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If I had a nickel for every terrible biology to computer processes analogy I saw on this website since joining, I’d probably have enough money to buy a beer. Wh

If I had a nickel for every terrible biology to computer processes analogy I saw on this website since joining, I’d probably have enough money to buy a beer. Which is what I feel I need after I see something like this. Biology does not act like a computer. You cannot reduce biology to an operating system

TeMPOraL 3y ago
> Biology does not act like a computer. You cannot reduce biology to an operating system Nobody is doing that. Analogies are drawing rough outlines in the thought-space[0], they aren't a definition. As such, they are helpful. -- [0] - Or latent space, if I want to make an analogy inside the analogy apologia.
- deleted 3y ago
  [deleted]
- fabian2k 3y ago
  I don't think the programming analogies are helpful here, they seem to cause a serious amount of confusion. The basic idea isn't so bad, but too many people seem to try and push them much, much further than they can work. For a developer this analogy also implies a lot of assumptions that they know to be true for code that are simply wrong for biology.
  - theGnuMe 3y ago
    One can view the cell as an information processing entity. If we agree with that view then it can be analyzed as an abstract computational process. If you are upset about using the word 'computational' then consider it to be a dynamical process. We can then use mathematics to analyze this system. In any event, genes (programming instructions) encode proteins (applications) that run in the cell (operating system). Now biology is weird and has multiple feedback steps, some of which we probably do not even know yet, but the basic approach is solid.
    - fabian2k 3y ago
      Those analogies imply things that simply aren't true. Genes and proteins aren't digital, they are real entities with physical and chemical properties that affect everything they do. Of course you can model various aspects of cells mathematically. But that doesn't require any analogies to software.
      - theGnuMe 3y ago
        There's no requirement that a computer or computational process be 'digital'. Analog computers exist, in fact, the first computers were analog. At any rate digital (0,1) strings aren't that different than DNA strings (A, T, C, G) and just because we have 4 characters in the alphabet doesn't mean you can't analyze it as an abstract computational process. You can also discretize the concentration of molecules such that above a threshold switch like behavior occurs (gene turns on or off). Also people have done experiments where they program DNA to perform computations to solve various problems like the traveling salesman problem. This is a direct application of using biology to solve a "digital problem" https://www.nature.com/articles/news000113-10 https://www.nature.com/articles/news000113-10 So here we have an example of an artificial logical problem encoded into DNA and solved using biology. That means biology can simulate computational algorithms.
      - FrustratedMonky 3y ago
        "model various aspects of cells mathematically" I think a lot of people here will equate software/programming to mathematically modeling. Saying you can model/math it, but not use software analogies, is just really trying to split hairs, since models/math is also software.
- getoffmycase 3y ago
  The fundamentals of biology are not difficult to grasp. Evolution, DNA -> RNA -> Protein, basic cell signalling, etc are all really easy to grasp with just the tiniest bit of effort. There's really no place for bad analogies, especially such a misleading one. Sorry to bite your head off, but the reason that I'm passionate about this topic is, and I'm not joking, young earth Creationism. An analogy like the grandparent is something simple to grasp by many people, and then the Creationists can quickly turn around and say, "Well you see how biology is like a computer; somebody built a computer; therefore, God created us in six days, 6000 years ago."
