[HN Gopher] How not to think about cells
___________________________________________________________________
How not to think about cells
Author : rrampage
Score : 81 points
Date : 2022-11-23 14:30 UTC (8 hours ago)
(HTM) web link (www.subanima.org)
(TXT) w3m dump (www.subanima.org)
| vic_nyc wrote:
| 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.
| Kalanos wrote:
| dense, shaky mix of proteins that bump into each other at the
| right angle to make stuff happen
| csours wrote:
| Sounds like my kind of party
| pencilguin wrote:
| dkarl wrote:
| 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.
| 1auralynn wrote:
| People like this are one of the reasons biology visualization
| is so difficult: Nothing less than a perfect simulation is good
| enough, and any editorial/design choices to make certain
| processes perceptible to humans are problematic in some way.
| It's all true really, but there are many valid reasons to
| create visualizations that are less-than-perfect. But yeah it's
| a fine balance between accuracy and the appearance of accuracy
| (e.g presenting a process as linear when it's really
| stochastic)
| ouid wrote:
| 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 wrote:
| 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".
| ouid wrote:
| Your "guarantee" is insufficient evidence that lying to the
| population is worthwhile. The burden of evidence is on you,
| I think.
|
| You're also making unreasonable assumtpions about the
| burden associated with not lying. You don't have to
| completely solve the miscommunication problem in order to
| do something about it, and even if you were to try to
| completely solve the miscommunication problem, it would not
| require you to include a million caveats. Basically you
| could solve the whole problem by not making analogies.
| pixl97 wrote:
| You're falling into your own trap of what is and isn't a
| lie.
|
| Lets go with the common aphorism 'all models are wrong,
| but some are useful'. As it puts forth there are a large
| number of useful models, but wouldn't that fall under
| your term of a lie since it's not the truth of a
| situation.
|
| The problem with reality is it feels no need to be
| explainable.
|
| I think I meant to post this to the user above you....
| 1auralynn wrote:
| Exactly? I wasn't the one who classified Drew Barry's
| work, widely acknowledged as some of the very best and
| most accurate in molecular animation, as "lies" ... so,
| not really sure what you're saying? In reality, humans
| can't see down to the nanoscale with their eyes, yet
| there are real 3D structures down there that have a
| physical form. If we display them as being a couple of
| inches large so that humans can see the shape, is that
| misleading? Should we never try to visualize anything for
| fear of it not accurately representing reality?
|
| I guess my point is, as someone who has done a ton of
| work in this area, there are a million choices one can
| make when choosing what to visualize, and the lines
| between truth/reality/lies/accuracy can get muddled. A
| lot of it depends on context, use cases etc. For example,
| a star high school teacher may show one of Drew Barry's
| animations to their class and use it as an example of the
| limitations of visualization. A creationist could use the
| same animation as evidence of "God's perfect design".
|
| What I'm understanding from the article and from your
| arguments, is that unless you can guarantee that a piece
| of work 100% represents reality in all its complexity, it
| does more harm than good. I'm politely disagreeing, I
| think it's better for these works to exist: "Perfection
| is the enemy of done".
| 1auralynn wrote:
| Yeah I mean, we could just never use real structural data
| and just communicate purely in symbols that way users
| would know it's "not real", or inherit a billion dollars
| and come up with a perfect simulator and high-end
| computers for all of humanity to view it. This stuff is
| HARD to make, and nearly impossible to satisfy everyone.
| Drew Barry's animations are "lying" because they're not a
| perfect representation of reality? In my opinion, it's
| better for his animations to exist and be "lying" than
| have nothing.
| tejohnso wrote:
| 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.
| omginternets wrote:
| 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.
| jerf wrote:
| 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.
| omginternets wrote:
| 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.
| adamredwoods wrote:
| 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.
| bsder wrote:
| > 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".
|
| Erm, a lot of the "nanomachine" people think exactly like
| this. Even simple things like "gears" do weird things an the
| nano level.
|
| Nevertheless, the biggest problems with the conception of a
| "cell" would be solved if we _quit drawing them in 2D_. Draw
| some cells as spheres. Draw muscle cells as slightly
| elongated cylinders. etc.
|
| If we drew the cells in 3D with chunks missing for labels,
| students would have a much better conception. Starting with:
| "Oh, hey, there _isn 't_ a huge amount of empty space--
| there's crap _everywhere_. These things are _packed_ ".
| akomtu wrote:
| 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 wrote:
| > 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.htm...
|
| [1] For those tempted to construe reality in computational
| terms:
| https://drive.google.com/file/d/0B4SjM0oabZazckZnWlE1Q3FtdGs...
| Daniel_sk wrote:
| 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 wrote:
| 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
|
| 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 wrote:
| The only response I can really give here is
|
| 'insufficient data for meaningful answer'
|
| Time will tell if this is true or not.
| bryan0 wrote:
| 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 wrote:
| 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 wrote:
| 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.
| oh_my_goodness wrote:
| 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_differen...
| omginternets wrote:
| "What is a machine" is hardly the realm of science.
| oh_my_goodness wrote:
| 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 wrote:
| 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/post
| s/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.
| oh_my_goodness wrote:
| I'm saying that for practical purposes, "What is
| machine?" has no unique answer.
|
| I can't understand whether you agree, disagree, or what.
| daveguy wrote:
| 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 wrote:
| 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/
|
| > _Why Biology BREAKS Physics_
|
| https://www.subanima.org/biology-breaks-physics/
| prolyxis wrote:
| Those two titles are good examples of when click-bait is
| stretched to the point of complete inaccuracy.
| joshuahedlund wrote:
| > 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]
| jakear wrote:
| > 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 wrote:
| 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/ and
| other things written by Schneider
| turtledragonfly wrote:
| 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-
| crowde...
| TeeWEE wrote:
| 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 wrote:
| > 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).
| volleygman180 wrote:
| Within cells interlinked.
|
| Within cells interlinked.
|
| Within cells interlinked.
| pizlonator wrote:
| 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 wrote:
| 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 wrote:
| "Machine moves faster than some people thought previously; hence
| it is not a machine."
|
| What kind of logic is this?
| greenbit wrote:
| 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 wrote:
| 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..
| hirenj wrote:
| 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 wrote:
| 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.
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