6 ms·

How not to think about cells

103 points by rrampage 4y ago

greenbit 4y ago
My TL;DR take on this: thinking of proteins like rigid little single-purpose parts might fall short of the mark. Proteins are kind of wiggly, and nature can easily multi-purpose a given molecule. Backed up with lots of references. Good read.
- qikInNdOutReply 4y ago
  Its also, the situation deforms the outcome. Plants deform and grow different in zero gravity, so its carbon nano-machinery, but machinery that uses the circumstances to shape itself. Like a liquid metal terminator, that becomes a bell when meating the casting mold. Take allergies, here is a hyper active defense system that wants to fight for its life and looks for a challenge. And it will find its fight and find its challenge, shaping itself accordingly, and if there is no opponent, it will take on the things close enough to it. Which is why its such a folly to take a creature completely out of its natural environment, like taking away half of what defines the creature. And instead of accepting the mistake, some even dig in further, developing phobias against dirt, parasites and "nature contamination". Resulting in melting humans. But i digress..
Kalanos 4y ago
dense, shaky mix of proteins that bump into each other at the right angle to make stuff happen
- csours 4y ago
  Sounds like my kind of party
omginternets 4y ago
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.
dkarl 4y ago
There's one complaint here that seems valid: > gives us a false sense of confidence in how much we know about the biological world A false sense of confidence could make people vulnerable to bold false claims, which might lead to poor consumer choices and poor policy choices. Beyond that, the approach seems really wrong-headed. Popular science education has a successful approach when you want people to understand the limitations of a model: you hook people with a fun headline of "COOL NEWS, THINGS ARE MUCH WEIRDER THAN YOU THINK!" You teach forward from the oversimplified model. You aren't going to reach many people with a negative, moralizing message that people need to go backwards and give up a model that has given them insight. "Oh, we should never have given you this, you're not smart enough for it, you're going to make a mess." The sad thing is that the information conveyed here is really cool, and it could easily be framed in a fun way! Instead, it's presented in a way that sends the message, "Look, you need to understand how dumb and dangerous it was for you to think you had any insight into this." > It's finally dawning on us that the cell is not a machine I really, really, really don't understand the sense of moralistic fear infusing this whole presentation. Reading the piece and watching the video, I feel like I'm reading and watching a religious sermon on the spiritual dangers of materialism instead of a piece of popular education to help the public have a better-informed understanding of science.
- ouid 4y ago
  you are thinking about individual understanding, but science writers must be concerned with population understanding. People die and get born, and this is a force in the population making it know less over time. This force and education must reach some sort of equilibrium, and the author is concerned about the shape of the resulting steady state of knowledge. It is far more important, typically, to not lie to people than it is to tell them the truth, for if you are lying to them in service of later telling them the truth, and people don't seek out further education, then most people will just believe lies, and then eventually die, never having contributed their knowing the truth to the population knowledge distribution.
  - 1auralynn 4y ago
    On the other hand, if everything is always presented in its full complexity with a million caveats and you lose people because they don't have the prerequisite knowledge to be able to digest it, I guarantee this will result in many, many more potential contributions being lost than from those who were just "satisfied that it was all worked out already".
turtledragonfly 4y ago
I enjoy when the nice abstract models we work with are given a course-correction, and we are reminded of the profound, gargantuan complexity of the real world. Sometimes, we get lost in our models and start thinking that they are reality, rather than just poor approximations of the real mess that's out there. So, nice article (: For a shorter version, that also gives some of that sense of the real complexity of cells, I like "Cells are very fast and crowded places"[1]. One good quote: molecules move unimaginably quickly due to thermal motion. A small molecule such as glucose is cruising around a cell at about 250 miles per hour, while a large protein molecule is moving at 20 miles per hour. Note that these are actual speeds inside the cell, not scaled-up speeds. I'm not talking about driving through a crowded Times Square at 20 miles per hour; to scale this would be more like driving through Times Square at 20 million miles per hour! [1] http://www.righto.com/2011/07/cells-are-very-fast-and-crowded-places.html http://www.righto.com/2011/07/cells-are-very-fast-and-crowde...
pizlonator 4y ago
This is really cool! I just think that the definition of “machine” is too restrictive. To me a machine is a very broad word and no matter how complex we find our bodies to be, it’s still ok to think of them as machines. That doesn’t mean it’s ok to oversimplify how they work or to presume we know everything about them.
throw149102 4y ago
Reading this on mobile, I feel really lost about what the article is trying to say. The problem is all the sources are in between the essay-bits. I would prefer it if the author just used footnotes like Wikipedia when citing a claim and stuck all the sources on at the end.
amelius 4y ago
"Machine moves faster than some people thought previously; hence it is not a machine." What kind of logic is this?
TeeWEE 4y ago
It really depends on how you define a machine. A machine to me is a combination of elements that interact to perform some function. Wether those elements are multifunctional doesn’t matter. Also solid is not a requirement: ropes and pullies, expansion elements, self altering software: etc are all found in human made machines. And they are not solid. I disagree with this video: life is based on molecular machines. It just happens that these machines are really complex and dynamic. But machines nonetheless.
- isitmadeofglass 4y ago
  > It really depends on how you define a machine. Sure, and depending on how you define a computer program hamlet is a computer program, and depending on your definition of Christmas movie, Planet of the Apes is Christmas movie. The point is that for typical and sane definitions cells aren’t machines, hamlet isn’t a program and planet of the apes isn’t a Christmas movie (But Die Hard is).
