5 ms·

This is a very interesting article/video, and well-worth reading to get a sense of how complex proteins are, but I’m not convinced by the principle argument tha

This is a very interesting article/video, and well-worth reading to get a sense of how complex proteins are, but I’m not convinced by the principle argument that proteins don’t constitue “machinery”. The core philosophical question is actually interesting: what is a machine? The author suggests a machine is anything with solid parts of that have a specific function, and goes on to argue that the metabolic machinery or cells doesn’t correspond to any of these three criteria. I’m not sure it matters whether the parts are solid, I don’t think multifunctionality disqualifies something from being a machine, and despite the limitations presented, I am not even convinced that it is senseless to decompose a cell into components. On this last point, it bears emphasizing that his criticism bears the analytical method in general, and is not specific to biology. There are edge cases in any decomposition of a whole into parts. So while it’s interesting to see how these philosophical questions are at play in cellular biology, the case remains to be made that “machinery” is a fundamentally bad analogy. Here it also bears emphasizing that confusion between the subject of study and the metaphor is a risk with all metaphors (the map is not the territory), not especially this metaphor. In sum, I wish the author had focused on the philosophical substance of “what even is a machine?”. That’s bound to be a richer investigation.

323 4y ago
Sometimes it helps to approach these things at a meta-level. What would it mean if cells were machines? Would that make humans machines? Maybe this is the problem author has. Other articles on the site which might be considered controversial: > Organisms Are Not Made Of Atoms https://www.subanima.org/organisms/ https://www.subanima.org/organisms/ > Why Biology BREAKS Physics https://www.subanima.org/biology-breaks-physics/ https://www.subanima.org/biology-breaks-physics/
- prolyxis 4y ago
  Those two titles are good examples of when click-bait is stretched to the point of complete inaccuracy.
jerf 4y ago
I think the author covered it sufficiently, because the author is correct that if you just walk up to someone with the referenced videos, they are going to come away with the mistakes the video author discusses. They're going to think things have specific functions, in specific ways, in the super-orderly manners presented, etc. Redefining machine to the point that it happens to cover what cells really are won't change those misconceptions, or at least, it won't change them for a very long time and until you get those definitions propagated far and wide. Which will be an uphill battle because they are frankly less useful than the current definition we have, which works in the real world we all interact with. Nobody is hearing "the cell is a machine" and then goes off thinking "ah, what they clearly mean is that it is a whole lot of goop interacting in shocking complicated ways with each other all the time resembling literally nothing else a human calls a machine". Playing games with definitions is, well, exactly that: Playing games with definitions. It doesn't actually change anything in the world.
- adamredwoods 4y ago
  This was similar to my understanding (with my limited insight). If we are researching a particular cell interaction, thinking it as a machine, we may walk away with wrong conclusions if we hypothesize, set up a test, and study results, thinking that this machine is expected to work the same way every time.
- omginternets 4y ago
  I suppose that's fair. I guess I'm lamenting the missed opportunity for an interesting philosophical discussion, and perhaps wishing the author had presented his (otherwise very interesting!) thoughts through a more nuanced lens. I don't think he would even need to change the title. I still enjoyed the article, and would upvote it again if I could.
  - mxkopy 4y ago
    GEB explores a similar idea in investigating where a program is written It's implied that the distinctions are somewhat arbitrary. For example, a song is "written" on a record with a bunch of grooves, and the record-player is the machine that plays it. But if the record-player spun backwards instead of forwards, you'd hear something completely different. So in some sense, the record-player also holds part of the program. And all this runs parallel to the idea that a program is also data, IMO. I think a 'non-arbitrary' definition of a machine would be very general.
Daniel_sk 4y ago
A cell is not a machine in what most people would understand under this word. It's almost like it's full of agents that each have their own goal and through endless evolutionary selection these goals between those agents became interconnected in such way a complicated way that they play this "orchestra" that is a cell. But when you look inside it's a huge biological mess. There is no central part that controls everything - cells and multicellular organisms are hugely distributed systems.
kmtrowbr 4y ago
