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I wouldn't recommend trying to understand it through analogy to CS - I'm a biologist and know enough CS to feel uncomfortable really using any of the usual ana

I wouldn't recommend trying to understand it through analogy to CS - I'm a biologist and know enough CS to feel uncomfortable really using any of the usual analogies. The problem is that they work ok for a layperson understanding, but are fundamentally wrong enough that if you want to understand it at the level of something like virology you'll be lead constantly astray. I dont know of a better recommendation than "watch some recorder bio 101 lectures or pick up a textbook, and learn it like a bio major instead of a CS major." It's a lot of time commitment, but I think you have to put in the time to actually learn it from first principles. For context, imagine if I as a biologist asked you, what's a good read on CS for a biologist? And generally how algorithms, data science, AI, and operating systems work? You can understand why it would be difficult to recommend any readings on it. For me to learn to code at any level, I had to spend the time learning it from the fundamentals, and it was worth spending the time for me as it was far more rewarding than trying to wrap my mind around something like "so imagine source code is this thing that's like DNA + epigenetics + dna topology that codes for the information you want, but instead of a complex set of chemical and physical interactions, it's math, and you can change it at will and nothing is leaky on purpose, and the code you write doesnt evolve unless you tell it to which you might want to do sometimes for AI stuff, but usually not."

Retric 7y ago
It’s hard to disagree with what your saying, but analogies are fun. I think the best analogy is DNA is a series of automated assembly lines. The workers, raw materials, and signals to turn sections on or off are separate. Each nucleotide station is called A, T, C, or G and adds a single element at a time to long chains which then get folded up into useful tools. DNA can also be used to manufacture either more stands of DNA or to do very simple repairs. Alternatively, a stack of computer punch cards with a program on them. In that it’s a standard format for information transfer that is physically altered by the message it carries. Further, on it’s own nothing happens but connected to the right machinery it’s useful.
- vikramkr 7y ago
  Edit - I'll concede that analogies are absolutely fun haha. They might be useful to come up with when you yourself are trying to better understand something by drawing connections to other things you know and all. But I don't think they're ideal for being taught the subject. And again, for a layperson, analogies are totally fine if you just want a surface level understanding of "oh, mitochondrias are powerhouses of the cell." But if you want to do anything with that, beware the dangers. The second analogy is ok, but again not really great if you want to understand what's actually going on. If you just want to get an intuition that DNA has something to do with storing information, as long as that comes with an understanding that information evolves (biology is really the study of evolution in many ways), that's probably more than enough for a layperson. But it's a dangerous understanding if you plan on using it as a foundation to try and explore more complicated topics in biology. There's no need to do so, but if you are going to, it's far far better to spend the time getting the correct first-principles understanding and get rid of this idea of "DNA as source code" so you can better grapple with the subject. I don't think the first analogy makes much sense since it makes nucleotides the sort of active agents here and needlessly focuses on individual nucleotides when codon triplets are what are involved in coding for proteins (probably better to, if you have to use an analogy, treat nucleotides as letters instead of words). And, especially in the context of this thread, neither analogy build the understanding needed to really dive into what RNA is, which is important for understanding what RNA viruses are, and what the coronavirus is.
  - salty_biscuits 7y ago
    Source code, but pretend there is no error correction and your logic circuit is noisy? (or the details of the error correction are murky)
    - vikramkr 7y ago
      And it also doesn't contain all of the source code and the error correction is when it tries to copy itself? I mean, just thinking of it as a type of biological source code that makes more of itself with mistakes and is messy is a decent enough analogy, and again I think most of these are fine just to be able to know as a layperson "oh right, DNA is that thing that has a lot of information about what the living thing is going to be like." You don't really need to know more than that day to day as long as other people do - I don't know how to fix my car but i know there are people out there that know how it works. If you are going to be more involved with it or want to know more about it for whatever reason though it's maybe worth diving into the bio 101 stuff then.
umvi 7y ago
It's hard not to draw analogies though. For example, the covid-19 virus's RNA ends with AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA (33 As) which, as someone pointed out, looks suspicially like a "NOP sled"[1] (i.e. so that a protein coming in hot can hit anywhere on the sled and then slide down to the actual information) [1] https://en.wikipedia.org/wiki/NOP_slide https://en.wikipedia.org/wiki/NOP_slide
- vikramkr 7y ago
  A poly A tail is at the end of the transcript, not the start. This is a perfect example of the dangers of analogies because this one is completely incorrect. Poly A tails protect RNA from degradation. A ribosome will not bind to that part, it will bind to something within the 5' untranslated region on the other end of the genome) ribosome binding site, kozak consensus sequence, etc). If you bound to the poly A tail and slide "down," you'd just slide right off the end of the gene. Definitely nothing wrong with trying to find things that look similar across fields and try and gain differentiated insights, it's certainly an admirable thing and an important part of making many discoveries. But a first principles understanding of the structure of DNA, what a 5' end and a 3' end is, and how transcription/translation works (all bio 101 type stuff) would provide a much better foundation to do that with. You don't need a degree in biology to know the basics, just like you don't need a degree in CS to know the basics, but it's worth learning the basics if you want to get an understanding of the field or work with it. https://en.wikipedia.org/wiki/Polyadenylation https://en.wikipedia.org/wiki/Polyadenylation
- deleted 7y ago
  [deleted]
Hnrobert42 7y ago
Can you recommend any sites like HN, but for biology?
- vikramkr 7y ago
  I dont actually know of any. I've heard of like biostar and maybe a couple others but I dont know how good those are. Researchgate is kind of a forum I guess? But most of the questions I've seen in the social media side of that are like "how do I turn this experiment" I think most of the discussions I've had have been journal clubs during lab meetings. An hn style website for virtual journal clubs would be super cool...