joshuahedlund 4y ago
> I like when humans finally caught up to this advanced biological process and had to compare it to machines that humans created that led to this discovery just to understand it. The solar system is like a clock. Cells are like machines. Brains are like computer networks. It's interesting to realize how regularly we map our discoveries about the physical world to the technologies of the day, "just to understand it," and also interesting to be reminded of the limitations of such analogies. The best and most literal parallel I can think of is DNA is like code. Yet I find it interesting, almost uncanny, that we discovered that right around the same time we started developing prgoramming languages.
- deleted 4y ago
  [deleted]
- jakear 4y ago
  > The best and most literal parallel I can think of is DNA is like code. Yet I find it interesting, almost uncanny, that we discovered that right around the same time we started developing prgoramming languages. Eh... codons were only discovered in 1961 (Crick, Brenner et al. experiment), the Jacquard Loom was invented in 1804.
  - dekhn 4y ago
    I think the better parallel is information theory and DNA coding, which happened around the same time, and there was a lot of flow from the IT folks to the DNA folks when people were trying to deduce the "code". See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220916/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220916/ and other things written by Schneider
tejohnso 4y ago
I couldn't figure out if the author is trying to make a point about the definition of machine, or if they're trying to make a point that the animations are misleading. Because they say the animations are misleading, but then they go into a discussion about what makes a machine a machine. > the animations are misleading. Ok, why are the animations misleading? Are they representing a process that does not occur? > Let's go from the start. Why isn't the cell run by molecular machines like the animations suggest? Well, first we need to come up with some criteria to distinguish machines from non-machines. Wait, what? No, we don't first need to define what we mean by machine. I just want to know why the animation is misleading as an approximate model. Does the animation represent the interactions occurring in the cell or not? > I also know that many machines have bendy parts, and that some machines have multi-functional parts. Ok, further digging into what people think about when they talk about a machine. I still just want to know if the thing in the video is misleading, as accused. > the structure of proteins isn't hard and rigid like we see in the animations. They're actually more like "dense liquids" that constantly jiggle around inside the cell. But do they do what is shown in the video? Maybe just in a less rigid manner? It's just a model! In the ted talk there's another video of some process and you can see it's all liquid. Can we focus on the animation and why it's misleading? > This is already strike one for the machine metaphor because, if my bike jiggled this much I wouldn't be able to go very far. Well yeah, it wouldn't work very well as a bicycle, but a jiggly machine wouldn't be a bicycle, it would be something else. Doesn't mean it's not a machine. And we're still not talking about the accusation of misleading videos. > Proteins almost never have one shape, they have a bunch of different configurations that they shift between. But for the model in the video, for that particular protein shape, does it represent the interactions that are occurring? Does the Helicase process the DNA strands? Does the DNA wrap around Histones? > It is finally dawning on us that the cell is not a machine. No, there was an accusation made that was not backed up aside from an elaborate side argument about whether the cell is machine-like. Obviously the animations don't completely represent reality. They're just models after all. Simplified for presentation and communication of a particular concept. I still don't know if the interactions in the animation are false or not. Or if the author is really calling them misleading because they're more rigid than in real life, and they don't represent the full complexity of every possible protein type.
- 4y ago
pencilguin 4y ago
volleygman180 4y ago
Within cells interlinked. Within cells interlinked. Within cells interlinked.
hirenj 4y ago
I have been wondering if a better representation of a cell would actually be a large centralised message “queue”, which represents the state of the cell somehow (one entry for each metabolite molecule, or for each proteoform). The enzymes/proteins would then sample this queue, and return the message, process the message, or add new state to the queue. So this is essentially a large decentralised message processing mechanism, and what you would expect is that over time the state of the queue would shift, representing a shift in the state of the cell.
dekhn 4y ago
There's some good stuff in this but while I agree with many of his points, I don't agree with his fundamental conclusion. I see several examples of "machines" in biology which satisfy all my requirements. In particular DNA and RNA transcriptase, the ribosome, and motor proteins are all machines. They act with very high fidelity, have a specific and necessary purpose (to the extent that an evolved system can have a well-defined purpose), consume energy to achieve their goals, and eventually break down and make mistakes. The current belief about alphafold is that its confidence is actually a "disorder predictor": when it makes low confidence predictions, it's really that the protein itself doesn't adopt a well-defined structure. But further than this, we actually do protein design and create new proteins that have well-defined functions. FOr example there is a class of proteins known as proteases that "cut proteins" (conceptually like scissors, but physically using enzymatic activity). A well-known protein designer at Genentech took an existing protease and made it more heat-stable (IE, didn't stop working when you raised the temperature). This protein was then sold licensed to laundry manufacturers who added it to their detergent (it does a great job cleaning up protein stains, hence the advertisement "protein gets out protein"). It's literally a machine you put in your machine to make your machine machine better.
vic_nyc 4y ago
I wonder how this relates to the "mystical realm" - the yogic concept that a certain "life-force" (prana / chi) exists that coordinates, at a higher level, the behavior of cells.
- Koshkin 4y ago
  It seems you are taking the notion of "the cell not being a machine" a little too far. Molecular biology has not shown the need for the hypothesis of a "higher level life-force" to explain what is going on inside a cell.

