5 ms·

As a biologist and programmer, nothing makes me roll my eyes harder than SV types talking about biology like a computer. The analogy might hold if we treated

As a biologist and programmer, nothing makes me roll my eyes harder than SV types talking about biology like a computer. The analogy might hold if we treated CPUs like a magical artifact that we don't have the technology to understand.

vikramkr 6y ago
I don't know if that would be enough to make the analogy hold, since what we do know about biology includes a lot of things that are distinctly non-computer like. At the end of the day, one is a system designed by humans for humans, while the other is a system that's an emergent phenomena of billions of years of chemistry, physics, and statistics. In computers you create the rules and then build systems that follow the rules, and then push the rules to their limits to see what you can do. In bio the only rule is that an arrangement of atoms that's more likely to replicate a version if itself into a future time period will be more likely to be found in that future time period compared to an arrangement of atoms that isn't. And that principle has had 4+ billion years to play with the rules of physics to see what it can do, and we're just trying to decipher that now.
- shpongled 6y ago
  I mean, I think that there is some merit to biology-computer analogies, I just don't think anyone can expect those analogies to hold in reality. But you are exactly on point. There are presumably "rules" in biology, but they are occluded by spooky action a distance and oodles of hidden and ever-changing state.
  - jfarlow 6y ago
    I think it's important not to say that biology is somehow 'spooky', or not governed by physical rules. We actually know the outlines of those rules pretty well - they're just complicated. The really big difference is that biology computes at overlapping time and distance scales, simultaneously. There are biological computational processes that occur at microseconds, to millennia, from fractions of a nanometer to kilometers all happing in concert and referencing each other. In the building of our own computational tools we generally try to avoid mixing physical scales like that. The analogies to computers aren't inherently wrong, they just need to mix in a lot more complexity.
    - shpongled 6y ago
      "Spooky action at a distance" doesn't imply that it's not governed by physical rules - and I think it's certainly a valid descriptor for biological systems as a whole. Yes, we can break down aspects of biology into nice subsystems that we can define rules for - e.g. we have a pretty good idea of how DNA polymerase, or the ribosome carry out their duties (in isolation). It's when we start looking at the emergent properties of having all of these things in one larger system that our understanding starts to break down.
      - seamyb88 6y ago
        Just out of interest: Spooky action at a distance was Einstein's quote, his way of dismissing a genuine physical rule - quantum entanglement - which he did not believe to be true.
      - ethbro 6y ago
        Valid / invalid for metaphors, to me, depends on the audience. For laypeople, ill equiped to deal with high orders of complexity: spooky. For people in the field: details. For some audiences being accurate is less descriptive than being reductionist. Because if you lose your audience's attention, you've communicated no accuracy.
Johnjonjoan 6y ago
Biology is more like a class where everything's private and there was no documentation on the public methods (for us)
- Barrin92 6y ago
  in biology nothing is private or even in a class because in biology there is no designer, so there is no need for encapsulation. One of the more and more prominent insights in biology is that almost every gene apparently appears to influence everything else.[1] Which is why I think methods like CRISPR are fundamentally misguided for anything but the most simple problems. Trying to impose deliberate change on biological systems by editing a single gene is like trying to turn a story from drama into comedy by switching out individual letters. [1]https://www.quantamagazine.org/omnigenic-model-suggests-that-all-genes-affect-every-complex-trait-20180620/ https://www.quantamagazine.org/omnigenic-model-suggests-that...
  - Johnjonjoan 6y ago
    I'm curious why you're so sure there isn't a designer.
    - discreteevent 6y ago
      One can never be sure, but from all the evidence it looks like that if there was a designer, they weren't operating at this level, so the parents point is unaffected by this concern.
      - Johnjonjoan 6y ago
        I'm unsure, the only contradictory point to my proposition was that there was no designer. "in biology nothing is private or even in a class because in biology there is no designer, so there is no need for encapsulation." How can the point be unaffected if you are rightly saying the point is in question? Are we on the same level as the implementation when we write our classes?
    - 6y ago
Melting_Harps 6y ago
> This highlights why it was so irresponsible to create CRISPR babies, and why you take things slow in science. Don't let the analogies about bio being programmable just like a computer fool you - it's not that easy or that simple. Bio is messy and complex. > As a biologist and programmer, nothing makes me roll my eyes harder than SV types talking about biology like a computer. Same. But in truth, I'm glad this experiment took place, we need to adhere to the rigors that uphold the notion of incremental progress for a desirable end, and this begins by quantifying just how immense this problem really is. I'm glad that Dr. Jiankui He did it anyway. It cost him his career and he will likely remain as a cautionary tale for all other future biologists in academia, but in Biohacking scene he is really no different then the pioneers in cell biology that often resorted to self experimentation, History in Biology is such a fickle thing: we'll laud them when the outcomes favour conventional wisdom and it accepts there methods, but infamy awaits anyone who defies to go out of its per-ordained confines. Even though we all accept that the walled garden of peer-reviewed publication is flawed and riddled with so many unnecessary things that encumber its ability to live up to its potential when it can use unorthodox or unconventional means and methods. The Health Sciences, specifically that of genetics and cellular and molecular biology, has a history of being the punk-rock branch. Where even a monk playing with peas in his free time can help establish the notion of inheritable mutation (Mendelian genetics) based on adaption created by a British Medical school drop out who took to sea-fairing and island hopping to create the concept of what we'd eventually call Darwinian Evolution. This is our History and as a Cell/Molecular Biologist myself, I take great pride in it and I have tried my best to live up to this reputation and apply this to my work in Agricultural and Food Sciences after abandoning my career as a lab scientist. Dr. He got consent from the parents to undergo this procedure and move Biology in a territory it otherwise would never go for another couple of decades at the earliest. This is more than what some physicians did not too long ago, and the data we obtained from those experiments proved incredibly useful to this day.
- throwaway4666 6y ago
  Peer-review has its problems but I don't think the solution is 'we need more people carelessly injecting themselves and others with things with unknown effects'. I think the covid crisis aptly showed that the 'plucky outsider that defies a reactionary authority' archetype doesn't actually exist in real life. And biohacking itself is largely a grift.
CWuestefeld 6y ago
SV types What's "SV"?
- tyingq 6y ago
  Silicon Valley.
crawfordcomeaux 6y ago
I wonder what your take is on this. "Brain computation by assemblies of neurons" https://www.pnas.org/content/117/25/14464 https://www.pnas.org/content/117/25/14464

