[HN Gopher] Cells are fast and crowded places
___________________________________________________________________
Cells are fast and crowded places
Author : gmays
Score : 240 points
Date : 2020-10-05 12:30 UTC (10 hours ago)
(HTM) web link (www.righto.com)
(TXT) w3m dump (www.righto.com)
| DoreenMichele wrote:
| I had no idea.
|
| I am really glad to see this piece. I've spent more than 19 years
| getting myself healthier while the world spit in my face and
| called me _crazy_. I did so by focusing on trying to understand
| my genetic disorder at the cellular level.
|
| Most genetic disorder involve a miscoded protein. Your DNA serves
| as the blue prints for a complex factory called a "cell" and when
| there is a bug in the code of your DNA, the 3D printer mechanisms
| translating those instructions into physical reality create
| something broken.
|
| That something broken is typically a bit of protein that normally
| gets folded up and used as a tool within the cell. When it is
| miscoded, it can't do it's job. It's sometimes kind of like a cog
| missing a tooth.
|
| As the cell gets more chemically deranged from the tools
| misfiring, you see more misfolded proteins. If either salinity or
| pH balance are off, those proteins are more likely to misfold.
|
| I think this accounts for what gets called "The normal
| progression of CF." It's a positive feedback loop -- aka a
| vicious cycle.
|
| More broken proteins leads to worse chemical derangement and
| worse chemical derangement leads to more broken proteins and we
| are off and running on a highway to hell.
|
| In cystic fibrosis, the protein that gets miscoded is known as
| the CFTR -- the cystic fibrosis transmembrane conductance
| regulator. It serves as a channel in the cell membrane.
|
| You can think of it like a traffic light managing traffic into
| and out of the cell of certain proteins or an air lock and only
| certain proteins with the right ID card get to use it.
|
| It causes the body to misprocess salt (NACL -- sodium chloride)
| and also sodium bicarbonate -- aka baking soda. I think the
| misprocessing of sodium bicarbonate is a large factor in why
| people with CF are so prone to being very acid.
|
| I initially thought this my big discovery. It turns out everyone
| who knows anything about CF knows it causes excess acidity,
| including patients and doctors. They just don't bother to do a
| damn thing about it and act like it isn't clinically significant
| information.
|
| "You are people are dying. We know you are too acid. Meh. Can't
| be related. Moving on."
|
| Even though if you get ketoacidosis they promptly hospitalize you
| because you can be dead within three days.
|
| Ketoacidosis is typically rooted in diabetes and people with CF
| are at high risk of developing a special form of diabetes known
| as Cystic Fibrosis Related Diabetes (CFRD). But lets not confuse
| any poor doctors and scientists with the facts. The slow boiling
| of the tissues of people with CF in acid couldn't possibly be
| anything like this extremely deadly condition for which they
| promptly hospitalize you. No. Let's just ignore the acidification
| of people dying of CF. Can't possibly be clinically significant.
|
| The salt wasting we do has significant implications because as
| the salt gets sweated out at high rates, it drags other
| electrolytes with it. Reading up on Altitude Sickness was hugely
| helpful to my understanding of what was going on with my body and
| finally gave me a direct connection between the respiratory
| problems and the gut issues that both occur in CF.
|
| When you are altitude and can't get enough oxygen, you begin
| peeing more. You do this because the body cannot breath out all
| of the wastes accumulating in your blood and your body starts
| shunting those wastes through the kidneys as a backup system.
|
| So your blood chemistry directly connects what is going on in
| your lungs to what is going on in your gut. These are not
| "separate and unrelated systems that never interact." It is not
| "mere coincidence" that people with CF have both gut and
| respiratory issues.
|
| Of course, a more fundamental issue is that CF significantly
| impacts all epithelial tissues and all mucus membranes and your
| lungs and gut both fall in both categories. (Your skin is also
| epithelial tissue, but not a mucus membrane.)
|
| Anyway, glad to see cell biology getting some attention. This
| helps explain a lot about what I have accomplished and I am sort
| of glad I didn't get the memo earlier. Thinking of the cell in
| relatively simple terms was helpful to me, if only to make me
| feel less intimidated by the process of trying to get well while
| the entire world treated me abusively for not liking what was
| happening to my body and not wanting to quietly and meekly go
| along with their plans to gruesomely murder me so doctors and
| scientists could feel like they are smart and know things and
| former homemakers are clearly all "dumb blondes" or some shit.
|
| Yes, I have baggage. No, I'm not apologizing. The world could
| have been less awful to me. It chose not to be.
| selestify wrote:
| That was really interesting, thanks for writing all that out!
|
| Given this sort of knowledge and understanding, what do you do
| about your CF then? Is there a way to prevent your body from
| being so acidic, or to mitigate the effects of it?