103 points by rrampage 4y ago

My TL;DR take on this: thinking of proteins like rigid little single-purpose parts might fall short of the mark. Proteins are kind of wiggly, and nature can easily multi-purpose a given molecule. Backed up with lots of references. Good read.

qikInNdOutReply 4y ago
Its also, the situation deforms the outcome. Plants deform and grow different in zero gravity, so its carbon nano-machinery, but machinery that uses the circumstances to shape itself. Like a liquid metal terminator, that becomes a bell when meating the casting mold. Take allergies, here is a hyper active defense system that wants to fight for its life and looks for a challenge. And it will find its fight and find its challenge, shaping itself accordingly, and if there is no opponent, it will take on the things close enough to it. Which is why its such a folly to take a creature completely out of its natural environment, like taking away half of what defines the creature. And instead of accepting the mistake, some even dig in further, developing phobias against dirt, parasites and "nature contamination". Resulting in melting humans. But i digress..

Kalanos 4y ago

dense, shaky mix of proteins that bump into each other at the right angle to make stuff happen

csours 4y ago
Sounds like my kind of party

omginternets 4y ago

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.

dkarl 4y ago

There's one complaint here that seems valid: > gives us a false sense of confidence in how much we know about the biological world A false sense of confidence could make people vulnerable to bold false claims, which might lead to poor consumer choices and poor policy choices. Beyond that, the approach seems really wrong-headed. Popular science education has a successful approach when you want people to understand the limitations of a model: you hook people with a fun headline of "COOL NEWS, THINGS ARE MUCH WEIRDER THAN YOU THINK!" You teach forward from the oversimplified model. You aren't going to reach many people with a negative, moralizing message that people need to go backwards and give up a model that has given them insight. "Oh, we should never have given you this, you're not smart enough for it, you're going to make a mess." The sad thing is that the information conveyed here is really cool, and it could easily be framed in a fun way! Instead, it's presented in a way that sends the message, "Look, you need to understand how dumb and dangerous it was for you to think you had any insight into this." > It's finally dawning on us that the cell is not a machine I really, really, really don't understand the sense of moralistic fear infusing this whole presentation. Reading the piece and watching the video, I feel like I'm reading and watching a religious sermon on the spiritual dangers of materialism instead of a piece of popular education to help the public have a better-informed understanding of science.

