaryotic cell, but it abstracts much farther than the data can bear and leaves the reader without the intellectual tools to work with the material in it. And so you get computer scientists thinking about assembly language and compiling and physicists building little stochastic models of state transitions without knowing the biological considerations that lead those efforts astray. Not that I have a book to recommend instead...

entee 9y ago
I disagree, it's a decent overview that introduces the major concepts and how they work. It's not intended to be at the cutting edge or to provide all caveats. By definition all textbooks in biochemistry, biology and the like are out of date by the time they go to press. The average MBOC provides is enough of a basic understanding of molecular biology to move on to more advanced work including papers that start to get into the nitty gritty details. Note that many people haven't been even exposed to the basics!
- madhadron 9y ago
  I'm not worried about it being out of date. I worry about the misconceptions it leaves in the minds of those who learn from it. They can parrot the words, but the mental models that result from studying it regularly lead people astray. At least, that's my anecdotal observation from as a research biologist.
collyw 9y ago
Wow that's a blast from the past. I started a Molecular Biology undergrad in 1992 and that was one of the books we had to buy. Mr Alberts must be doing alight if that is a course text on many courses for so many years.

AllegedAlec 9y ago

> If you want an analogy with computer code: it’s most like a spaghetti-code hair ball of assembly coding it’s own compiler, IDE, vim, a few games, and a neural network ten magnitudes the size of anything tensorflow can do. It does it all on hardware that works only probabilistically. And it is constantly starved for resources, leading to hacks such as DNA sequences that code for two completely different functioning proteins depending on reading it either forward or backward, or starting to read at an offset (what’s called a “reading frame”). Not only that, but it's also (quite literally) radiation hardened: the genome has evolved to a state where most changes to the DNA do very little. Or, if the environment is changing frequently, it'll have evolved to a place in the genome space where it has a higher chance to obtain more beneficial mutations (for more info on this sort of stuff, look up articles by Hogeweg, Colizzi or Crombach). As a computational biologist, I can tell you that evolution works in many ways, but most likely not in the way you'd expect it to.