| DoreenMichele wrote:
| The short answer is "I've made a lot of dietary and lifestyle
| changes."
|
| I eat very carefully with an eye towards food chemistry. If
| you have no idea I have CF and I do this, you wouldn't notice
| that I eat any differently from anyone else.
|
| For example, pizza is a staple part of my diet. But I mostly
| get takeout pizza from Little Caesar's.
|
| They are the only national franchise that makes their dough
| fresh in house daily. Everyone else ships it in from
| elsewhere in frozen form.
|
| They also use corn meal to help make it not stick. This was
| something I did when I used to make homemade pizza with a
| pizza stone.
|
| The corn meal is more alkaline than wheat. Most wheat only
| crusts leave me too acid, but Little Caesar's pizza doesn't
| because of the addition of a small amount of corn meal to the
| crust.
|
| I also avoid certain oils. It is well established that people
| with CF misprocess oils and I got very interested in the
| chemistry of oils.
|
| They come in three forms: long chain triglycerides, short
| chain triglycerides and medium chain triglycerides. Medium
| chain triglycerides also get called MCT oil and it has long
| been established that MCT oil is medically beneficial for CF
| and certain other conditions.
|
| This is the basis for why coconut oil is popular in some
| circles: it is high in MCTs. MCT oil has long been prescribed
| by doctors to people with CF and coconut oil has an even
| longer history of being medically prescribed for various gut
| issues, including stomach cancer (though I can no longer find
| the link supporting that statement, sadly).
|
| I not only favor MCT oils, including butter which is a good
| source of such, I actively avoid long chain triglycerides
| because my body fails to break them down and it wreaks havoc
| and makes me really sick. So I avoid peanut oil, canola oil
| and some other things.
|
| I am a butter fiend and I tolerate animal fats well, such as
| bacon (though bacon is high in something that is hard on the
| lungs and I had to be careful with it when my lungs were in
| worse shape).
|
| So I pay a lot of attention to food chemistry and I do eat
| what other people see as "junk food" but one brand of potato
| chips is perfectly fine because they cook with oils I
| tolerate well and another makes me dog sick because they use
| different oils. If you don't know that, you see me eating
| pizza and potato chips and don't think I'm some kind of super
| extreme "health food nut" though I am.
|
| I also am very careful about what I touch. Skin is epithelial
| tissue and people with CF are prone to aquagenic wrinkling --
| aka we get extremely pruney in bath water. This is so extreme
| that they are now using it a cheap initial screening in rural
| clinics in India.
|
| I've actually already written about the skin stuff so let me
| give a link rather than repeat myself on too little sleep and
| yadda:
|
| https://atypicalcysticfibrosis.blogspot.com/2020/01/skin-
| and...
|
| That even has a link to the PDF about the test they are
| developing (or have developed) in India for rural clinics.
|
| I spent a long time taking $300/month worth of supplements. I
| now manage my condition with diet and lifestyle and I am
| mostly well, having resolved that backlog of malnourishment,
| chemical derangement, accumulated infections, etc etc. I'm
| trying to figure out how to solve my financial problems
| because I remain dirt poor and it sucks and I hates it.
|
| I wanted to be an urban planner and now I am trying to figure
| out how to provide low cost services to small communities and
| I have fantasies the world will support my Patreon so I can
| pay my bills while doing a lot of stuff mostly "for free" for
| small communities so we can reverse this trend out in the
| world of everyone going to big cities and mostly hating it
| because that's where the jobs are and small communities
| shriveling up and dying. I think it is part of why our world
| is so dysfunctional.
| nobrains wrote:
| Wow! So, molecular transports and reactions within cells happens
| to be probabilistic, and not mechanical. For me, this is new
| mind-blown level info.
| mncharity wrote:
| Does anyone know of resources or groups with a focus on
| educationally conveying a feel for foundational biochemistry
| mechanics: extreme violence; random; crowded; with locality and
| concentration enhancement?
|
| For instance, there's a video of simulated viral icosahedral
| capsid assembly, where the panels are tethered together to
| maintain proximity, so you get to see realistic assembly and
| disassembly, temporary misfits and irreversible fails, and just a
| whole lot of flailing and slamming around until something clicks.
| It's ok for showing 10 nm scale object violence, but I've never
| seen anything good for 1 nm or 100 nm scale violence. And for
| concentration enhancement, I've only ever seen nice slides in
| research talks.
|
| Given how pervasive related misconceptions are, it'd be
| interesting to have a page to point to where the best available
| misconception antigens are slowly accumulated.