vikramkr 6y ago

I don't know if that would be enough to make the analogy hold, since what we do know about biology includes a lot of things that are distinctly non-computer like. At the end of the day, one is a system designed by humans for humans, while the other is a system that's an emergent phenomena of billions of years of chemistry, physics, and statistics. In computers you create the rules and then build systems that follow the rules, and then push the rules to their limits to see what you can do. In bio the only rule is that an arrangement of atoms that's more likely to replicate a version if itself into a future time period will be more likely to be found in that future time period compared to an arrangement of atoms that isn't. And that principle has had 4+ billion years to play with the rules of physics to see what it can do, and we're just trying to decipher that now.

shpongled 6y ago
I mean, I think that there is some merit to biology-computer analogies, I just don't think anyone can expect those analogies to hold in reality. But you are exactly on point. There are presumably "rules" in biology, but they are occluded by spooky action a distance and oodles of hidden and ever-changing state.
- jfarlow 6y ago
  I think it's important not to say that biology is somehow 'spooky', or not governed by physical rules. We actually know the outlines of those rules pretty well - they're just complicated. The really big difference is that biology computes at overlapping time and distance scales, simultaneously. There are biological computational processes that occur at microseconds, to millennia, from fractions of a nanometer to kilometers all happing in concert and referencing each other. In the building of our own computational tools we generally try to avoid mixing physical scales like that. The analogies to computers aren't inherently wrong, they just need to mix in a lot more complexity.
  - shpongled 6y ago
    "Spooky action at a distance" doesn't imply that it's not governed by physical rules - and I think it's certainly a valid descriptor for biological systems as a whole. Yes, we can break down aspects of biology into nice subsystems that we can define rules for - e.g. we have a pretty good idea of how DNA polymerase, or the ribosome carry out their duties (in isolation). It's when we start looking at the emergent properties of having all of these things in one larger system that our understanding starts to break down.
    - seamyb88 6y ago
      Just out of interest: Spooky action at a distance was Einstein's quote, his way of dismissing a genuine physical rule - quantum entanglement - which he did not believe to be true.
    - ethbro 6y ago
      Valid / invalid for metaphors, to me, depends on the audience. For laypeople, ill equiped to deal with high orders of complexity: spooky. For people in the field: details. For some audiences being accurate is less descriptive than being reductionist. Because if you lose your audience's attention, you've communicated no accuracy.