ouid 4y ago
you are thinking about individual understanding, but science writers must be concerned with population understanding. People die and get born, and this is a force in the population making it know less over time. This force and education must reach some sort of equilibrium, and the author is concerned about the shape of the resulting steady state of knowledge. It is far more important, typically, to not lie to people than it is to tell them the truth, for if you are lying to them in service of later telling them the truth, and people don't seek out further education, then most people will just believe lies, and then eventually die, never having contributed their knowing the truth to the population knowledge distribution.
- 1auralynn 4y ago
  On the other hand, if everything is always presented in its full complexity with a million caveats and you lose people because they don't have the prerequisite knowledge to be able to digest it, I guarantee this will result in many, many more potential contributions being lost than from those who were just "satisfied that it was all worked out already".

turtledragonfly 4y ago

I enjoy when the nice abstract models we work with are given a course-correction, and we are reminded of the profound, gargantuan complexity of the real world. Sometimes, we get lost in our models and start thinking that they are reality, rather than just poor approximations of the real mess that's out there. So, nice article (: For a shorter version, that also gives some of that sense of the real complexity of cells, I like "Cells are very fast and crowded places"[1]. One good quote: molecules move unimaginably quickly due to thermal motion. A small molecule such as glucose is cruising around a cell at about 250 miles per hour, while a large protein molecule is moving at 20 miles per hour. Note that these are actual speeds inside the cell, not scaled-up speeds. I'm not talking about driving through a crowded Times Square at 20 miles per hour; to scale this would be more like driving through Times Square at 20 million miles per hour! [1] http://www.righto.com/2011/07/cells-are-very-fast-and-crowded-places.html http://www.righto.com/2011/07/cells-are-very-fast-and-crowde...

pizlonator 4y ago

This is really cool! I just think that the definition of “machine” is too restrictive. To me a machine is a very broad word and no matter how complex we find our bodies to be, it’s still ok to think of them as machines. That doesn’t mean it’s ok to oversimplify how they work or to presume we know everything about them.

throw149102 4y ago

Reading this on mobile, I feel really lost about what the article is trying to say. The problem is all the sources are in between the essay-bits. I would prefer it if the author just used footnotes like Wikipedia when citing a claim and stuck all the sources on at the end.

amelius 4y ago

"Machine moves faster than some people thought previously; hence it is not a machine." What kind of logic is this?

TeeWEE 4y ago

It really depends on how you define a machine. A machine to me is a combination of elements that interact to perform some function. Wether those elements are multifunctional doesn’t matter. Also solid is not a requirement: ropes and pullies, expansion elements, self altering software: etc are all found in human made machines. And they are not solid. I disagree with this video: life is based on molecular machines. It just happens that these machines are really complex and dynamic. But machines nonetheless.

isitmadeofglass 4y ago
> It really depends on how you define a machine. Sure, and depending on how you define a computer program hamlet is a computer program, and depending on your definition of Christmas movie, Planet of the Apes is Christmas movie. The point is that for typical and sane definitions cells aren’t machines, hamlet isn’t a program and planet of the apes isn’t a Christmas movie (But Die Hard is).

joshuahedlund 4y ago

> I like when humans finally caught up to this advanced biological process and had to compare it to machines that humans created that led to this discovery just to understand it. The solar system is like a clock. Cells are like machines. Brains are like computer networks. It's interesting to realize how regularly we map our discoveries about the physical world to the technologies of the day, "just to understand it," and also interesting to be reminded of the limitations of such analogies. The best and most literal parallel I can think of is DNA is like code. Yet I find it interesting, almost uncanny, that we discovered that right around the same time we started developing prgoramming languages.