https://www.etymonline.com/word/machine https://www.etymonline.com/word/machine machine (n.) 1540s, "structure of any kind," from Middle French machine "device, contrivance," contrive: to form or create in an artistic or ingenious manner According to these definitions a machine is something that humans create. We understand what we create. When trying to understand complex things, we form metaphors based on our actual understanding. Whichever is the most advanced thinking of the age is used at a metaphor to describe life and nature. When it was steam, we used popularly understood concepts of steam engines to describe life. When it was electricity, we used electrical metaphors. Now that it is computers, we use those concepts. We are also very overconfident regarding how well we understand and control the world. Having achieved smashing success in some areas, we then think we have total control. Chronological snobbery, if you will: https://en.wikipedia.org/wiki/Chronological_snobbery https://en.wikipedia.org/wiki/Chronological_snobbery The danger is then, at a popular level, we take the metaphor literally and turn it around to be something reductive: "Life is no more than a machine." That is frankly not true: this is where the metaphor falls apart & it's the danger the article describes. Life is more than a steam engine, it's more than electrical circuits, and it's also not a computer. Life may be a purely material phenomenon (i.e. no more than atoms, void, and time), but that does not mean it is "just a steam engine / computer" etc.
- pixl97 4y ago
  The only response I can really give here is 'insufficient data for meaningful answer' Time will tell if this is true or not.
oh_my_goodness 4y ago
Yes, the core philosophical question is very interesting. Unfortunately at this time we can't resolve that core philosophical question. When we can resolve it, I think we'll be able to move it into the part of philosophy that's also called "science." The cell might be understandable as a giant machine, but I think the author is claiming that we either don't know that yet, or that the machine may be enormously more complex than some folks are suggesting. Physicist Philip Anderson has written about reductionism (which he claims works very well) and "constructionism" (which he says is much more confusing). https://www.tkm.kit.edu/downloads/TKM1_2011_more_is_different_PWA.pdf https://www.tkm.kit.edu/downloads/TKM1_2011_more_is_differen...
- omginternets 4y ago
  "What is a machine" is hardly the realm of science.
  - oh_my_goodness 4y ago
    Either it's a philosophical question, or it's some other kind of question. "Philosophical question" implies that we can't answer it at this time. (Or, equivalently, we can build equally convincing but conflicting answers.) One claim in the article is that we can't answer the (much narrower) question, "Is the cell a machine?" I don't see that saying "well that's a philosophical question" is so different from saying "as scientists, we don't know."
    - nosianu 4y ago
      There really is no great mystery question - because "machine" is a word not defined by the universe and is controlled by humans, who can use whatever definition they want. So whatever definition you use, this word has no external objective constraints, there will be a common ground between people or not and there is no objective way to make everybody agree on one definition, it's all voluntary. (Even if they do, the agreement is never complete because it's only about the aspects talked about, and then words are not reality and come about indirectly through many processes in the brain and never completely match between different people, or even the same person over time) "What is a machine" is a great way to waste time doing nothing, unless you can beforehand agree on constraints, e.g. by looking for a definition for one clearly defined purpose. But that's just moving the goal post to a little outside the box that then this definition is tied to. There is this strange movement, or maybe it isn't strange, when I was younger I followed it too, to take words way too seriously. There's entire fantasy stories about "true names", some kind of absolute comprehension about something expressed as a word. There also are practical examples, for example I once read about a father whose daughter had some rare disease about which nothing really was known. The only thing that had happened, at least by the time of the story, was that somebody had encountered this disease previously and attached a word to it. But without any content, there was no knowledge about how it occurred or how to treat it. But when the father was told that name he said something like "Finally we know what the problem is, I can breath much easier" (words partially made up because I don't remember, but that meaning was there). Just look at unrestraint, non-concrete discussions about words and there arbitrary definitions, looking for something "philosophical" behind those words. In this context, a blog post I once bookmarked (hey, I finally get to use my bookmarks!): https://www.lesswrong.com/posts/7X2j8HAkWdmMoS8PE/disputing-definitions https://www.lesswrong.com/posts/7X2j8HAkWdmMoS8PE/disputing-... - with some practical advice, not an attempt to solve anything "philosophically". I see sooo many comments here basing their agreement or disagreement on some definition of the word "machine". The default these days is to try to find something wrong with somebody's statement(s), by exploring the edges or even beyond of definitions of some word or words, making discussions very tiring. When instead one could just try to find the idea the person wanted to express and not get hung up about some words. Because deep inside the brain there are no words, the ideas one tries to express are much more fuzzier and flexible and trying to turn them into words is a very inexact process. Our brains don't think in words, except for a tiny part under our direct attention. The concepts leading to the use of this or that word, and the