  - silent_cal 3y ago
    [flagged]
    - getoffmycase 3y ago
      What are the proper qualifications to criticize evolution?
      - jononomo 3y ago
        Well, you could start by reading these books: 1. Darwin on Trial by Phillip E. Johnson 2. The Stairway To Life: An Origin-Of-Life Reality Check by Tan & Stadler 3. Darwin's Doubt by Stephen C. Meyer
        jibal 3y ago
        Those are by people not qualified to criticize evolution.
        silent_cal 3y ago
        I'm not sure about the others (don't know who they are), but Meyer certainly is.
        3y ago
- Viliam1234 3y ago
  How exactly is the analogy "DNA: file.c" helpful to answer the question from the article "Where did DNA come from?"?
Ralfp 3y ago
This is sometimes called „Andrew Grove Fallacy” after Intel Ceo’s interview in Newsweek where he famously commented how drug research should look at CPU engineering for inspiration to improve itself, missing point that in biology we dont have privilege of knowing how each part of the system works, compared to, eg. designing CPUs, and making invalid analogies.
- tivert 3y ago
  I've also heard this described as "Engineer's Disease": "We think because we're an expert in one area, we're automatically an expert in other areas." (https://news.ycombinator.com/item?id=10812804 https://news.ycombinator.com/item?id=10812804). I think the core lazy assumption that enables is the idea that all the other fields are properly understood as just like your field. Sometimes it's so bad that a software engineer will outright dismiss the ideas of actual experts as misguided, and insist on some "disrupting" the fields with some half-ass software-thinking.
deleted 3y ago
[deleted]
jibal 3y ago
How does a computer act? I think your understanding of that is too narrow ... consult the Church-Turing thesis; biology computes. And an operating system is just one sort of program ... it makes no sense to talk about reducing to an operating system; that's a category mistake.
FrustratedMonky 3y ago
Is there an alternative to analogies and metaphors when using language? What terms/concepts should be used in their place?
dekhn 3y ago
Parts of biology act like analog computers even if the whole of biology exceeds what we see in computing. But more importantly: the existence of DNA demonstrates that information processing is universal and that there are many common aspects between current approaches to silicon-based information processing and biology-based information processing.
dang 3y ago
Ok, but can you please make your substantive points informatively? Just putting someone else or the community down doesn't help. It just makes the thread shallow and dyspeptic. If you know more than others do, that's great, but then please share some of what you know, so the rest of us can learn (edit: like you did here! https://news.ycombinator.com/item?id=36330052 https://news.ycombinator.com/item?id=36330052) If you don't want to do that, that's fine too, but in that case the thing to do is remind oneself that the internet is more or less wrong about everything and move on. I know it's tempting to leave an empty negative comment to relieve oneself of annoyance, but this is the worst choice, at least on HN. It not only isn't the curious conversation we're looking for, it actively impedes it. p.s. You're a good HN commenter generally - so thanks for that! https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sort=byDate&type=comment&query=share%20know%20learn%20by:dang https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sor...

