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I think what is described here comes down to the fact that we don't have much (any?) _deep_ understanding of biology. The most concrete aspects of biology are o

by axg11 4y ago

I think what is described here comes down to the fact that we don't have much (any?) _deep_ understanding of biology. The most concrete aspects of biology are observations. For example, anatomy is very well understood because it's essentially observations of structures within living organisms, as field it has been relatively stable for a long time, hence there are well-established methods for teaching anatomy. There's a huge gap between the fundamental units of biology (biochemistry) and the resulting emergent behaviour (living things). We don't have a good bottom-up system to predict the emergent behaviour so we're mostly left with observing from the top down and poking/prodding sub-systems, hoping to gain some insight. When so much of biology is observation without deep insight, it shouldn't be a surprise that biology is difficult to teach, and even more difficult to find beauty in for new students.

shpongled 4y ago
I would argue that depends on your definition of deep - we are certainly getting better at developing both genetic and chemical tools that allow us to probe specific pathways/sub-systems of biology, and read out the resulting perturbed phenotype(s). > There's a huge gap between the fundamental units of biology (biochemistry) and the resulting emergent behaviour (living things). We don't have a good bottom-up system to predict the emergent behaviour so we're mostly left with observing from the top down and poking/prodding sub-systems, hoping to gain some insight. I think this is just about the last thing that we will ever solve/figure out. There are just a mind-boggling number of parameters, feedback loops, dynamic modifications, interactions, etc that are effecting cellular state (let alone organism state) - something that I think many CS oriented folks ignore when talking about "DNA as source code" (perhaps if program behavior depended on the size of indents, font, variable names, how many lines of code you wrote, the proximity in source location of different functions, etc).
- AlecSchueler 4y ago
  > (perhaps if program behavior depended on the size of indents, font, variable names, how many lines of code you wrote, the proximity in source location of different functions, etc) I think I've seen all of those functionalities implemented in esoteric programming languages! Nice comparison.
  - marcosdumay 4y ago
    What you haven't seen is a CD-ROM sized program with no abstraction, encapsulation, or modularization, all implemented on a language that has all of those. Oh, and that is being interpreted by more than one incompatible interpreter at the same time.
- randcraw 4y ago
  Yeah, I think programmers would better appreciate the complexity and subtlety of biology much better if they had to evolve their programs rather than code them up explicitly. (I say this as someone with degrees in both subjects.)
onychomys 4y ago
> There's a huge gap between the fundamental units of biology (biochemistry) and the resulting emergent behaviour (living things). And then a very similar gap between the fundamental units of one small branch of biology, ecology, where the fundamental units are living things and the emergent behavior is everything you see outside your window! We have a lot of math that explains how things act and evolve together and it's all just the tiniest little smidge of what actually happens.
atty 4y ago
You can have what I would consider deep knowledge of a system without the ability to manufacture it or modify it. For instance, we have pretty deep knowledge of how the sun or other stars work, but we can’t even begin to dream about creating one, or controlling one. In the same way, we know a lot of how biology works. Obviously nowhere near all of it; but we are far beyond just scratching the surface. It just turns out that modifying a working complex system is pretty hard.
- h2odragon 4y ago
  > ow the sun or other stars work, but we can’t even begin to dream about creating one Wolfram didn't answer "how much would a solar mass of hydrogen cost" for me, but it did tell me that the solar mass is 1.988435×10^33 grams, and another search found hydrogen prices [1] in the range of US$ 250 to 1350 per MT ... So just the financing on building another sun is going to be tricky. [1] I know it's not all hydrogen but we'll burn those bridges when we get to them.
  - PebblesRox 4y ago
    Gotta budget for some extra hydrogen to burn the bridges.
  - burnished 4y ago
    Oof, and you didn't even factor in extra-solar shipping costs. Thats most of the expense, really.
ramraj07 4y ago
Hard disagree. We understand biology for the most part. The issue is in the exact implementations. An analogy would be like understanding how a computer works. We know how chips are made, the physics behind them. We know how bits are stored and processing steps are executed. We also know generally how operating systems work. We have the full compiled code as assembly instructions. But we don’t have the source code of the OS. We just use crude tools to figure out The details of the OS and how it works on particular subsystems but because of the crude nature of the tools the knowledge we gain is ambiguous at times.
- randcraw 4y ago
  Biology is incomparable to computers, or to any other man-made machine. In computers the components interact in well-defined separable and independent roles. In a biological organism, all components depend heavily on not just one or two other components, but many. The role we impute for each mechanism often interfere and/or collaborate with other seemingly unrelated mechanisms, often in hierarchical and nonlinear fashion. That's why the function of even simple biological subsystems is so challenging to decipher. Context and interdependency are everywhere. That's why the oxymoronicism of a biologist “fixing a radio” rings so true.
  - dinvlad 4y ago
    > Context and interdependency are everywhere. Very much applicable to software as well :-) Modern systems are so complex there're very few people (if at all) who understand everything in them, even though they were man-made over time.
- Balgair 4y ago
  Having done a lot of biology, I'd disagree that we understand biology. My background is neuro, so take that into account. But in neuro, we've nearly no idea about the larger parts of how it all works. Sure, yeah, electrically active neurons, we have that down. But the non electrically active parts? I mean, we're still debating about how much of the brain is glia. Like, we can't even agree on how to count. Don't get me started on synapses.