many words accompanying it, are never the same in different brains, and not the same in the same brain over time. To make the best use of our very limited communication tools that serialized extremely intricate four-dimensional patterns (brain structure plus the dynamic behavior) into rigid words you have to want to communicate and to understand and be positive, at least when something is a little off-center from the usual things that everybody involved in the communication has already established a good synchronization on. When discussing if we need to buy more milk because there is none in the fridge we have a much easier time with the communication and with agreements, because we are not going anywhere near the edges of well-used concepts (what is milk, what is a fridge, what does "empty" mean, etc. etc. - all of those can lead to deep disagreements at the edges). For a text like the one here some more allowances would be better to get something useful out of the communication. IMHO the best way to make something out of this article is if you already have a pretty good and somewhat deep comprehension of organic chemistry at least. The many stages of going deeper and deeper down the rabbit hole from the beginning teachings of atoms and chemical bonds to more and more complex understanding that you get from university chemistry, where it gets more like physics, coupled with seeing it "in use" for large and complex organic molecules, is I think a good preparation to understand the article's point.
akomtu 4y ago
Intuituvely, a machine is a thing with an internal state and behaviour that predictably depends only on that state. However, what if the internal state exists, but cannot be completely known or reproduced?
lo_zamoyski 4y ago
> The core philosophical question is actually interesting: what is a machine? [...] I wish the author had focused on the philosophical substance of “what even is a machine?” Indeed, and here we enter the land of metaphysics. Empirical science is not inherently mechanistic, though you cannot be blamed for making the mistake of thinking so given the crude metaphors we learn in school or how the methodological presumptions within scientific disciplines affect how we model and make predictions about phenomena. Even when not intended as literal characterizations of reality, against the backdrop of scientism, it is easy to reify metaphors into metaphysical truths if you don't know any better, when an authority figure compels you to do so, or when you fail to detect the whiff of contradiction. From experience, I will say that it is difficult to dislodge the mechanistic bias after a childhood spent having it reinforced in school and educational material. It might take a while to heal from the brain damage. But where this article is concerned, I think the author missed what is the essential difference between a machine and a living thing, namely, that while the parts of a machine are arranged according to ends external to the arrangement (the artificer) and, more importantly, have no inherent tendency to operate the way they do, the "parts" of living things are inherently ordered toward an end. To put it in technical language, the parts of a machine (or artifact) are joined together by an accidental form, while what makes an organism is a substantial form. Of course, a mechanistic view of the world excludes substantial form and telos as a presupposition of its founding charter, not as the conclusion of a demonstration from observation or logical necessity, and so a "mechanist" is conceptually prevented from distinguishing machines from living things from the start. [0] A nice article about mechanism: https://edwardfeser.blogspot.com/2010/05/deus-ex-machina.html https://edwardfeser.blogspot.com/2010/05/deus-ex-machina.htm... [1] For those tempted to construe reality in computational terms: https://drive.google.com/file/d/0B4SjM0oabZazckZnWlE1Q3FtdGs/view?resourcekey=0-9o43hlDMbPHyAnPzxOn1iQ https://drive.google.com/file/d/0B4SjM0oabZazckZnWlE1Q3FtdGs...
bryan0 4y ago
The author said specifically that he did not want to make the video about this philosophical point: > I imagine I'll get some pushback on my definition of a machine. I didn't want to turn the video into a definitional debate so I glossed over it pretty quickly. That was intentional. The specific definition is kind of besides the point, basically what he’s saying that if the cell is a “machine” then it is quite unlike any machine we are familiar with. It is far more complicated than anything humans have built or even imagined.
- omginternets 4y ago
  I’m not sure it’s entirely beside the point though, especially as his warnings and criticisms hinge on that very definition. To my point: there’s a nuanced (and, I would argue, more exact) definition of a machine that cellular systems meet. That lay people (and the occasional person who really ought to know better) misinterpret the metaphor is not a terribly interesting point, and, I think, not a reason to throw out the metaphor. To the authors credit, the explanation of how cells and proteins differ from everyday machines was a fascinating read.
  - bryan0 4y ago
    Yeah I agree with you. I think the author’s main point that this is a harmful analogy is not correct. We need some model to make progress on the complexities.
daveguy 4y ago
This is a great point. Maybe the focus should be, "how not to think about machines." If we build more complex functional systems (with the complexity, reliability, and efficiency of a cell) then we will certainly have to rethink what a "machine" is.

