7 ms·

Reminder of Complexity

199 points by azhenley 6y ago

rantwasp 6y ago
i independently ran across this when going through: https://www.edx.org/course/principles-of-biochemistry https://www.edx.org/course/principles-of-biochemistry As someone who is formally trained in computer science I was literally blown away by biochemistry. Once you see that any organism that involved organic chemistry is in fact an insanely complicated, biological computer you cannot unsee it. It's amazing. In case someone is wondering what the author of the blog post zoomed in, that's the Krebs cycle - ie how we derive energy (ie ATP) from the food we eat (https://en.wikipedia.org/wiki/Citric_acid_cycle https://en.wikipedia.org/wiki/Citric_acid_cycle). See: https://www.youtube.com/watch?v=juM2ROSLWfw https://www.youtube.com/watch?v=juM2ROSLWfw and https://www.youtube.com/watch?v=7J4LXs-oDCU https://www.youtube.com/watch?v=7J4LXs-oDCU
- neilpanchal 6y ago
  > Once you see that any organism that involved organic chemistry is in fact an insanely complicated, biological computer you cannot unsee it. It's amazing. This blew my mind. In addition to the computer analogy, I think Bio-mechanics is incredibly fascinating. The fact that I can close my eyes and still be able to touch the nose with my index finger repetedly from any starting position of the hand is mind boggling. I cannot fathom the type of inverse-kinematics that is involved in the cerebellum.
  - rantwasp 6y ago
    hah. technically your brain is a prediction machine and, when you are trying to touch your nose, it’s really good at minimizing the prediction error.
    - klipt 6y ago
      Also you're not just relying on sight, the sense of proprioception is providing constant feedback of your finger's position even with your eyes closed. So it's not an open loop control problem, it's a closed loop, which is much easier.
- dnautics 6y ago
  Ok as someone who has been programming computers since age five (and currently in the industry) and has a PhD in biochemistry... It's not a computer. If you think of it that way you can wind up in deep trouble with critical nuances. That said, it can be fruitful to treat a small percentage of the systems (my gut says 10%), and exploit their computer-like features for fun and profit.
  - coolgeek 6y ago
    I'd like to hear more about this. My understanding is that these things are not Turing complete, and don't resemble Von Neumann machines (or any other architecture we use for computers). But the processes themselves can be understood in terms of computation and/or communication. Is that wrong? If so, why/how? Also, could you point out an example or two of the nuances that tend to get people in trouble?
    - dnautics 6y ago
      The big one is it's nondeterministic. An obvious example of nondeterminism is the genotype which determines mirror-body, it's caused by a defective cilium. Normally that cilium enforces torquoselectivity -it only rotates in one direction which establishes chiral directionality, but a certain genotype disables its rotation, so the orientation of your body is a factor of random chance based on how your cell was rotating at the single cell level. The mendelian inheritance is basically 50/50 stochastic based on the genotype. That's a pretty macro example (both at the genotypic ratio and phenotype levels), but it can happen at the micro level, too. You can have grossly nonlinear effects (well actually many effects are O(n^k) in concentration n, where k is the oligomer size, 2->12->20++) and sometimes even the phenotypically important species is like 10%? 1%? 0.1%? 0.01%? of the molecule population. And the proportion of the species could depend on the temperature. Are you running at 35C? 38C? 40C? 42C? In a reductionistic way you could say that any system that follows logical rules is "like a computer" but I think at that point it ceases to be a meaningful statement. Computers are great because if you give them an input they can give a deterministic answer (you can also choose to have them not give a deterministic answer, as in ML, and yes sometimes at Google scale you have to deal with cosmic radiation) but the choice is inverted for biological systems. You can try really hard to make biological systems give deterministic answers, and in some systems you don't have to try that hard, especially nowadays, but the default still is "nondeterministic".
- rstuart4133 6y ago
  This video blew me away: https://www.youtube.com/watch?v=wJyUtbn0O5Y https://www.youtube.com/watch?v=wJyUtbn0O5Y It's an animation of the bio-chemistry a lymphocyte uses to move between cells (maybe - that's a guess?). It covers what I can only assume is a few milliseconds, it's just a tiny slither of the cells behaviours, yet how much is going on to make that happen is off the charts. I showed in it a club consisting of mostly software engineers, and the universal reaction was "thank god I didn't do bio-chemistry".
nafey 6y ago
This reminds me of Tesler's law says something quite useful about how complexity works: "Every application has an inherent amount of complexity that cannot be removed or hidden. Instead, it must be dealt with, either in product development or in user interaction."
cxr 6y ago
Half-related: Reality has a surprising amount of detail http://johnsalvatier.org/blog/2017/reality-has-a-surprising-amount-of-detail http://johnsalvatier.org/blog/2017/reality-has-a-surprising-... https://news.ycombinator.com/item?id=16184255 https://news.ycombinator.com/item?id=16184255 https://news.ycombinator.com/item?id=22020495 https://news.ycombinator.com/item?id=22020495
WJW 6y ago