TeMPOraL 3y ago

> Biology does not act like a computer. You cannot reduce biology to an operating system Nobody is doing that. Analogies are drawing rough outlines in the thought-space[0], they aren't a definition. As such, they are helpful. -- [0] - Or latent space, if I want to make an analogy inside the analogy apologia.

deleted 3y ago
[deleted]
fabian2k 3y ago
I don't think the programming analogies are helpful here, they seem to cause a serious amount of confusion. The basic idea isn't so bad, but too many people seem to try and push them much, much further than they can work. For a developer this analogy also implies a lot of assumptions that they know to be true for code that are simply wrong for biology.
- theGnuMe 3y ago
  One can view the cell as an information processing entity. If we agree with that view then it can be analyzed as an abstract computational process. If you are upset about using the word 'computational' then consider it to be a dynamical process. We can then use mathematics to analyze this system. In any event, genes (programming instructions) encode proteins (applications) that run in the cell (operating system). Now biology is weird and has multiple feedback steps, some of which we probably do not even know yet, but the basic approach is solid.
  - fabian2k 3y ago
    Those analogies imply things that simply aren't true. Genes and proteins aren't digital, they are real entities with physical and chemical properties that affect everything they do. Of course you can model various aspects of cells mathematically. But that doesn't require any analogies to software.
    - theGnuMe 3y ago
      There's no requirement that a computer or computational process be 'digital'. Analog computers exist, in fact, the first computers were analog. At any rate digital (0,1) strings aren't that different than DNA strings (A, T, C, G) and just because we have 4 characters in the alphabet doesn't mean you can't analyze it as an abstract computational process. You can also discretize the concentration of molecules such that above a threshold switch like behavior occurs (gene turns on or off). Also people have done experiments where they program DNA to perform computations to solve various problems like the traveling salesman problem. This is a direct application of using biology to solve a "digital problem" https://www.nature.com/articles/news000113-10 https://www.nature.com/articles/news000113-10 So here we have an example of an artificial logical problem encoded into DNA and solved using biology. That means biology can simulate computational algorithms.
    - FrustratedMonky 3y ago
      "model various aspects of cells mathematically" I think a lot of people here will equate software/programming to mathematically modeling. Saying you can model/math it, but not use software analogies, is just really trying to split hairs, since models/math is also software.
getoffmycase 3y ago
The fundamentals of biology are not difficult to grasp. Evolution, DNA -> RNA -> Protein, basic cell signalling, etc are all really easy to grasp with just the tiniest bit of effort. There's really no place for bad analogies, especially such a misleading one. Sorry to bite your head off, but the reason that I'm passionate about this topic is, and I'm not joking, young earth Creationism. An analogy like the grandparent is something simple to grasp by many people, and then the Creationists can quickly turn around and say, "Well you see how biology is like a computer; somebody built a computer; therefore, God created us in six days, 6000 years ago."
- silent_cal 3y ago
  [flagged]
  - getoffmycase 3y ago
    What are the proper qualifications to criticize evolution?
    - jononomo 3y ago
      Well, you could start by reading these books: 1. Darwin on Trial by Phillip E. Johnson 2. The Stairway To Life: An Origin-Of-Life Reality Check by Tan & Stadler 3. Darwin's Doubt by Stephen C. Meyer
      - jibal 3y ago
        Those are by people not qualified to criticize evolution.
        silent_cal 3y ago
        I'm not sure about the others (don't know who they are), but Meyer certainly is.
        3y ago
Viliam1234 3y ago
How exactly is the analogy "DNA: file.c" helpful to answer the question from the article "Where did DNA come from?"?

Ralfp 3y ago

This is sometimes called „Andrew Grove Fallacy” after Intel Ceo’s interview in Newsweek where he famously commented how drug research should look at CPU engineering for inspiration to improve itself, missing point that in biology we dont have privilege of knowing how each part of the system works, compared to, eg. designing CPUs, and making invalid analogies.

tivert 3y ago
I've also heard this described as "Engineer's Disease": "We think because we're an expert in one area, we're automatically an expert in other areas." (https://news.ycombinator.com/item?id=10812804 https://news.ycombinator.com/item?id=10812804). I think the core lazy assumption that enables is the idea that all the other fields are properly understood as just like your field. Sometimes it's so bad that a software engineer will outright dismiss the ideas of actual experts as misguided, and insist on some "disrupting" the fields with some half-ass software-thinking.

deleted 3y ago

[deleted]

jibal 3y ago

How does a computer act? I think your understanding of that is too narrow ... consult the Church-Turing thesis; biology computes. And an operating system is just one sort of program ... it makes no sense to talk about reducing to an operating system; that's a category mistake.

FrustratedMonky 3y ago

Is there an alternative to analogies and metaphors when using language? What terms/concepts should be used in their place?

dekhn 3y ago

Parts of biology act like analog computers even if the whole of biology exceeds what we see in computing. But more importantly: the existence of DNA demonstrates that information processing is universal and that there are many common aspects between current approaches to silicon-based information processing and biology-based information processing.

dang 3y ago

Ok, but can you please make your substantive points informatively? Just putting someone else or the community down doesn't help. It just makes the thread shallow and dyspeptic. If you know more than others do, that's great, but then please share some of what you know, so the rest of us can learn (edit: like you did here! https://news.ycombinator.com/item?id=36330052 https://news.ycombinator.com/item?id=36330052) If you don't want to do that, that's fine too, but in that case the thing to do is remind oneself that the internet is more or less wrong about everything and move on. I know it's tempting to leave an empty negative comment to relieve oneself of annoyance, but this is the worst choice, at least on HN. It not only isn't the curious conversation we're looking for, it actively impedes it. p.s. You're a good HN commenter generally - so thanks for that! https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sort=byDate&type=comment&query=share%20know%20learn%20by:dang https://hn.algolia.com/?dateRange=all&page=0&prefix=true&sor...