323 4y ago

Sometimes it helps to approach these things at a meta-level. What would it mean if cells were machines? Would that make humans machines? Maybe this is the problem author has. Other articles on the site which might be considered controversial: > Organisms Are Not Made Of Atoms https://www.subanima.org/organisms/ https://www.subanima.org/organisms/ > Why Biology BREAKS Physics https://www.subanima.org/biology-breaks-physics/ https://www.subanima.org/biology-breaks-physics/

prolyxis 4y ago
Those two titles are good examples of when click-bait is stretched to the point of complete inaccuracy.

jerf 4y ago

I think the author covered it sufficiently, because the author is correct that if you just walk up to someone with the referenced videos, they are going to come away with the mistakes the video author discusses. They're going to think things have specific functions, in specific ways, in the super-orderly manners presented, etc. Redefining machine to the point that it happens to cover what cells really are won't change those misconceptions, or at least, it won't change them for a very long time and until you get those definitions propagated far and wide. Which will be an uphill battle because they are frankly less useful than the current definition we have, which works in the real world we all interact with. Nobody is hearing "the cell is a machine" and then goes off thinking "ah, what they clearly mean is that it is a whole lot of goop interacting in shocking complicated ways with each other all the time resembling literally nothing else a human calls a machine". Playing games with definitions is, well, exactly that: Playing games with definitions. It doesn't actually change anything in the world.

adamredwoods 4y ago
This was similar to my understanding (with my limited insight). If we are researching a particular cell interaction, thinking it as a machine, we may walk away with wrong conclusions if we hypothesize, set up a test, and study results, thinking that this machine is expected to work the same way every time.
omginternets 4y ago
I suppose that's fair. I guess I'm lamenting the missed opportunity for an interesting philosophical discussion, and perhaps wishing the author had presented his (otherwise very interesting!) thoughts through a more nuanced lens. I don't think he would even need to change the title. I still enjoyed the article, and would upvote it again if I could.
- mxkopy 4y ago
  GEB explores a similar idea in investigating where a program is written It's implied that the distinctions are somewhat arbitrary. For example, a song is "written" on a record with a bunch of grooves, and the record-player is the machine that plays it. But if the record-player spun backwards instead of forwards, you'd hear something completely different. So in some sense, the record-player also holds part of the program. And all this runs parallel to the idea that a program is also data, IMO. I think a 'non-arbitrary' definition of a machine would be very general.

Daniel_sk 4y ago

A cell is not a machine in what most people would understand under this word. It's almost like it's full of agents that each have their own goal and through endless evolutionary selection these goals between those agents became interconnected in such way a complicated way that they play this "orchestra" that is a cell. But when you look inside it's a huge biological mess. There is no central part that controls everything - cells and multicellular organisms are hugely distributed systems.

kmtrowbr 4y ago

https://www.etymonline.com/word/machine https://www.etymonline.com/word/machine machine (n.) 1540s, "structure of any kind," from Middle French machine "device, contrivance," contrive: to form or create in an artistic or ingenious manner According to these definitions a machine is something that humans create. We understand what we create. When trying to understand complex things, we form metaphors based on our actual understanding. Whichever is the most advanced thinking of the age is used at a metaphor to describe life and nature. When it was steam, we used popularly understood concepts of steam engines to describe life. When it was electricity, we used electrical metaphors. Now that it is computers, we use those concepts. We are also very overconfident regarding how well we understand and control the world. Having achieved smashing success in some areas, we then think we have total control. Chronological snobbery, if you will: https://en.wikipedia.org/wiki/Chronological_snobbery https://en.wikipedia.org/wiki/Chronological_snobbery The danger is then, at a popular level, we take the metaphor literally and turn it around to be something reductive: "Life is no more than a machine." That is frankly not true: this is where the metaphor falls apart & it's the danger the article describes. Life is more than a steam engine, it's more than electrical circuits, and it's also not a computer. Life may be a purely material phenomenon (i.e. no more than atoms, void, and time), but that does not mean it is "just a steam engine / computer" etc.