| reubenswartz wrote:
| Yeah, it's pretty mind boggling... Amazing that it "works". And I
| think debugging single-threaded code can be hard. ;-)
| qwertox wrote:
| It's crazy what happens in there. It's as if other lifeforms
| exist at this cellular level, which wouldn't even care if they
| form part of a human or a plant, acting as if they have their
| own life, their own motivation and ability to execute it, their
| own purpose and will to live by it.
|
| As if what applies to us individuals, with our thoughts and
| actions, also applies to these subsystems of a cell, in a
| different form.
|
| What could be their motivation to build humans, to assemble
| brains that can reflect, eyes that can see, senses built to
| enable interaction with this world?
|
| Where do these instructions come from?
| nneonneo wrote:
| I think the main thing you're looking for is
| "differentiation". Unicellular organisms are generally
| homogenous, as each must be adapted to surviving on its own.
| Simple multicellular organisms are often just masses of
| individual cells. But, as you start increasing the number of
| cells, it becomes evolutionarily advantageous for some of
| them to take on more specialized roles, rather than have
| every one be capable of everything. That is differentiation.
|
| As these organisms get more complex and develop more and more
| differentiated cells, mechanisms also evolve to prohibit
| cells from "regressing" to undifferentiated forms, and to
| tightly control aspects of cell growth. Unlike unicellular
| organisms, a functioning multicellular organism needs to have
| all its cells coordinate in order to survive. Human cells for
| instance contain a regulation mechanism which detects
| abnormal behaviour and directs the cell to commit suicide (a
| key protein in this mechanism, p53, is widely studied in
| cancer research).
|
| So no, your cells don't get their own "will". They do what
| they are genetically fated to do. Those that don't either
| die, or wind up as a cancer that chokes the life out of their
| host.
| Schinken_ wrote:
| With things like these I always like to visualize it
| backwards.
|
| These things don't want anything. It's just the way things
| work.
|
| If you manage to form an organism that survives better than
| other organisms, there will be more of you (and your cells).
| There is no "want" and "like" in evolution, just "works" and
| "replication".
| qwertox wrote:
| Don't you sometimes "want" to eat some chocolate, or an ice
| cream, or even better, a nice, juicy, salty steak? I
| definitely do, and I "like" what I feel when I get to eat
| it.
|
| Yet I may be no more than a replicating machine whose
| purpose it is to build these new machines which may likely
| replace us one day, maybe keep us in a zoo, or as pets, if
| we get lucky.
|
| I can't imagine what motivates these molecules to behave,
| to group the way they do; why the existing energies get
| channeled to make them move that way, since there is no
| need for the energy to do anything at all.
|
| Something motivates me, and I see no reason why there isn't
| motivation in these molecules; what they do is already
| complex enough to be considered as something which may have
| a special purpose.
|
| We do have consciousness. There is this something in me
| which sees and tastes, which experiences life. It's hard to
| believe that this is something material. To me it feels as
| if complex enough structures of molecules allow something
| to plug into this universe, to absorb its information and
| to feed something into it, like instructions which allow
| this "me" to interact with it.
|
| The same could well be applicable to bacteria or to the
| most rudimentary lifeforms. Because a bacteria forms part
| of my body doesn't mean that it can't have its own
| consciousness; the same may be valid for all this stuff
| that (maybe) "lives" inside my cells. Lucky me, that I get
| to stand on its shoulders in order to perceive this
| universe the way I can and interact with it.
|
| "Works" and "replication" isn't wrong, but removing the
| "wants" and "likes" from this equation doesn't feel right.
| wombatmobile wrote:
| You're onto something when you link "wants" with
| "energies".
|
| Think back 4 billion years to some of the first lifeforms
| on earth, colonies of slime mould clinging to a rock in
| the ocean.
|
| The first behaviour of these organisms was to respond to
| the movement of the sun overhead. They'd orient
| themselves to regulate their exposure to the sun's rays,
| arranging themselves in a horizontal plane on top of the
| rock when the sun was overhead, and vertically along the
| side of the rock when the sun was at an angle.
|
| The first "desire" was the want of energy. The first
| behaviour was to move towards the sun.
|
| The first communication was the signal that was passed
| through the colony of cells to coordinate the movement of
| the whole community into a mutually beneficial
| configuration.
|
| The first conflict was when the colony became large
| enough and so diversely distributed that a part of the
| community "decided" it would rather not obey the signal
| to move and instead would move to its own preferred
| surface of the rock.
| jmoss20 wrote:
| Sure, but the parent's claim was that there is no "want"
| and "like" _in evolution_.
|
| You might want and like things; perhaps ( _perhaps_ )
| cells and bacteria might want and like things, but
| evolution certainly does not.
