It's pretty crazy just how computationally intense biological simulations are. The timesteps are just so tiny and the number of nodes involved is insane...
I think it's because we learn biology with a textbook cartoon illustration of the cell with sparse organelles floating in a clear sea of cytoplasm. The packed reality looks more like the halftime bathroom line at the Rose Bowl. Tons of heterogenous proteins and metabolites and mRNA and everything seemingly diffusing to its destination, shouldering past everything else. The sheer combinatorial complexity of the number of neighbors each molecule is imparting force on, combined with the constantly shifting conformational changes of many proteins which change the forces they receive, it's overwhelming. Recall that only recently AlphaFold was able to decently solve protein structures in isolation - add in dozens of shifting neighbors and that's suddenly a dynamic problem.
I am not sure where whole-cell simulation is at the moment since I've been away from the field for about 15 years, but I recall a rather difficult multi-month simulation that was trying to model an "empty" volume of cytoplasm away from the organelles, about 1/50th of total cell volume, and with all proteins and metabolites replaced by hard spheres of varying "stickiness". It was considered a huge success to just get a few of the diffusion rates for various compounds in the right order of magnitude. I mean, if you really want to get the fleeting interactions right you need to be modeling individual water molecules. I know there have been large advances in computing in the intervening years, but this was on I think #20 in the TOP500 at the time. Unlike AlphaGo I don't see any immediate avenue for AI to help with this because unlike protein crystal structures there is no wealth of quality training data for cellular dynamics at the molecular level.
It’s not simply diffusion complexity. A lot of cellular transport is dependent on directed transport via the cytoskeleton and myosin. For example a 1m long neutron would need years to move proteins from one end to the other if it just relied on diffusion.
Great point on the chaos! I'm planning to pursue atomic simulation in college, so I've tried to read as much as I can about the field short of the advanced math (hence college, lol). It seems to me that cross cluster synchronization is a massive scaling issue, since you essentially have global state both reduced and broadcasted every couple timesteps.
I've been thinking it would be cool to design chips to be realtime safe—that way there's no need to synctronize—and have further away information delayed (just like relativity) to deal with speed of light communication issues.
Never heard of fleeting interactions, would you mind to elaborate?
"Fleeting" in this context is just a synonym for "short lived" or "momentary".
the heterogeneity and packedness scratches the surface of the oversimplified complexity. particles are moving (usually with 6 degrees of freedom -- though biology can cheat this) randomly. lets say a protein docks with another protein... the number of unproductive collisions per docking is on the order of millions.
Yeah, I found this when I was Boinc protein folding for Covid. The work units ran for hours, my towercPC nearly melted, and then I found that this produced mere milliseconds of simulation!
Now consider that the Planck time is actually 1e-44 secs.
Hardly any actual physical simulations simulate every possible moment in time. We just calculate consequences of current events and put them in the queue to happen sometime in the future. And there's evidence that the real world works in a similar way.
Bonds jiggle and wiggle with characteristic times in femtoseconds, and most people believe it's not necessary to simulate at higher frequencies than that.
Yes, I agree with that. My point was just that stimulating a rudimentary model of reality is hard work, but reality is way more complex than even that.
> nearly melted
I’ll be that guy, but a computationally complex problem won’t push your computer to a temperature beyond design limits.
It’s just a turn of the phrase.
When someone says that the sky is falling, that also doesn’t need to be explained
You're welcome to come to my attic office in summer, as they ambient temperature reaches 200F m a sunny day and my obsolete-but-powerful tower PC consumes 350W power and adds to the tropical heat :)
> a computationally complex problem won’t push your computer to a temperature beyond design limits.
Allegedly. It allegedly won't do that.
Practically, running your CPU at design limits for a very long period of time tends to cause the temperature of the rest of the chassis to want to equalize to that temperature, which can be above comfort limits.
Except this isn't computational biology, it's fluid dynamics with an agent inside running a neural network.
You'd think they'd try something like smooth particle hydrodynamics so that it can be done more efficiently on a GPU cluster but I think they are just doing classic CFD
My (religious, spiritual, please-don’t-downvote-because-of-hate) opinion is the aspect of free will which extends even to the lowest creatures means computers will never simulate them accurately
No hate from me! You can believe what you like but I do disagree I'm afraid.
I think any rule-following (ie ~computational) system is either below, or at the same level of dynamic complexity as all others.
I also think that it's truly impossible to draw a sharp line between alive and not-alive, so the idea of 'free will' would have to extend all the way down to the smallest things like atoms/quarks/space etc.
Is it really meaningful to suggest that it could be anything like 'free will' at that size? Sure some quantum stuff seems indeterminate but could be fed by something that looks random to us - it might not actually be (dunno!?), but the idea that things at a larger scale could be meaningfully controlled by feeding-in different values (that still somehow have to look perfectly random!) seems extremely far-fetched to me.