pixl97 4y ago
The only response I can really give here is 'insufficient data for meaningful answer' Time will tell if this is true or not.

oh_my_goodness 4y ago

Yes, the core philosophical question is very interesting. Unfortunately at this time we can't resolve that core philosophical question. When we can resolve it, I think we'll be able to move it into the part of philosophy that's also called "science." The cell might be understandable as a giant machine, but I think the author is claiming that we either don't know that yet, or that the machine may be enormously more complex than some folks are suggesting. Physicist Philip Anderson has written about reductionism (which he claims works very well) and "constructionism" (which he says is much more confusing). https://www.tkm.kit.edu/downloads/TKM1_2011_more_is_different_PWA.pdf https://www.tkm.kit.edu/downloads/TKM1_2011_more_is_differen...

omginternets 4y ago
"What is a machine" is hardly the realm of science.
- oh_my_goodness 4y ago
  Either it's a philosophical question, or it's some other kind of question. "Philosophical question" implies that we can't answer it at this time. (Or, equivalently, we can build equally convincing but conflicting answers.) One claim in the article is that we can't answer the (much narrower) question, "Is the cell a machine?" I don't see that saying "well that's a philosophical question" is so different from saying "as scientists, we don't know."
  - nosianu 4y ago
    There really is no great mystery question - because "machine" is a word not defined by the universe and is controlled by humans, who can use whatever definition they want. So whatever definition you use, this word has no external objective constraints, there will be a common ground between people or not and there is no objective way to make everybody agree on one definition, it's all voluntary. (Even if they do, the agreement is never complete because it's only about the aspects talked about, and then words are not reality and come about indirectly through many processes in the brain and never completely match between different people, or even the same person over time) "What is a machine" is a great way to waste time doing nothing, unless you can beforehand agree on constraints, e.g. by looking for a definition for one clearly defined purpose. But that's just moving the goal post to a little outside the box that then this definition is tied to. There is this strange movement, or maybe it isn't strange, when I was younger I followed it too, to take words way too seriously. There's entire fantasy stories about "true names", some kind of absolute comprehension about something expressed as a word. There also are practical examples, for example I once read about a father whose daughter had some rare disease about which nothing really was known. The only thing that had happened, at least by the time of the story, was that somebody had encountered this disease previously and attached a word to it. But without any content, there was no knowledge about how it occurred or how to treat it. But when the father was told that name he said something like "Finally we know what the problem is, I can breath much easier" (words partially made up because I don't remember, but that meaning was there). Just look at unrestraint, non-concrete discussions about words and there arbitrary definitions, looking for something "philosophical" behind those words. In this context, a blog post I once bookmarked (hey, I finally get to use my bookmarks!): https://www.lesswrong.com/posts/7X2j8HAkWdmMoS8PE/disputing-definitions https://www.lesswrong.com/posts/7X2j8HAkWdmMoS8PE/disputing-... - with some practical advice, not an attempt to solve anything "philosophically". I see sooo many comments here basing their agreement or disagreement on some definition of the word "machine". The default these days is to try to find something wrong with somebody's statement(s), by exploring the edges or even beyond of definitions of some word or words, making discussions very tiring. When instead one could just try to find the idea the person wanted to express and not get hung up about some words. Because deep inside the brain there are no words, the ideas one tries to express are much more fuzzier and flexible and trying to turn them into words is a very inexact process. Our brains don't think in words, except for a tiny part under our direct attention. The concepts leading to the use of this or that word, and the many words accompanying it, are never the same in different brains, and not the same in the same brain over time. To make the best use of our very limited communication tools that serialized extremely intricate four-dimensional patterns (brain structure plus the dynamic behavior) into rigid words you have to want to communicate and to understand and be positive, at least when something is a little off-center from the usual things that everybody involved in the communication has already established a good synchronization on. When discussing if we need to buy more milk because there is none in the fridge we have a much easier time with the communication and with agreements, because we are not going anywhere near the edges of well-used concepts (what is milk, what is a fridge, what does "empty" mean, etc. etc. - all of those can lead to deep disagreements at the edges). For a text like the one here some more allowances would be better to get something useful out of the communication. IMHO the best way to make something out of this article is if you already have a pretty good and somewhat deep comprehension of organic chemistry at least. The many stages of going deeper and deeper down the rabbit hole from the beginning teachings of atoms and chemical bonds to more and more complex understanding that you get from university chemistry, where it gets more like physics, coupled with seeing it "in use" for large and complex organic molecules, is I think a good preparation to understand the article's point.