| benlivengood wrote:
| The fascinating question is where the line is between
| action and reaction and our qualitative experience of
| wanting and liking. Our wants and likes are (probably)
| physically implemented as a sequence of electrochemical
| reactions; almost certainly with nothing more than
| electromagnetism.
|
| So which instantiations/states of the electromagnetic
| field experience feelings and desires? Are they held in
| the energy potential or in the energy transfer, or both?
| Is it enough to have a sufficiently complex feedback loop
| simulating/predicting itself?
|
| The answer is likely to be both sort of simple but also
| profound. Eventually we'll have an a-ha moment studying
| electrocardiographs or FMRI or individual neural networks
| and be able to replicate experience in other
| electromagnetic substrates, and knowing precisely what we
| are, in a sense, will be pretty neat.
|
| Then what will we really know about experience? Is it
| truly in the electromagnetic field or does it exist in
| the mathematical relationships that determine the
| evolution of the fields? That might be a question we
| never definitely answer from an outside perspective, but
| is endlessly fascinating to me.
| selestify wrote:
| Fascinating question indeed :)
|
| > So which instantiations/states of the electromagnetic
| field experience feelings and desires?
|
| Personally this is why I think that perhaps qualia is not
| an emergent phenomenon after all, and must come from
| outside the system. I.e. I suspect that philosophical
| zombies are possible
| pharke wrote:
| It's more interesting to think that evolution is guided by
| the selective pressures that exist in the environment. That
| means that all of the current forms of life are finding the
| optimal design for their environment and interaction with
| other life forms. Human beings have evolved to fit this
| world and if we continue to expand beyond it we will
| continue to evolve to fit the solar system, the galaxy, and
| the universe. It's hard not to feel that there is some
| optimal thing that we are heading towards, the solution to
| the question posed by reality.
| leetcrew wrote:
| > It's hard not to feel that there is some optimal thing
| that we are heading towards, the solution to the question
| posed by reality.
|
| depends how optimistic/pessimistic you are. I find it far
| more likely that humans will eventually hit some local
| maximum in a trough too deep to ever escape.
| benlivengood wrote:
| There are no platonic ideals for humans or beings in
| general; we explore a giant solution space for
| reproducing thinking-machines. For every utility function
| there's a globally maximal physical being or society, but
| there are also a lot of utility functions.
| jszymborski wrote:
| I mean, getting there took millennia of evolution, which is a
| long-time of brute-forcing. It's an incredible and beautiful
| thing to think about, and it's wilder than any one person's
| imagination, but I don't know that it's efficient ;)
| ahelwer wrote:
| I don't know... look at ATP Synthase, it's basically an
| electric motor made out of crazy nanotech from the future.
| Seems pretty efficient to me.
| dllthomas wrote:
| Whether the design is efficient is a different question
| than whether the design _process_ is efficient.
| jszymborski wrote:
| Yes, this is precisely what I was trying to get at.
|
| The process is inefficient in that it takes a long time
| for it to get to a workable solution, but the solutions
| are usually incredibly efficient.
| reubenswartz wrote:
| Yeah, pretty crazy that these things have been turning like
| mad for billions of years... ;-)
| reubenswartz wrote:
| Not saying it's efficient, in the way we would think of
| "coding" things.
|
| One way I like to think of evolution is how long it takes to
| get from one state to another. So it took hundreds of
| millions of years for the first "life" to evolve-- perhaps
| close to a billion. This includes RNA, DNA, ATP, etc. Then it
| took about a billion-ish years to go from prokaryotic to
| eukaryotic life. Then about another billion-ish years to get
| multicellular eukaryotic life. Then it only took about a
| quarter billion years to have dinosaurs. It only took about
| 10-20 million years to go from the ancestors of all apes to
| having chimps, gorillas, and people. (!!!) And when you have
| people directing evolution, like with dogs or crops, you can
| make things happen very "quickly".
| Terr_ wrote:
| Efficiency tends to come at the cost of not being robust
| against the unknown. The crazy mutant random number generator
| might not go fast, but perhaps it's less likely to get
| stuck...
| unavoidable wrote:
| DNA is spaghetti code... but it all works somehow.
| crehn wrote:
| How frequent are outages and operational issues with DNA?
| quesera wrote:
| Miscarriage is common.
| Schinken_ wrote:
| Literally, as even the tangling and folding ("packing") of
| DNA changes its behaviour.
| agumonkey wrote:
| let's take polymer, thermodynamics and statistical physics and
| make a new harder field out of these..
| ramraj07 wrote:
| What's more interesting is its not just crowded but organized. We
| are starting to discover that large patches of cell membrane as
| well as the cellular volume might also be highly structured (p
| granules, etc) and gel like, and God knows what other mechanisms
| are involved.