Johnjonjoan 6y ago

Biology is more like a class where everything's private and there was no documentation on the public methods (for us)

Barrin92 6y ago
in biology nothing is private or even in a class because in biology there is no designer, so there is no need for encapsulation. One of the more and more prominent insights in biology is that almost every gene apparently appears to influence everything else.[1] Which is why I think methods like CRISPR are fundamentally misguided for anything but the most simple problems. Trying to impose deliberate change on biological systems by editing a single gene is like trying to turn a story from drama into comedy by switching out individual letters. [1]https://www.quantamagazine.org/omnigenic-model-suggests-that-all-genes-affect-every-complex-trait-20180620/ https://www.quantamagazine.org/omnigenic-model-suggests-that...
- Johnjonjoan 6y ago
  I'm curious why you're so sure there isn't a designer.
  - discreteevent 6y ago
    One can never be sure, but from all the evidence it looks like that if there was a designer, they weren't operating at this level, so the parents point is unaffected by this concern.
    - Johnjonjoan 6y ago
      I'm unsure, the only contradictory point to my proposition was that there was no designer. "in biology nothing is private or even in a class because in biology there is no designer, so there is no need for encapsulation." How can the point be unaffected if you are rightly saying the point is in question? Are we on the same level as the implementation when we write our classes?
  - 6y ago

Melting_Harps 6y ago

> This highlights why it was so irresponsible to create CRISPR babies, and why you take things slow in science. Don't let the analogies about bio being programmable just like a computer fool you - it's not that easy or that simple. Bio is messy and complex. > As a biologist and programmer, nothing makes me roll my eyes harder than SV types talking about biology like a computer. Same. But in truth, I'm glad this experiment took place, we need to adhere to the rigors that uphold the notion of incremental progress for a desirable end, and this begins by quantifying just how immense this problem really is. I'm glad that Dr. Jiankui He did it anyway. It cost him his career and he will likely remain as a cautionary tale for all other future biologists in academia, but in Biohacking scene he is really no different then the pioneers in cell biology that often resorted to self experimentation, History in Biology is such a fickle thing: we'll laud them when the outcomes favour conventional wisdom and it accepts there methods, but infamy awaits anyone who defies to go out of its per-ordained confines. Even though we all accept that the walled garden of peer-reviewed publication is flawed and riddled with so many unnecessary things that encumber its ability to live up to its potential when it can use unorthodox or unconventional means and methods. The Health Sciences, specifically that of genetics and cellular and molecular biology, has a history of being the punk-rock branch. Where even a monk playing with peas in his free time can help establish the notion of inheritable mutation (Mendelian genetics) based on adaption created by a British Medical school drop out who took to sea-fairing and island hopping to create the concept of what we'd eventually call Darwinian Evolution. This is our History and as a Cell/Molecular Biologist myself, I take great pride in it and I have tried my best to live up to this reputation and apply this to my work in Agricultural and Food Sciences after abandoning my career as a lab scientist. Dr. He got consent from the parents to undergo this procedure and move Biology in a territory it otherwise would never go for another couple of decades at the earliest. This is more than what some physicians did not too long ago, and the data we obtained from those experiments proved incredibly useful to this day.

throwaway4666 6y ago
Peer-review has its problems but I don't think the solution is 'we need more people carelessly injecting themselves and others with things with unknown effects'. I think the covid crisis aptly showed that the 'plucky outsider that defies a reactionary authority' archetype doesn't actually exist in real life. And biohacking itself is largely a grift.

CWuestefeld 6y ago

SV types What's "SV"?

tyingq 6y ago
Silicon Valley.

crawfordcomeaux 6y ago

I wonder what your take is on this. "Brain computation by assemblies of neurons" https://www.pnas.org/content/117/25/14464 https://www.pnas.org/content/117/25/14464