I love that it comes with a piece of paper reminding the viewer that this is a small selection of reality. Biochemistry is much, MUCH more complex than even these two 26 square foot posters. I'd love to get a similar poster of the entire Linux kernel or, alternatively, the total supply chain for an everyday item like the proverbial pencil.
- rantwasp 6y ago
  the complexity of the linux kernel (and in man-made things in general) is usually really small compared to biological systems.
  - WJW 6y ago
    I'm sure you could still fill a good-size poster if you make a nice inefficient representation, like every function call is a separate node in the graph and you include every single device driver even for decades old stuff like tape drives. I agree though, Mother Nature has an inordinate love for making everything a global variable and She definitely hates comments.
    - rantwasp 6y ago
      the analogy is good but i think it kinda breaks down when you consider the machine the kernel runs on. so you would mostly represent the machine the software run on.
- azhenley 6y ago
  I'd buy a similar poster of the Linux kernel. I'm sure some astute HN reader could whip up a script that generates illustrative posters of static call graphs given a Git repo!
  - cmrx64 6y ago
    https://makelinux.github.io/kernel/map/ https://makelinux.github.io/kernel/map/ my uni had some different, older posters about linux. one was radial with most non driver files represented. can’t seem to find them on the web though
0d9eooo 6y ago
Related: https://arxiv.org/abs/0708.1362 https://arxiv.org/abs/0708.1362 At some point the complexity of a system becomes great enough that it's impossible to simulate it perfectly. The interesting question for me lately is how and under what circumstances can you ignore the complexity for some purpose. For example, underlying what is represented in that poster is some set of physical processes that are ignored in that poster. The system at that physical level of description would be even more complex, probably too complex to represent on a poster. So why the level of analysis of the poster? Similarlly, at some point it's easier to talk about eating and fatigue than it is the citric acid cycle. How and why do you move from one level of analysis to another? Some of it probably depends on what is being explained, but some of it might not.
- fulafel 6y ago
  Interesting looking paper. From the abstract it seems that the claim is about about perfectly replicating a future state of the simulated system? Simulation with a less ambitious fidelity level still seems useful to understand these kind of systems.
  - di4na 6y ago
    Yes, that is called a model. Usually people that study complexity will say that all models are wrong but some are useful. In software, we usually prefer the term abstraction. The trick is to remember that our model are wrong. This gap between "system-as-modeled" and "system-as-reality" can be inconsequential in a lot of time, but it is also a place in which failure mode can rise. It is important to always keep exploring it and change the model depending on situations.
mark_l_watson 6y ago
John’s blogs always set me off in one direction or another. Now he has me thinking: Our human minds can only hold a finite amount of information in long term and short term memories. I don’t too much buy into direct brain augmentation in the sense of NeuralLink or my friends in the SingularityNET community. What I am hoping for is external augmentation using smart glasses that record everything I study and that I hear, and sufficient AI (doesn’t have to be AGI) on the backend to learn when to prompt or remind. Ideally this would be paired with something like an iPad that the system could draw on top of what I am looking at. This is the startup I would like to work for. Apple is supposed to be releasing smart glasses sometime. I hope the hardware and software support is hackable and extensible.
- emsy 6y ago
  That’s really more of a “flying cars” startup than a “140 characters” one. You should pitch the idea :P
  - mark_l_watson 6y ago
    Someone just emailed me with the idea of making it open source. That would work if/when there is commodity and hackable hardware to support it.
    - otoburb 6y ago
      There are some movements in this area with the inevitable and inexorable march of progress that drops the prices of high-speed low-rez cameras using mostly off-the-shelf components. If video can be lossy while key features from the feed are processed in-stream, one can get creative with high frame rates (>2000 fps, 256x256 monochrome).[1] [1] https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232788 https://journals.plos.org/plosone/article?id=10.1371/journal...
- fineline 6y ago
  I expect smart glasses to be the next UI paradigm. Very conveniently portable. AR style visual interfaces. Built in speakers for personal audio (bose already do this in sunglasses). The AR interface could be directly manipulated by hand gestures using cameras and other sensors. I know there have been a couple of false starts (Google Glass) and current products with bigger form factors (Hololens), but I expect spectacles size devices with good UI in the not too distant future, and I look forward to the development opportunities.
splittingTimes 6y ago
You can download the posters here: https://www.roche.com/sustainability/philanthropy/science_education/pathways/pathways-ordering.htm https://www.roche.com/sustainability/philanthropy/science_ed...
reidacdc 6y ago
I ran across an early version of this, on paper, in the university library at my undergraduate institution, and took the same lesson of humility and respect in the face of complexity that the article does. The positive side is that we actually can and do effectively intervene in this system, and systems like it, to improve outcomes, so even very high levels of complexity don't mean analysis is impossible.