deleted 4y ago
[deleted]
jakear 4y ago
> The best and most literal parallel I can think of is DNA is like code. Yet I find it interesting, almost uncanny, that we discovered that right around the same time we started developing prgoramming languages. Eh... codons were only discovered in 1961 (Crick, Brenner et al. experiment), the Jacquard Loom was invented in 1804.
- dekhn 4y ago
  I think the better parallel is information theory and DNA coding, which happened around the same time, and there was a lot of flow from the IT folks to the DNA folks when people were trying to deduce the "code". See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220916/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3220916/ and other things written by Schneider

tejohnso 4y ago

I couldn't figure out if the author is trying to make a point about the definition of machine, or if they're trying to make a point that the animations are misleading. Because they say the animations are misleading, but then they go into a discussion about what makes a machine a machine. > the animations are misleading. Ok, why are the animations misleading? Are they representing a process that does not occur? > Let's go from the start. Why isn't the cell run by molecular machines like the animations suggest? Well, first we need to come up with some criteria to distinguish machines from non-machines. Wait, what? No, we don't first need to define what we mean by machine. I just want to know why the animation is misleading as an approximate model. Does the animation represent the interactions occurring in the cell or not? > I also know that many machines have bendy parts, and that some machines have multi-functional parts. Ok, further digging into what people think about when they talk about a machine. I still just want to know if the thing in the video is misleading, as accused. > the structure of proteins isn't hard and rigid like we see in the animations. They're actually more like "dense liquids" that constantly jiggle around inside the cell. But do they do what is shown in the video? Maybe just in a less rigid manner? It's just a model! In the ted talk there's another video of some process and you can see it's all liquid. Can we focus on the animation and why it's misleading? > This is already strike one for the machine metaphor because, if my bike jiggled this much I wouldn't be able to go very far. Well yeah, it wouldn't work very well as a bicycle, but a jiggly machine wouldn't be a bicycle, it would be something else. Doesn't mean it's not a machine. And we're still not talking about the accusation of misleading videos. > Proteins almost never have one shape, they have a bunch of different configurations that they shift between. But for the model in the video, for that particular protein shape, does it represent the interactions that are occurring? Does the Helicase process the DNA strands? Does the DNA wrap around Histones? > It is finally dawning on us that the cell is not a machine. No, there was an accusation made that was not backed up aside from an elaborate side argument about whether the cell is machine-like. Obviously the animations don't completely represent reality. They're just models after all. Simplified for presentation and communication of a particular concept. I still don't know if the interactions in the animation are false or not. Or if the author is really calling them misleading because they're more rigid than in real life, and they don't represent the full complexity of every possible protein type.

4y ago

pencilguin 4y ago

volleygman180 4y ago

Within cells interlinked. Within cells interlinked. Within cells interlinked.

hirenj 4y ago

I have been wondering if a better representation of a cell would actually be a large centralised message “queue”, which represents the state of the cell somehow (one entry for each metabolite molecule, or for each proteoform). The enzymes/proteins would then sample this queue, and return the message, process the message, or add new state to the queue. So this is essentially a large decentralised message processing mechanism, and what you would expect is that over time the state of the queue would shift, representing a shift in the state of the cell.

dekhn 4y ago

There's some good stuff in this but while I agree with many of his points, I don't agree with his fundamental conclusion. I see several examples of "machines" in biology which satisfy all my requirements. In particular DNA and RNA transcriptase, the ribosome, and motor proteins are all machines. They act with very high fidelity, have a specific and necessary purpose (to the extent that an evolved system can have a well-defined purpose), consume energy to achieve their goals, and eventually break down and make mistakes. The current belief about alphafold is that its confidence is actually a "disorder predictor": when it makes low confidence predictions, it's really that the protein itself doesn't adopt a well-defined structure. But further than this, we actually do protein design and create new proteins that have well-defined functions. FOr example there is a class of proteins known as proteases that "cut proteins" (conceptually like scissors, but physically using enzymatic activity). A well-known protein designer at Genentech took an existing protease and made it more heat-stable (IE, didn't stop working when you raised the temperature). This protein was then sold licensed to laundry manufacturers who added it to their detergent (it does a great job cleaning up protein stains, hence the advertisement "protein gets out protein"). It's literally a machine you put in your machine to make your machine machine better.

vic_nyc 4y ago

I wonder how this relates to the "mystical realm" - the yogic concept that a certain "life-force" (prana / chi) exists that coordinates, at a higher level, the behavior of cells.

Koshkin 4y ago
It seems you are taking the notion of "the cell not being a machine" a little too far. Molecular biology has not shown the need for the hypothesis of a "higher level life-force" to explain what is going on inside a cell.