akomtu 4y ago

Intuituvely, a machine is a thing with an internal state and behaviour that predictably depends only on that state. However, what if the internal state exists, but cannot be completely known or reproduced?

lo_zamoyski 4y ago

> The core philosophical question is actually interesting: what is a machine? [...] I wish the author had focused on the philosophical substance of “what even is a machine?” Indeed, and here we enter the land of metaphysics. Empirical science is not inherently mechanistic, though you cannot be blamed for making the mistake of thinking so given the crude metaphors we learn in school or how the methodological presumptions within scientific disciplines affect how we model and make predictions about phenomena. Even when not intended as literal characterizations of reality, against the backdrop of scientism, it is easy to reify metaphors into metaphysical truths if you don't know any better, when an authority figure compels you to do so, or when you fail to detect the whiff of contradiction. From experience, I will say that it is difficult to dislodge the mechanistic bias after a childhood spent having it reinforced in school and educational material. It might take a while to heal from the brain damage. But where this article is concerned, I think the author missed what is the essential difference between a machine and a living thing, namely, that while the parts of a machine are arranged according to ends external to the arrangement (the artificer) and, more importantly, have no inherent tendency to operate the way they do, the "parts" of living things are inherently ordered toward an end. To put it in technical language, the parts of a machine (or artifact) are joined together by an accidental form, while what makes an organism is a substantial form. Of course, a mechanistic view of the world excludes substantial form and telos as a presupposition of its founding charter, not as the conclusion of a demonstration from observation or logical necessity, and so a "mechanist" is conceptually prevented from distinguishing machines from living things from the start. [0] A nice article about mechanism: https://edwardfeser.blogspot.com/2010/05/deus-ex-machina.html https://edwardfeser.blogspot.com/2010/05/deus-ex-machina.htm... [1] For those tempted to construe reality in computational terms: https://drive.google.com/file/d/0B4SjM0oabZazckZnWlE1Q3FtdGs/view?resourcekey=0-9o43hlDMbPHyAnPzxOn1iQ https://drive.google.com/file/d/0B4SjM0oabZazckZnWlE1Q3FtdGs...

bryan0 4y ago

The author said specifically that he did not want to make the video about this philosophical point: > I imagine I'll get some pushback on my definition of a machine. I didn't want to turn the video into a definitional debate so I glossed over it pretty quickly. That was intentional. The specific definition is kind of besides the point, basically what he’s saying that if the cell is a “machine” then it is quite unlike any machine we are familiar with. It is far more complicated than anything humans have built or even imagined.

omginternets 4y ago
I’m not sure it’s entirely beside the point though, especially as his warnings and criticisms hinge on that very definition. To my point: there’s a nuanced (and, I would argue, more exact) definition of a machine that cellular systems meet. That lay people (and the occasional person who really ought to know better) misinterpret the metaphor is not a terribly interesting point, and, I think, not a reason to throw out the metaphor. To the authors credit, the explanation of how cells and proteins differ from everyday machines was a fascinating read.
- bryan0 4y ago
  Yeah I agree with you. I think the author’s main point that this is a harmful analogy is not correct. We need some model to make progress on the complexities.

daveguy 4y ago

This is a great point. Maybe the focus should be, "how not to think about machines." If we build more complex functional systems (with the complexity, reliability, and efficiency of a cell) then we will certainly have to rethink what a "machine" is.