by axg11 4y ago

shpongled 4y ago

I would argue that depends on your definition of deep - we are certainly getting better at developing both genetic and chemical tools that allow us to probe specific pathways/sub-systems of biology, and read out the resulting perturbed phenotype(s). > There's a huge gap between the fundamental units of biology (biochemistry) and the resulting emergent behaviour (living things). We don't have a good bottom-up system to predict the emergent behaviour so we're mostly left with observing from the top down and poking/prodding sub-systems, hoping to gain some insight. I think this is just about the last thing that we will ever solve/figure out. There are just a mind-boggling number of parameters, feedback loops, dynamic modifications, interactions, etc that are effecting cellular state (let alone organism state) - something that I think many CS oriented folks ignore when talking about "DNA as source code" (perhaps if program behavior depended on the size of indents, font, variable names, how many lines of code you wrote, the proximity in source location of different functions, etc).

AlecSchueler 4y ago
> (perhaps if program behavior depended on the size of indents, font, variable names, how many lines of code you wrote, the proximity in source location of different functions, etc) I think I've seen all of those functionalities implemented in esoteric programming languages! Nice comparison.
- marcosdumay 4y ago
  What you haven't seen is a CD-ROM sized program with no abstraction, encapsulation, or modularization, all implemented on a language that has all of those. Oh, and that is being interpreted by more than one incompatible interpreter at the same time.
randcraw 4y ago
Yeah, I think programmers would better appreciate the complexity and subtlety of biology much better if they had to evolve their programs rather than code them up explicitly. (I say this as someone with degrees in both subjects.)

onychomys 4y ago

> There's a huge gap between the fundamental units of biology (biochemistry) and the resulting emergent behaviour (living things). And then a very similar gap between the fundamental units of one small branch of biology, ecology, where the fundamental units are living things and the emergent behavior is everything you see outside your window! We have a lot of math that explains how things act and evolve together and it's all just the tiniest little smidge of what actually happens.

atty 4y ago

You can have what I would consider deep knowledge of a system without the ability to manufacture it or modify it. For instance, we have pretty deep knowledge of how the sun or other stars work, but we can’t even begin to dream about creating one, or controlling one. In the same way, we know a lot of how biology works. Obviously nowhere near all of it; but we are far beyond just scratching the surface. It just turns out that modifying a working complex system is pretty hard.

h2odragon 4y ago
> ow the sun or other stars work, but we can’t even begin to dream about creating one Wolfram didn't answer "how much would a solar mass of hydrogen cost" for me, but it did tell me that the solar mass is 1.988435×10^33 grams, and another search found hydrogen prices [1] in the range of US$ 250 to 1350 per MT ... So just the financing on building another sun is going to be tricky. [1] I know it's not all hydrogen but we'll burn those bridges when we get to them.
- PebblesRox 4y ago
  Gotta budget for some extra hydrogen to burn the bridges.
- burnished 4y ago
  Oof, and you didn't even factor in extra-solar shipping costs. Thats most of the expense, really.

ramraj07 4y ago

Hard disagree. We understand biology for the most part. The issue is in the exact implementations. An analogy would be like understanding how a computer works. We know how chips are made, the physics behind them. We know how bits are stored and processing steps are executed. We also know generally how operating systems work. We have the full compiled code as assembly instructions. But we don’t have the source code of the OS. We just use crude tools to figure out The details of the OS and how it works on particular subsystems but because of the crude nature of the tools the knowledge we gain is ambiguous at times.

randcraw 4y ago
Biology is incomparable to computers, or to any other man-made machine. In computers the components interact in well-defined separable and independent roles. In a biological organism, all components depend heavily on not just one or two other components, but many. The role we impute for each mechanism often interfere and/or collaborate with other seemingly unrelated mechanisms, often in hierarchical and nonlinear fashion. That's why the function of even simple biological subsystems is so challenging to decipher. Context and interdependency are everywhere. That's why the oxymoronicism of a biologist “fixing a radio” rings so true.
- dinvlad 4y ago
  > Context and interdependency are everywhere. Very much applicable to software as well :-) Modern systems are so complex there're very few people (if at all) who understand everything in them, even though they were man-made over time.
Balgair 4y ago
Having done a lot of biology, I'd disagree that we understand biology. My background is neuro, so take that into account. But in neuro, we've nearly no idea about the larger parts of how it all works. Sure, yeah, electrically active neurons, we have that down. But the non electrically active parts? I mean, we're still debating about how much of the brain is glia. Like, we can't even agree on how to count. Don't get me started on synapses.