Larger things like a molecule, a transistor or a human! generally stay as coherent and predictable/controllable (or self-controlling) things, even in the face of indeterminate-ness at the smallest scales underneath. I just can't see how there's any utility in connecting the idea of free-will/consciousness to this indeterminacy.. it's like saying free will is just fuzziness, and how does that really help in understanding life, the universe and everything?
isn't free will, more about inner control, in opposition to external control?
What a great, thought-provoking question! Thanks mromanuk!
I started reading the Wikipedia page about free-will to try to work out where I stand on this. I think I quite like the classical way of thinking about free will as simply: Being free from coercion in one's decision-making! I guess the source of such limits could be either internal or external or both though! So I don't know whether that helps much in answering your question.
The Wikipedia page says about 'compatibilism' (which holds that free will and determinism are compatible) that it is "the absence of various impediments" and that "a coerced agent's choices can still be free if such coercion coincides with the agent's personal intentions and desires", so that still doesn't really help answer the question.
I accept quantum-mechanics enough to be slightly skeptical of strict-determinism, so I guess maybe I fall more into the 'metaphysical libertarianism' point of view, but I still feel like the non-determinism that QM introduces probably acts more like a limit to how 'free' free-will can possibly be, rather than being a kind of 'secret sauce' that makes it possible for us or some external factor to be able to meddle with what reality (or ourselves) get up to in a meaningful way.
I also think that the internal/external distinction breaks down when examined very closely. For me this leads to the idea that I am actually the same thing (same 'wavefront' or whatnot?) as what caused the existence of the universe that I am a part of. I am both myself and the environment at the same time, but with a limited ability to sense very far into the external universe and its workings, beyond input from senses like sight/hearing/etc (I guess realms of pure-thought should also be included too though! Do we 'sense' reason/philosophy/mathematics/algorithms when we think about them?).
I think one answer (or the avoidance of a clear answer) to your question is that people have been arguing about this for thousands of years, and we (as a collective/species) are still really not very close to being firmly decided about it at all!
Interesting. This kind of dont-understand-therefore-fill-in-the-gaps-with-magic is the same mental shortcut that would lead you to believe that cryptocurrency is a good thing.
Well of course Shakespeare got it wrong with ‘There are more things in heaven and earth, Horatio, than are dreamt of in your philosophy.’. At least, that's seems to be the acceptably prevalent view.
That was Hamlet, wanting to believe in ghosts, so that his dead dad could reveal that he'd been poisoned in the ear, for the purpose of the plot. So yeah, in the original context it was some paranormal investigator or Scooby Doo level of crap. But subsequently people have picked it up and made it deep and meaningful due to having been wrote by The Bard. Even so, what do we want it to mean? That just about anything could maybe be discovered one day, therefore we can imagine arbitrary things right now and say they're real? Doesn't follow.
My primary reason I like cryptocurrency is it takes money out of the hands of government, which is run by people and is therefore fallible
Every component of cryptocurrencies, every crypto exchange etc is created and run by fallible people as well.
And as could be seen with the FTX debacle the outcome was basically the same but without helpful government regulations.
I trust the source code and decentralized network of miners doing 1 thing - securing the network with predictable emissions policy - over the central bank and politicians
There are many things that we don't consider to have free will that is very hard to simulate accurately. Like the weather, and generally any chaotic system. We can't even simulate interactions between small molecules accurately.
I don't consider free will to be a scientific concept. It is philosophical, or religious. But if we give free will to things we can't simulate accurately, maybe planets like the Earth have free will. It is a common religious belief, and if you believe that simple life forms have free will, not too far fetched. The Earth, with its atmosphere, magnetism and geology is a really complex system we have a hard time understanding.
Life is already an analog computer running on hardware (the universe). You could be correct that if life is using the hardware to the fullest extent, simulating it again would you a horrendous double virtualization penalty.
We could already be living under that same double virt penalty.
I think we have an outsized focus on free will, partly because free will is a trick played on us by evolution. It takes an exorbitant amount of effort to exercise anything close to what most people would consider free will and the phase lag is measured in hours if not years.
Nature being continuous is exactly the reason why our universe is not a simulation.
Can't continuousness be simulated by lazy evaluation? Also you're assuming the simulator is bound by the same physical limitations that exist inside the simulation which seems unreasonable to me. Simulations are usually vastly simpler than the substrate they run on.
Has this been actually proven? I remember multiple experiments trying to prove the opposite - both effectively a discrete-like and a grid-like universe. Wolfram for example has some ideas about discrete graphs https://writings.stephenwolfram.com/2020/04/finally-we-may-h...
> Has this been actually proven?
Neither proven nor disproven in any capacity.
