[ajkjk]

Part of the problem is that the difficulty curve becomes, like, superexponential if you try to do the actual math. Fairly elementary atoms require the full theory of quantum mechanics to justify rigorously, and anything more complicated than that requires huge bodies of specialist knowledge on approximation schemes (I assume; I haven't studied them, but given that helium already requires approximations I'm assuming the trend continues..)

Of course, they could still do a much better job useful providing pointers into this knowledge, instead of just handwaving over it and insisting on rote memorization.

[DiscourseFan]

But oftentimes theoretical chemistry is not as important as what we get out of experiments because unlike physics, which attempts to derive general laws of nature, chemistry has to deal with the nitty gritty of the diversity of actual miscroscopic interactions of things. Any theory that is not entirely rigorous or even has slight room for an exception will be ignored by necessity, and physics is chock full of such examples. Biology is in a certain sense better (since it deals with larger things) and in a certain sense worse (as it relies on dogma and mysticism, at its essence, to explain the systems of life), and still nobody has gone beyond Aristotle and Kant in giving anything close to a rigorous definition of life as such.

[HarHarVeryFunny]

I think that as you ascend the scale of complexity, and just system size, then necessarily empiricalism and rote learning/memorization has to take over from more reductionalist explanations.

Physics, whether at atomic level, or on a much larger scale, is simple enough that reductionism usually works and you can calculate behavior from first principles using a few memorized "laws"

Biology is well past the point of complexity where you can do this most of the time, unless perhaps you are at the level of aspects of cellular behavior that can be analyzed in terms of chemistry.

Chemistry is in-between physics and biology in terms of complexity. In simple cases chemistry can be explained in terms of physics, but as AlphaFold has shown when you get to a certain level of complexity (in this case protein folding) empiricism takes over and you need to perform experiments and memorize results.

I think modern science and philosophy has a reasonable understanding of what life is, even if you disagree. This is certainly more a matter of philosophy than science, but it seems the best definition of life is based on the ability of a system to actively maintain a boundary between itself and the external world, thereby combating the 2nd "law" (statistical tendency) of thermodynamics. Maybe an interesting/useful definition (which is somewhat arbitrary) also needs to involve something like consuming energy/resources from the environment.

[fc417fc802]

> unless perhaps you are at the level of aspects of cellular behavior that can be analyzed in terms of chemistry.

Only in the most hand-wavey sense. Actual simulation of the cell interior with even comically coarse grained models is prohibitively expensive. It comes up a lot in neuroscience where it sure would be nice to be able to credibly simulate even a single neuron at the molecular level. (I'm several years out of date on the state of that field so it's possible someone managed to pull it off in the meantime but even if so the broader point still stands.)

[vasco]

> and still nobody has gone beyond Aristotle and Kant in giving anything close to a rigorous definition of life as such

You stopped reading after the 1800's? Schrödinger told us life is what feeds on negative entropy and that is pretty good.

[DiscourseFan]

I guess that is true, but it isn't much. But my basic point was that before you can have "life" you have to have a theory of life which ultimately requires metaphysics, and there hasn't been much of an update to our understanding of what would ground a definition of life beyond Aristotle and Kant, and even their work is not determinative by any means.

[vasco]

Just because you picked 2 guys it doesn't mean nobody else had any different ideas. What a weird position to have, unless you literally read everything. There's so many theories. You didn't even include religions

[applicative]

Look into Aristotle and Kant on ‘the organized /and self-organizing/ being’; apply a couple thermodynamic abstractions known to adolescents ; be named Erwin Schrödinger ; hackernews will respond accordingly.

[inigyou]

Freezing water is life?

[isomorphic_duck]

how does biology depend on "dogma and mysticism"? I am really curious - a Google search yielded nothing much relevant.

[nemothekid]

I think he's being a little facetious - what he probably means is that if you attempt to get any true scientific rigor of that is going on in biological or chemical systems you end up facing the limits of physics in being able to explain what is going on. So rather and try to have scientific rigor, you just accept things the way they are and memorize the outputs and if anyone asks "why is it like that", your answers are either:

* Because God said so

* Find out yourself and get a nobel prize

Either way, even if you don't know what the answers are, you can still do serious work at a higher level of abstraction.

[AngryData]

I would think just because everything is so cumulatively complicated and interconnected that if you tried to trace a line through a complex biological processes and explain it all you will end up with 1,000 PhD thesis topics to figure out and thousands more you just hadn't noticed yet. And at the end of the day none of that might be all that useful for describing the larger process at work. So at some point when someone ask "Why does X do Y" you gotta just settle on "because that's the way it is" and move on.

[not-a-llm]

biology is full of exceptions to exceptions to exceptions. like immunology

so there is no way to extrapolate/interpolate, anything which was not directly measured is basically unknown since it could be yet another exception

or in programming language, the worse spaghetti code you could imagine, full of feature flags randomly enabled inconsistently

[gmueckl]

Where is physics chock full pf exceptions?

[vessenes]

Maybe we’d say “physics” is really just the delineation between things we have an accurate model for and everything else (the exceptions?). Theoretical physics would be the search for the “why” of everything, inside and out of that line in that case.

I’m not a physicist, so I’ll let them pipe up on how much is in and out of the descriptive line, and how much is in and out of the theoretical explanation line. But I don’t know many physicists who think we’re close to “done” with either endeavor.

[dolni]

I'm not a physicist but I've always seen physics as a bit hand-wavy myself.

Dark matter is a great example.

Our understanding of gravitation didn't cleanly apply at ultra-large scales so we had to add a massive fudge factor.

You can't "go faster" than the speed of light, but space in between things can expand faster than the speed of light.

It seems like things that are "settled" regularly get an "ope, but except for this special case..." treatment.