199 points by azhenley 6y ago

i independently ran across this when going through: https://www.edx.org/course/principles-of-biochemistry https://www.edx.org/course/principles-of-biochemistry As someone who is formally trained in computer science I was literally blown away by biochemistry. Once you see that any organism that involved organic chemistry is in fact an insanely complicated, biological computer you cannot unsee it. It's amazing. In case someone is wondering what the author of the blog post zoomed in, that's the Krebs cycle - ie how we derive energy (ie ATP) from the food we eat (https://en.wikipedia.org/wiki/Citric_acid_cycle https://en.wikipedia.org/wiki/Citric_acid_cycle). See: https://www.youtube.com/watch?v=juM2ROSLWfw https://www.youtube.com/watch?v=juM2ROSLWfw and https://www.youtube.com/watch?v=7J4LXs-oDCU https://www.youtube.com/watch?v=7J4LXs-oDCU

neilpanchal 6y ago
> Once you see that any organism that involved organic chemistry is in fact an insanely complicated, biological computer you cannot unsee it. It's amazing. This blew my mind. In addition to the computer analogy, I think Bio-mechanics is incredibly fascinating. The fact that I can close my eyes and still be able to touch the nose with my index finger repetedly from any starting position of the hand is mind boggling. I cannot fathom the type of inverse-kinematics that is involved in the cerebellum.
- rantwasp 6y ago
  hah. technically your brain is a prediction machine and, when you are trying to touch your nose, it’s really good at minimizing the prediction error.
  - klipt 6y ago
    Also you're not just relying on sight, the sense of proprioception is providing constant feedback of your finger's position even with your eyes closed. So it's not an open loop control problem, it's a closed loop, which is much easier.
dnautics 6y ago
Ok as someone who has been programming computers since age five (and currently in the industry) and has a PhD in biochemistry... It's not a computer. If you think of it that way you can wind up in deep trouble with critical nuances. That said, it can be fruitful to treat a small percentage of the systems (my gut says 10%), and exploit their computer-like features for fun and profit.
- coolgeek 6y ago
  I'd like to hear more about this. My understanding is that these things are not Turing complete, and don't resemble Von Neumann machines (or any other architecture we use for computers). But the processes themselves can be understood in terms of computation and/or communication. Is that wrong? If so, why/how? Also, could you point out an example or two of the nuances that tend to get people in trouble?
  - dnautics 6y ago
    The big one is it's nondeterministic. An obvious example of nondeterminism is the genotype which determines mirror-body, it's caused by a defective cilium. Normally that cilium enforces torquoselectivity -it only rotates in one direction which establishes chiral directionality, but a certain genotype disables its rotation, so the orientation of your body is a factor of random chance based on how your cell was rotating at the single cell level. The mendelian inheritance is basically 50/50 stochastic based on the genotype. That's a pretty macro example (both at the genotypic ratio and phenotype levels), but it can happen at the micro level, too. You can have grossly nonlinear effects (well actually many effects are O(n^k) in concentration n, where k is the oligomer size, 2->12->20++) and sometimes even the phenotypically important species is like 10%? 