Also I have no clue how anyone could assert that the universe being "continuous" (whatever that means) could be casually claimed by anyone to have any link to our universe being "a simulation" (whatever that means) or not.
>Simulations are usually vastly simpler than the substrate they run on.
So to simulate continuum you need a transfinite VM. It will be more efficient to just run the universe bare metal.
Quantum mechanics teaches us nature isn't continuous though.
The energy levels of electrons bound to atoms/molecules are quantized, and therefore the energy levels of photons emitted/absorbed (when those electrons change energy levels) are quantized.
But as far as I understand that is just the result of constraints imposed by the atom/molecule "box". Like how a guitar string can only vibrate at certain frequencies because an integer multiple of wavelengths of the standing wave must fit on the string.
Outside of such systems, energy levels are not quantized. For example, photons from distant galaxies appear to be redshifted on a continuous spectrum.
And even within the box the energy levels can be varied continuously if, for example, you squeeze the molecule or put it in an electric field.
Does that mean you believe there is something beyond the physical realm that gives free will? Otherwise, it seems to me like another physical process should be able to simulate a creature.
There is still the general fact that plenty of processes are 'chaotic' making them impossible to accurately simulate (because errors in the initial state compound exponentially). But it seems to me like a good enough simulation of a chaotic system is phenemologically indistinguishable from the real thing.
My (similarly religious) opinion is that because we _can_ simulate biological systems, computers can and will have free will too. Human brain is just a physical object that has some particular structure. We have free will (yes, I believe in free will). Then, we are not special, there can be other systems with free will, and we can build them.
If consciousness can be recreated by a computer, then a billion people holding flags up and down could recreate a computer, and consciousness could exist within the flags people are holding. But I do not believe in this form of consciousness and I don’t see a computer simulation as the same.
> computers can and will have free will too
What is free will if it's simply causation? i.e., environmental inputs leading to differences in charge, altering other differences in charge, leading to outputs, leading to environmental outputs, leading to changed environmental inputs, etc. If the chain can be examined and is entirely deterministic, be it neuronal or silicon circuits, where's the escape hatch?
Another thought experiment: if there's something that is you, that decides, and presented two different realities where the environment, brain, etc. were precisely the same, what would cause there to be a difference in decision? If it's deterministic, how is that free will? If it's random, how is that free will?
Physics is famously non-deterministic. Quantum physics is built on irreducible randomness, it is incompatible with determinism (except for evolutions of probability quasidistributions). And we don't even need to try to find "quantum interactions" in human brain — every physical system is quantum, for every photon that touches retina. There's enough indeterminism to hide entire universes.
Free will is the interplay between determinism and randomness, an emergent phenomenon with multiple self-recursive feedback loops and path dependence. Even if we could trace it through all these loops and find all the mixtures of quantum randomness and classical deterministic patterns it emerges from, it wouldn't make it any less magical.
Appreciate the thoughtful comment. Yes, under the hood indeed "every physical system is quantum", yet at the macro level physical systems are more or less predictable, including the brain. The brain's immensely complex structure and extensive interactivity make understanding how it works largely a mystery. The relatively simplistic models we're able to create have so far illuminate only a small part of its functionality.
The idea of free will has been a subject of eternal debate. I suspect this reflects lack of consistent definition. I would posit that free will isn't absolute but necessarily constrained by the nature of individual exercising its will. The stochastic attributes of a system or entity mean its actions are to an extent unpredictable, providing an "opening" for willful behavior.
Humans imagine they have free will because they're aware of their decisions or actions while unaware of the range of factors contributing to a decision or action. Intuitive (vs. analytical) cognition is the operational default. By definition intuition is a computation occurring outside of the person's awareness.[0] Consequently, it augments the impression of exercising unfettered free will.
Perhaps it's most accurate to say we have will or volition but not free of constraints imposed by our biology and physical/social environments. While the randomness inherent in biological systems allows volition to evolve, it also limits what an organism can will itself to do.
[0] Journal of Cognitive Engineering and Decision Making 2017, Volume 11, Number 1, March 2017, pp. 5–22
> Perhaps it's most accurate to say we have will or volition but not free of constraints imposed by our biology and physical/social environments.
You might be talking about compatiblism.
> Humans imagine they have free will because they're aware of their decisions or actions while unaware of the range of factors contributing to a decision or action.
Or more likely there’s no evolutionary fitness benefit to being able to understand this, and perhaps it’s even detrimental if it leads to nihilistic or egocentric impulses.
I’ll repeat the question you might have missed
> If it’s random how is it free will?
Stochastic processes won’t get you to free will any more than determinism.
Aren't we just saying that matter is complex enough to form an input to a model of the world and self which results in a really complex feedback loop where organisms which adjusted actions to increasingly complex projected model state had more descendants?
The self is just the only part of the model directly wired to our neurons and self awareness is just correct labeling.