| gambler wrote:
| Reminds me of some Alan Kay talks:
|
| https://youtu.be/YyIQKBzIuBY?t=1384
|
| He actually mentions the book that is the source for the first
| illustration in the article. He also often talks about the speed
| of molecules and how it's counter-intuitive to the commonplace
| idea of cell operation.
|
| Cell biology was an inspiration for original OOP (which wasn't
| much like Java/C++ at all).
|
| When reading about Covid stuff and immunity, I often think how
| these mechanism could be imitated in engineering. I definitely
| believe there are some general principles that we could benefit
| from without trying to "simulate" biology.
|
| Edit: Sorry, same author/illustrator, but different book.
| selestify wrote:
| Any chance you could provide a summary of how OOP was
| originally much more similar to cell biology? :)
| amatic wrote:
| OOP could only have been inspired by the then-available
| knowledge of cell biology, and it seems that even today we
| still have a lot to learn.
| ncmncm wrote:
| We know way less than we don't know. And much of what we
| think we know is wrong.
| gambler wrote:
| Some of the ideas that were translated to reality are covered
| here:
|
| https://www.youtube.com/watch?v=QjJaFG63Hlo
|
| Some of them never got fully translated to reality at Xerox
| because of various reasons (e.g. memory limitation of
| hardware at the time). This is worth a read:
|
| http://alumni.media.mit.edu/~mt/thesis/mt-thesis-
| Contents.ht...
| agumonkey wrote:
| life was described as a miracle but facts like that make it even
| more so.. how organized processes emerges from this HF mess is ..
| surprising.
| aylmao wrote:
| I'm always awe-struck thinking about the fact we know this. For
| example the ATP synthase motors in the Mitochondria-- we have
| figured out ways to discover these sorts of things without seeing
| them, just by chemical analysis, computer modeling, trial and
| error.
|
| Moreover, this is just what we know, but there must be so much
| more we don't know. It's astounding to think just how much more
| might be hiding in these very complex systems.
| acomjean wrote:
| > but there must be so much more we don't know.
|
| I was pretty surprised at the amount of biology we don't know
| (I'm writing software to help geneticists, a recent development
| for me). We know a lot, but its astounding how complex these
| biological systems are.
|
| It is kinda amazing we're alive.
| ncmncm wrote:
| Biology is unusual among sciences in that a five year old can
| ask questions it can't answer.
|
| To get an idea about what life processes are like, you need
| to read endocrinologists like Robert Sapolski or Robert
| Lustig.
|
| A lot of processes only work because there are so many moving
| parts each pushing only a little of the way, so that when
| something is wrong it doesn't all collapse.
| HenryKissinger wrote:
| To think that the machinery of the human body evolved from
| water and basic elements. It's hard to believe sometimes.
| mdavidn wrote:
| Most of life's history on this planet was single-celled.
| That's especially astounding when you consider the short
| generation time of single-celled life. The building blocks
| for these complex molecular machines existed before
| multicellular life was possible.
| wombatmobile wrote:
| The first 2 billion years was single celled. Since then,
| life on earth has been a combination of single celled
| prokaryotic cells, and much larger (100x) eukaryotic cells.
|
| The evolution of eukaryotes, which comprise all the plants
| and animals you see on David Attenborough's Life on Earth
| show, didn't occur until the Earth had developed an oxygen
| rich atmosphere.
|
| What's amazing about eukaryotic cells is that they formed
| from colonies of prokaryotic cells, in a process called
| endosymbiosis.
|
| There's a reason why the mitochondria in eukaryotic cells
| look like little bacteria like organisms. They actually
| were once separate prokaryotic organisms. Same for
| chloroplasts in plant cells.
|
| How Two Microbes Changed History
|
| https://www.youtube.com/watch?v=lhF5G2k45vY&t=343s
| hi41 wrote:
| Nice work by op. When I see the world and space, I cannot stop
| being awestruck by how everything is so beautiful. I am not able
| to explain all of this just based on randomness and Darwin's
| evolutionary theory. I think there is God. Does anyone else get
| the same feeling? I also admit that I don't know who the real God
| is. I also feel terrible sadness that the real God does not
| reveal himself to each individual when the expectation is that
| being the father he has responsibility to lead each individual.
| tt433 wrote:
| Please explain how the complexity of God arose independently of
| natural cumulative selection processes like evolution. The
| Blind Watchmaker might be an interesting read for you.
| reubenswartz wrote:
| Not trying to pick a fight, just asking a question-- if you
| think the natural world as we see it could not have arisen
| "on its own" through the laws of nature, how did something
| even more amazing come to be?
| shuntress wrote:
| The same way as everything else: On its own through the
| laws of nature.