1%? 0.1%? 0.01%? of the molecule population. And the proportion of the species could depend on the temperature. Are you running at 35C? 38C? 40C? 42C? In a reductionistic way you could say that any system that follows logical rules is "like a computer" but I think at that point it ceases to be a meaningful statement. Computers are great because if you give them an input they can give a deterministic answer (you can also choose to have them not give a deterministic answer, as in ML, and yes sometimes at Google scale you have to deal with cosmic radiation) but the choice is inverted for biological systems. You can try really hard to make biological systems give deterministic answers, and in some systems you don't have to try that hard, especially nowadays, but the default still is "nondeterministic".
rstuart4133 6y ago
This video blew me away: https://www.youtube.com/watch?v=wJyUtbn0O5Y https://www.youtube.com/watch?v=wJyUtbn0O5Y It's an animation of the bio-chemistry a lymphocyte uses to move between cells (maybe - that's a guess?). It covers what I can only assume is a few milliseconds, it's just a tiny slither of the cells behaviours, yet how much is going on to make that happen is off the charts. I showed in it a club consisting of mostly software engineers, and the universal reaction was "thank god I didn't do bio-chemistry".

nafey 6y ago

This reminds me of Tesler's law says something quite useful about how complexity works: "Every application has an inherent amount of complexity that cannot be removed or hidden. Instead, it must be dealt with, either in product development or in user interaction."

cxr 6y ago

Half-related: Reality has a surprising amount of detail http://johnsalvatier.org/blog/2017/reality-has-a-surprising-amount-of-detail http://johnsalvatier.org/blog/2017/reality-has-a-surprising-... https://news.ycombinator.com/item?id=16184255 https://news.ycombinator.com/item?id=16184255 https://news.ycombinator.com/item?id=22020495 https://news.ycombinator.com/item?id=22020495

WJW 6y ago

I love that it comes with a piece of paper reminding the viewer that this is a small selection of reality. Biochemistry is much, MUCH more complex than even these two 26 square foot posters. I'd love to get a similar poster of the entire Linux kernel or, alternatively, the total supply chain for an everyday item like the proverbial pencil.

rantwasp 6y ago
the complexity of the linux kernel (and in man-made things in general) is usually really small compared to biological systems.
- WJW 6y ago
  I'm sure you could still fill a good-size poster if you make a nice inefficient representation, like every function call is a separate node in the graph and you include every single device driver even for decades old stuff like tape drives. I agree though, Mother Nature has an inordinate love for making everything a global variable and She definitely hates comments.
  - rantwasp 6y ago
    the analogy is good but i think it kinda breaks down when you consider the machine the kernel runs on. so you would mostly represent the machine the software run on.
azhenley 6y ago
I'd buy a similar poster of the Linux kernel. I'm sure some astute HN reader could whip up a script that generates illustrative posters of static call graphs given a Git repo!
- cmrx64 6y ago
  https://makelinux.github.io/kernel/map/ https://makelinux.github.io/kernel/map/ my uni had some different, older posters about linux. one was radial with most non driver files represented. can’t seem to find them on the web though