In that context will is certainly a function of a how much a things internal model of self encoding the idea that its actions are moreso based on its own model than the tgings its model is built with and ability to make this distinction right or wrong and free will is basically meaningless.
Its certainly not a magical out for determinism all the qualities that we imbue with such meaning are as based on the same principals as anything else.
I’m curious if you think plants, single-cell algae, or single-cell animals like amoebas will be simulatable?
But simulate-able how? Not like they would exist in reality, interacting with the rest of the universe
Why not? Most simulations (flight sims, etc) include external stimulus.
And my magical belief is there is no free will so that means you’re wrong, right?
Both are silly statements that can’t add anything.
I sympathize with your point of view, but they stated opinion based on faith, which is wholly (holy?) different from stating truth
IMHO "free will" is about motivation, the drive to survive which is inherent to all life. And I don't think we have as much free will as we might think we do - if you've ever seriously starved, you'd maybe understand "free will" a little bit more, and how you aren't really free from your mortal coil at all. Motivation is all a computer is really lacking to have free will. Computers are good at following instructions, but they aren't good at surviving yet since we can just cut their power. God forbid someone like Elon Musk teaches a computer to have real motivation and not just follow instructions. I do think "a computer" in the far distant future could simulate every atomic interaction sufficiently to simulate a living organism, but we are nowhere near that yet. A virtual organism of this type would still be a blank slate and need to learn what free will is to really have any beyond satisfying whatever need it has to survive. Do newborn babies have free will, or are they operating on the instinct coded into their DNA? I subscribe to the latter, because science is my religion.
Musk is an idiot who hires people a lot smarter than him. Every company he has he bought and succeeds only to the extent that he leaves it alone.
No downvotes from me, but where do you think the free will lives? What mechanism produces it? What about that mechanism, if not purely stochastic, is not predictable? If free will can have a real measurable physical effect on this universe, then why can't it be isolated?
I believe our consciousness is separate from our physical body. This metaphysical line of thinking is embodied by “idealism” which is opposed to “physicalism” or materialism. I am also not a determinist and I don’t believe you can replay the universe from first principles and get the exact same timeline.
I’m also religious and I believe in God (and the Holy Trinity) in the core of my being.
In some kind of quantum space probably.
We still don't know so much, yet we claim so much.
Even quantum space can be described by both deterministic and stochastic elements. The stochastic elements of quantum uncertainty are about as much free will as a PRNG – though even more predictable as they don't have a flat statistical distribution. And there are also known exploitable and predictable mechanisms behind quantum mechanics (emphasis added), so much so, that they can be leveraged for computation.
I think when most people say free will they mean dualism, in that there's some sentience in the spiritual plane that directs their bodies in the physical plane. But if this spiritual plane has no observable effect on the physical plane, it's completely incompatible with free will. And if it is observable, then it is indeed a measurable part of physical reality, but yet we haven't measured it - not even stochastic effects (which can still be observed statistically).
Sabine Hossenfelder has a much better informed take on this, and it's worth a watch.
https://www.youtube.com/watch?v=TI5FMj5D9zU
Also of interest, a study where fMRI readings were used to predict a persons decisions well in advance of them executing the decision. The success rate was only 60%, but still better than chance, and this study was way back in 2008:
> fMRI machine learning of brain activity (multivariate pattern analysis) has been used to predict the user choice of a button (left/right) up to 7 seconds before their reported will of having done so.
https://en.wikipedia.org/wiki/Neuroscience_of_free_will#Neur...
Yes, for example we make wild claims like 'biological sentience is incomputable'
a random number generator in base reality? ;) really i'm just using this as a more accessible (to rational materialists) example of how processes can exist outside of our measurable physical reality.
> processes can exist outside of our measurable physical reality
If it can't be measured in reality, how can it be relevant to reality?
> a random number generator in base reality?
How does randomness pertain to free will?
they may have measurable effects in our physical reality, eg. the behavior of the individual and even be correlated with other physical processes.
however, there may be hidden variables outside of our physical reality that are actually mechanizing the result. some such processes may be non-deterministic, which is why i used randomness as an example.
what i'm implying is analogous but opposite to the concept of a philosophical zombie. there may be a ghost in the machine which no measurement can reveal.
P-zombies, conceptually, actually have no ghost in the machine, but are indistinguishable from sentient beings. Sentience and free will are two different things.
> they may have measurable effects in our physical reality
If there’s something external that interfaces with the physical universe, such an externality could be observed. It’s strange that we haven’t found such a force. But if it were to exist, in some parallel universe, that external force would have its own mechanics and its own chain of causality – its own physics so to speak. Dualism doesn’t get you to free will, it just means there’s physics we can’t observe. (Or perhaps there’s some superset universe that interfaces with that universe, and then it’s still determinism or stochastic processes all the way down.)