| tt433 wrote:
| To be frank, I have no idea. It would be folly for me to
| guess. Still, the notion of intelligent design explaining
| the awesome complexity of life by waiving it away with an
| additional, spontaneous and inexplicable divine entity of
| essentially infinite complexity just occurring out of
| nowhere makes even less sense to me personally than the
| spontaneous existence of a "basic" "unguided" universe with
| the potential for cumulative selection to cause complex
| life independently of a guiding hand. Intelligent design
| postulates that a divine entity spontaneously existed and
| all complexity is the result of that entity, whereas
| evolution explains complexity via long term cumulative
| selection. I struggle to rationalize the spontaneous
| complexity that intelligent design must justify.
| ksk wrote:
| I think you have the right approach. We all have to be humble
| and accept wherever science leads us. If god is part of the
| natural order, and we find evidence for this phenomenon, then
| it should be accepted.
| dev_tty01 wrote:
| Agree. The difficulty is that as we learn more, we often (not
| always) tend to believe that we have most of the answers and
| become less open to other possibilities with respect to God
| or simply more understanding. We have to keep in mind how
| much of our current knowledge has been acquired in perhaps
| the last one or two hundred years. In other words, we are
| probably complete neophytes with respect to our understanding
| of the universe as a whole. As a result we have to resist our
| more arrogant tendencies and try to keep an open mind to
| things that we may not yet be able to sense or measure. As
| scientists, I think we have to recognize that God may not
| exist, but we must also recognize that it may exist, keeping
| in mind that our definition of "God" is probably way off base
| from what we might eventually come to recognize.
| ksk wrote:
| Yes, and we have to guard against knowledge regressions
| (dark ages) too. It is critical that we preserve our human
| tradition of passing inter-generational knowledge to the
| next generation. As an example, I see several older nerds
| complain that the new generation keeps re-inventing the
| same-old same-old tech, and I do see a small grain of truth
| there, but by and large I think we have successfully
| managed to transfer our knowledge and experience to the new
| generation so that they can push the boundaries even
| further.
|
| I remember reading (think it was Neil Tyson) that at some
| point in the future, if the universe continues at its
| current rate of expansion, we (earth) might arrive at a
| future state where we cannot detect the cosmic b/g
| radiation and other markers which confirm certain physical
| characteristics of the universe. I wonder if the future
| humans will accept that the humans who came before them
| really observed this phenomenon and that they can rely on
| that data :)
| aylamao wrote:
| "I don't understand" - "then call it god" is a false premise
| that was uttered many times in history:
|
| https://evolutionspace.wordpress.com/2007/04/17/then-call-it...
|
| Since you've identified what you don't understand, evolution,
| there is some hope.
|
| Try a basic programming exercise: evolutionary growing 2d or 3d
| "walkers" on a simulation on a PC, or alternatively running
| core wars.
|
| It's enlightening to see order, logic and machines arise from
| total randomness.
| acomjean wrote:
| >It's enlightening to see order, logic and machines arise
| from total randomness.
|
| https://en.wikipedia.org/wiki/Emergence
| shuntress wrote:
| Funny, I lean towards the opposite conclusion: That system
| based entirely on random coincidental collision of matter is
| more likely to have sprung forth from pure random chance rather
| than the mind of some individual omniscient being. No matter
| how all-powerful she might be.
| ksk wrote:
| There are multiple definitions of god. The crude one that is
| commonly used doesn't have to be only one. Its within the
| realm of possibility that there are entities that exist in a
| completely different substrate of existence. For us, time is
| experienced in a particular way because we also exist inside
| the same space-time. Maybe the 13 billion years of the
| universe, is like 13 billion cycles of a CPU which are tiny
| in our time-scale.
| phkahler wrote:
| I've always felt that putting our universe inside some
| larger context is a punt (American Football reference).
| Weather that's saying we are a thing within some creators
| context, or that it's a simulation, all that does is push
| the questions of "what is all this" and "where did it come
| from" to a next level up that we can't see and have no hope
| of answering those questions.
|
| If you think we live in the Matrix then all fundamental
| questions of existence can be asked about the "outer" world
| instead. It can't be turtles all the way down.
| ksk wrote:
| Oh, I didn't mean to imply that we should simply accept
| it as fact. I'm merely saying that we can have multiple
| theories. Certainly, we should only go where the evidence
| leads us.
| selestify wrote:
| Can we ever answer those most fundamental of questions?
| What pushing it one level up _does_ do is show that we do
| not have enough information to answer it at our current
| level --- and if we ever create simulated universes of
| our own, it shows that perhaps you could never know the
| answer at any level.