Retric 7y ago

It’s hard to disagree with what your saying, but analogies are fun. I think the best analogy is DNA is a series of automated assembly lines. The workers, raw materials, and signals to turn sections on or off are separate. Each nucleotide station is called A, T, C, or G and adds a single element at a time to long chains which then get folded up into useful tools. DNA can also be used to manufacture either more stands of DNA or to do very simple repairs. Alternatively, a stack of computer punch cards with a program on them. In that it’s a standard format for information transfer that is physically altered by the message it carries. Further, on it’s own nothing happens but connected to the right machinery it’s useful.

vikramkr 7y ago
Edit - I'll concede that analogies are absolutely fun haha. They might be useful to come up with when you yourself are trying to better understand something by drawing connections to other things you know and all. But I don't think they're ideal for being taught the subject. And again, for a layperson, analogies are totally fine if you just want a surface level understanding of "oh, mitochondrias are powerhouses of the cell." But if you want to do anything with that, beware the dangers. The second analogy is ok, but again not really great if you want to understand what's actually going on. If you just want to get an intuition that DNA has something to do with storing information, as long as that comes with an understanding that information evolves (biology is really the study of evolution in many ways), that's probably more than enough for a layperson. But it's a dangerous understanding if you plan on using it as a foundation to try and explore more complicated topics in biology. There's no need to do so, but if you are going to, it's far far better to spend the time getting the correct first-principles understanding and get rid of this idea of "DNA as source code" so you can better grapple with the subject. I don't think the first analogy makes much sense since it makes nucleotides the sort of active agents here and needlessly focuses on individual nucleotides when codon triplets are what are involved in coding for proteins (probably better to, if you have to use an analogy, treat nucleotides as letters instead of words). And, especially in the context of this thread, neither analogy build the understanding needed to really dive into what RNA is, which is important for understanding what RNA viruses are, and what the coronavirus is.
- salty_biscuits 7y ago
  Source code, but pretend there is no error correction and your logic circuit is noisy? (or the details of the error correction are murky)
  - vikramkr 7y ago
    And it also doesn't contain all of the source code and the error correction is when it tries to copy itself? I mean, just thinking of it as a type of biological source code that makes more of itself with mistakes and is messy is a decent enough analogy, and again I think most of these are fine just to be able to know as a layperson "oh right, DNA is that thing that has a lot of information about what the living thing is going to be like." You don't really need to know more than that day to day as long as other people do - I don't know how to fix my car but i know there are people out there that know how it works. If you are going to be more involved with it or want to know more about it for whatever reason though it's maybe worth diving into the bio 101 stuff then.

umvi 7y ago

It's hard not to draw analogies though. For example, the covid-19 virus's RNA ends with AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA (33 As) which, as someone pointed out, looks suspicially like a "NOP sled"[1] (i.e. so that a protein coming in hot can hit anywhere on the sled and then slide down to the actual information) [1] https://en.wikipedia.org/wiki/NOP_slide https://en.wikipedia.org/wiki/NOP_slide

vikramkr 7y ago
A poly A tail is at the end of the transcript, not the start. This is a perfect example of the dangers of analogies because this one is completely incorrect. Poly A tails protect RNA from degradation. A ribosome will not bind to that part, it will bind to something within the 5' untranslated region on the other end of the genome) ribosome binding site, kozak consensus sequence, etc). If you bound to the poly A tail and slide "down," you'd just slide right off the end of the gene. Definitely nothing wrong with trying to find things that look similar across fields and try and gain differentiated insights, it's certainly an admirable thing and an important part of making many discoveries. But a first principles understanding of the structure of DNA, what a 5' end and a 3' end is, and how transcription/translation works (all bio 101 type stuff) would provide a much better foundation to do that with. You don't need a degree in biology to know the basics, just like you don't need a degree in CS to know the basics, but it's worth learning the basics if you want to get an understanding of the field or work with it. https://en.wikipedia.org/wiki/Polyadenylation https://en.wikipedia.org/wiki/Polyadenylation
deleted 7y ago
[deleted]

Hnrobert42 7y ago

Can you recommend any sites like HN, but for biology?

vikramkr 7y ago
I dont actually know of any. I've heard of like biostar and maybe a couple others but I dont know how good those are. Researchgate is kind of a forum I guess? But most of the questions I've seen in the social media side of that are like "how do I turn this experiment" I think most of the discussions I've had have been journal clubs during lab meetings. An hn style website for virtual journal clubs would be super cool...