0d9eooo 6y ago

Related: https://arxiv.org/abs/0708.1362 https://arxiv.org/abs/0708.1362 At some point the complexity of a system becomes great enough that it's impossible to simulate it perfectly. The interesting question for me lately is how and under what circumstances can you ignore the complexity for some purpose. For example, underlying what is represented in that poster is some set of physical processes that are ignored in that poster. The system at that physical level of description would be even more complex, probably too complex to represent on a poster. So why the level of analysis of the poster? Similarlly, at some point it's easier to talk about eating and fatigue than it is the citric acid cycle. How and why do you move from one level of analysis to another? Some of it probably depends on what is being explained, but some of it might not.

fulafel 6y ago
Interesting looking paper. From the abstract it seems that the claim is about about perfectly replicating a future state of the simulated system? Simulation with a less ambitious fidelity level still seems useful to understand these kind of systems.
- di4na 6y ago
  Yes, that is called a model. Usually people that study complexity will say that all models are wrong but some are useful. In software, we usually prefer the term abstraction. The trick is to remember that our model are wrong. This gap between "system-as-modeled" and "system-as-reality" can be inconsequential in a lot of time, but it is also a place in which failure mode can rise. It is important to always keep exploring it and change the model depending on situations.

mark_l_watson 6y ago

John’s blogs always set me off in one direction or another. Now he has me thinking: Our human minds can only hold a finite amount of information in long term and short term memories. I don’t too much buy into direct brain augmentation in the sense of NeuralLink or my friends in the SingularityNET community. What I am hoping for is external augmentation using smart glasses that record everything I study and that I hear, and sufficient AI (doesn’t have to be AGI) on the backend to learn when to prompt or remind. Ideally this would be paired with something like an iPad that the system could draw on top of what I am looking at. This is the startup I would like to work for. Apple is supposed to be releasing smart glasses sometime. I hope the hardware and software support is hackable and extensible.

emsy 6y ago
That’s really more of a “flying cars” startup than a “140 characters” one. You should pitch the idea :P
- mark_l_watson 6y ago
  Someone just emailed me with the idea of making it open source. That would work if/when there is commodity and hackable hardware to support it.
  - otoburb 6y ago
    There are some movements in this area with the inevitable and inexorable march of progress that drops the prices of high-speed low-rez cameras using mostly off-the-shelf components. If video can be lossy while key features from the feed are processed in-stream, one can get creative with high frame rates (>2000 fps, 256x256 monochrome).[1] [1] https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0232788 https://journals.plos.org/plosone/article?id=10.1371/journal...
fineline 6y ago
I expect smart glasses to be the next UI paradigm. Very conveniently portable. AR style visual interfaces. Built in speakers for personal audio (bose already do this in sunglasses). The AR interface could be directly manipulated by hand gestures using cameras and other sensors. I know there have been a couple of false starts (Google Glass) and current products with bigger form factors (Hololens), but I expect spectacles size devices with good UI in the not too distant future, and I look forward to the development opportunities.

splittingTimes 6y ago

You can download the posters here: https://www.roche.com/sustainability/philanthropy/science_education/pathways/pathways-ordering.htm https://www.roche.com/sustainability/philanthropy/science_ed...

reidacdc 6y ago

I ran across an early version of this, on paper, in the university library at my undergraduate institution, and took the same lesson of humility and respect in the face of complexity that the article does. The positive side is that we actually can and do effectively intervene in this system, and systems like it, to improve outcomes, so even very high levels of complexity don't mean analysis is impossible.