| Schinken_ wrote:
| "Maybe the 13 billion years of the universe, is like 13
| billion cycles of a CPU which are tiny in our time-scale."
|
| That would be some hell of IPCs.
| lovecg wrote:
| Studying this stuff puts me in a spiritual mood though for a
| different reason. At the sub-cellular level it's just a bunch
| of chemistry. Molecules randomly bump into each other and stuff
| happens. It's all "push", not "pull". Yet we talk of the whole
| cell as if it has agency (e.g. an amoeba is "attacking" other
| organisms; a bacterium is "moving" and "eating"); we definitely
| think that about still larger animals. The more time I spend
| thinking about this duality the weirder it gets.
| modeless wrote:
| It always bothered me that in the standard explanations of how
| these processes work it always seemed that reaction ingredients
| would somehow magically seek each other out, such as in videos
| like this where the amino acids arrive at the ribosome in order:
| https://www.youtube.com/watch?v=TfYf_rPWUdY
|
| The molecules really do move randomly, not magically, and it's
| just that they go so fast and are so numerous and collide so
| often that even random chance puts the right molecules in the
| right place many times per second. This article was a revelation
| when I first read it and I'm quite disappointed that this was
| never explained properly in my entire school life.
| mindfulplay wrote:
| This is fascinating and new to me. I thought it was designed by
| say the DNA or the rna to behave in that coordinated manner and
| to seek specific molecules. But if it's just a random walk and
| somehow this success at this scale and speed, it is even more
| simple yet incredible to think.
| wombatmobile wrote:
| Don't be disappointed. Most of the things you were taught in
| school were simplifications of reality. The curriculum is
| taught this way to make it easier for you to incorporate a lot
| of axioms from different fields into your fledgling,
| inexperienced mind. Once you have a number of these axioms at
| your disposal, you are equipped to leave the nest and go out
| into the world and make sense of new things yourself, at
| whatever depth and speed suits your circumstances and
| interests.
| modeless wrote:
| This isn't a simplification though. It's a complification.
| It's both more important _and_ easier to understand than a
| lot of the biology stuff that I _was_ taught. The curriculum
| should be rearranged to prioritize this higher.
| sthnblllII wrote:
| Correct. In most class-based education, biology is treated
| just like history and math and everything else. All
| subjects are just collections of disconnected factoids
| handed down from on high. Intuition requires initiative,
| and initiative means asking questions, and asking questions
| takes away class time from the unintuitive students
| learning more factoids. The point is: go to your
| professors' office hours!
| shpongled wrote:
| What's also fascinating is that the shapes and biochemical
| properties of proteins and other molecules in the cell are so
| finely tuned that they can be flying into each other, and still
| have such a high degree of specificity (e.g. proteins
| interacting with certain other protein domains, substrates,
| etc) that life actually works.
| 01100011 wrote:
| I think what made it click for me was thinking of explosions.
| Think of something like the detonation of ammonium nitrate. It is
| _incredibly fast_ on a human timescale. It is just a chemical
| reaction. Chemistry can happen at insane speeds. Even the
| monstrous molecules of biology can interact at incomprehensible
| speeds. Think of all that needs to go on just to make a neuron
| fire, much less a million neurons forming a thought. It 's
| amazing that our bodies manage to last as long as they do. That
| is an awful lot of stuff that has to go right or else we die.
| rini17 wrote:
| What if, instead of monolithic chip we had "cells" filled by
| fluid with tiny chiplets in brownian motion. They would bump into
| each other or the wall to exchange packets of data or to recharge
| themselves.
| Aperocky wrote:
| You would have a computer that display the intelligence level
| of a bacteria.
| peterburkimsher wrote:
| (2011)
| nynx wrote:
| Honestly, some of these, like the ATP synthase, spin/move slower
| than I expected. The ATP synthase spins at ~700 Hz. I'm not sure
| what I was expected, but it was in the tens of kilohertz.
| koeng wrote:
| If you want beautiful representations of what cells look like,
| highly recommend David Goodsell's pictures. They're highly
| regarded in the field of biotech
| Emphere wrote:
| His book, "The Machinery of Life", is just wonderful.
| twic wrote:
| In case anyone missed the caption: the second picture on the
| page, "a representation of how crowded cells really are", is by
| Goodsell.
| flobosg wrote:
| I also like his renderings of protein structures:
| http://pdb101.rcsb.org/motm
| rattray wrote:
| Link?
| Klinky wrote:
| Some of them are at http://pdb101.rcsb.org/sci-art/goodsell-
| gallery/
| epistasis wrote:
| Here's a profile that includes some of his watercolors:
|
| https://www.sciencemag.org/news/2019/04/meet-scientist-
| paint...
| searine wrote:
| Yeah that "crowded" cell picture is iconic. I remember my
| biochemistry teacher showing it several times in undergrad years
| ago, and really trying to hammer home the density of the
| cytoplasm.
|
| Sometimes we have to reset our natural intuitions and I'm glad
| that professor did her job in making me more accurately imagine
| the interior of the cell.
| ncmncm wrote:
| 170 mV across a membrane only, what, 40 angstroms thick, is a
| field strength of >40 million volts/meter.
| Pulcinella wrote:
| I remember doing some back of the envelope calculations that
| showed the potential across the membrane was equivalent to only
| a few dozen potassium ions more on the outside or inside.
| Basically a countable number of atoms have to be moved by the
| cell to develop that potential.
| mncharity wrote:
| There's pretty video of bacteria with green-fluorescent-protein
| electric-field probes, flashing like (mostly on) fireflies, as
| they briefly drop membrane potential to dump charged waste
| without having to pump it against gradient.
| mncharity wrote:
| "Membrane potential changes results from very small net charge
| movements across the membrane"[2], like 10^-4th or 10^-5th[1]
| of the potassium ions in a cell.
|
| Bionumbers is a fun site: "membrane potential"
| https://bionumbers.hms.harvard.edu/search.aspx?trm=membrane+...
|
| [1]
| https://bionumbers.hms.harvard.edu/bionumber.aspx?id=106433&...
| [2]
| https://bionumbers.hms.harvard.edu/bionumber.aspx?id=110762&...
| munificent wrote:
| I find this initially unintuitive, but it makes sense when you
| think about it.
|
| Look at any other system that produces aggregate emergent
| behavior out the behavior of smaller parts. For example, here's
| Conway's Game of Life implemented using... Conway's Game of Life:
| https://www.youtube.com/watch?v=xP5-iIeKXE8 It takes many many
| steps of the inner game of life to produce a single iteration of
| the outer simulation.
|
| In general, with emergent behavior, it takes a lot of inner steps
| to produce a single meaningful step in the outer system. So it
| makes sense that our cells are much faster than we intuititively
| think of as "fast". Because our intuition about speed is itself
| the product an emergent system. We are that larger Game of Life
| there, so it looks incredibly fast to watch the inner one
| according to our own time scale.
| gotostatement wrote:
| what's interesting is that the GoL inception is (as far as I
| understand) highly sensitive to initial conditions and timing
| in order for everything to sync up properly, whereas the cell
| is really robust in terms of everything just jumping around
| randomly and yet still getting its tasks done
| elcritch wrote:
| One big difference is the dimensionality, of 2d vs 3d. Even
| within the 3d space, quantum chemistry effects produce an
| even higher order of "effective" dimensionality. Finding
| stable paths that don't interact in 2d is hard, but easier in
| 3d. Its even easier in hyper dimensional spaces where other
| chemical properties can be used to provide pathways for only
| specific reactions.
| Pulcinella wrote:
| Yeah it feels as if the cell is a ridiculously parallel array
| of molecules where every molecule in the array is rapidly
| iterating through the array (colliding with every molecule in
| the cell as it diffuses) and type checking those items to see
| if it can operate on them (e.g. a protein breaking down a
| small molecule). It all works out because the operations are
| atomic (heh) (don't need to worry about two proteins trying
| to break down the same molecule at the same time) and the
| type safety (proteins are highly specific on what kind of
| chemicals they target) means you don't need to worry about
| trying to perform some invalid operation.
|
| Turns out collision detection is real fast in real life!
| xwdv wrote:
| What would happen if a cell were somehow to be optimized
| such that every operation occurs in O(1) time rather than
| having to iterate?
| nsxwolf wrote:
| This is probably what happened to Tetsuo in Akira.
| shuntress wrote:
| Cancer, probably.
| kneel wrote:
| Another analogy: molecule interactions are like proof of
| work operations that unlock cell actions when the right fit
| (hash) is found. trillions of molecule interactions are
| required to find the right fit.
|
| the intricate network of transcription factors operate as a
| security system to unlock key processes in DNA regulation
| in eukaryotes. security must be maintain because the system
| is under constant attack from other information systems
| (viruses)
| thaumasiotes wrote:
| > the type safety (proteins are highly specific on what
| kind of chemicals they target) means you don't need to
| worry about trying to perform some invalid operation.
|
| You might want to look into the mechanics of heavy metal
| poisoning.
|
| There is no type safety, and there's no type checking.
| Everything attempts to interact with everything it
| encounters. Those interactions usually fail.
| foobarian wrote:
| So it's kind of like React hooks, except they are
| probabilistic and constrained by 3d geometry. And the
| things moving around fast inside the cell is the event
| loop. Fun!
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