[gmueckl]

There is no handwaving involved. The layman explanations of these phenomena are not that good. The quantitative derivations that leads to those results are totally fine, but hard to follow without deep knowledge of the subject.

Physics education sometimes aligns with historical evolution of the theories, mostly because that builds intuition and because the mathematical founsations of the improved theories need to be taught first. That leads to the "but in this case..." moments, but you need to realize that what you get taught as a "fix" is practically always a careful evolution that also reproduces all predictions from the less complete earlier theory.

[saghm]

I think they meant the opposite; physics throws things out as soon as there's a need for exceptions, and there are examples of that.

[IAmBroom]

Well, once they have a better explanation.

We know that mass of matter does not explain even half of the mass observed in the Universe; we haven't thrown out the explanations of mass and inertial gravity, but have a placeholder called "dark matter" to refer to the missing explanation.

[chanakya]

As you move up levels starting from physics (eg. physics-> chemistry-> biochemistry-> biology), each layer has several "laws" which are generally pretty established, but a causal connection between the layers is hard to provide satisfactorily. And that is how I think it'll always be, else we'll be expecting to explain Shakespeare's plays using physics.

Also, this is where Rutherford's "all science is either physics or stamp collecting" holds a lot of water. As you move up the science layers, the laws themselves become less mathematically rigid until by the time you get to the social sciences, explanations are all hand-waving, and all "laws" are statistical at best and empirical.

[RetroTechie]

Fundamental physics is also empirical. It's that as you move up to more 'fuzzy' sciences, the 'laws' become less strict, less formal defined, and (most importantly) less reliable.

Edit: and less universal. Physics underlies biology, chemistry, nuclear tech & more. Biology (so far) only applies to carbon-based life as we know it on Earth.

[tremon]

> and less universal

Yes, this is key in my mind. It's not really that the laws and definitions become less strict of themselves, it's that the subjects under study become less uniform. It's fine to study a few atoms in isolation and describe their features, but if you put a lot of them together they'd better be in a uniform lattice or your calculations will take more than a lifetime to complete. If you want to describe the interaction in a drop of water, you don't use the Standard Model to integrate over 3e22 baryon fields.

Yes, physics underlies all other fields. But fundamental physics is also completely untractable to solve problems in those other fields, even if Heisenberg would allow it.

[ohhnoodont]

> else we'll be expecting to explain Shakespeare's plays using physics.

This is just a data problem though. From the perspective of a deterministic universe, creative works theoretically can be explained as a physics outcome (ignoring the impact of potential quantum randomness).

[Sharlin]

Yeah, but that’s like saying predicting next week’s lottery numbers, or the precise weather exactly one year from now, is a data problem. There’s no simulation that could answer those questions even in principle even if the universe were fully classical.

[moring]

> From the perspective of a deterministic universe, creative works theoretically can be explained as a physics outcome

In other words, physics can explain Shakespeare's plays when you hand-wave away the biggest reason it cannot.

> theoretically

... meaning not in reality, but in an abstraction of reality that conveniently leaves out the hard part.

> This is just a data problem though.

The word "just" makes it sound like that data problem is a minor inconvenience, and not a fundamental obstacle.

Becoming a billionaire is simple, after all it's just a money problem.

I mean, you're right in that (leaving out quantum randomness), you could predict macroscopic outcomes based on a physics simulation that includes all elementary particles explicitly, if you assume that such a simulation can be scaled from <10 particles to macroscopic numbers. But there is no evidence that this assumption is true, so it remains an interesting thought experiment that gets confused with reality because people like to slap the "in theory" label on it.

[pestatije]

doesn't that also apply for the maths-> physics layer? id say maths is the bottom layer

[jeremyjh]

Yes, we've all seen the xkcd[1] but you've misunderstood it. Physics applies mathematics but mathematics cannot derive physics in the way that a complete physics (and a lot of compute) could derive chemistry and biochemistry.

Math isn't attempting to describe a physical universe. It provides the substrate upon which such a description can be expressed and validated - found to be consistent with itself - but many valid descriptions do not describe our universe. Physics is the empirical search for the correct mathematical description of our universe.

[1] https://xkcd.com/435/

[pestatije]

> mathematics cannot derive physics

thats just at the current state of the art...doesnt mean a complete maths cannot...its arguably debatable why physics follow some maths and why the specific constrains

[tremon]

I don't think that's true. Mathematics can model every conceivable universe; you cannot derive the values of c or G in our universe from a purely mathematical model. Even if there were a proof that the current values for cosmological constants are the only possible values, that proof would necessarily have to rely on lemmas from physics.

[ordersofmag]

It could be that once we truly understand math in a complete way it would lead inexorably to the definition of one and only one possible universe with only one possible set of rules and c and G would simply fall out naturally. I'd agree it seems unlikely given our current understanding of math and physics (and their relationship to each other). But given both are incomplete it remains a possibility. The one theme that seems to hold true as we dig deeper and deeper into how the world works is that the fundamental rules seem to get more and more unified.

[exe34]

Maths lacks the physical grounding, so in that sense, it's less "real", and more "made up", even though of course it's so pure.

[jeremyjh]

Downvoters are probably misunderstanding this. Mathematical theory is based on axioms and inference. The axioms do not have to be true in any cosmic sense for the math to be correct or even useful.

[pestatije]

its the same... physics hand-waves the 'why' all the same as chemistry or biology...the gap might be wider but its the same

[exe34]

Physics has a long history of throwing out laws with exceptions in favour of laws that cover larger and larger numbers of observations.

[not-a-llm]

yet there are problems there too we do not know the "true axioms of math", people disagree (math foundations)

[rnikander]

All this computing power. Can we even simulate a water molecule yet from scratch with QM?

[smj-edison]

Depends what level of accuracy you want. I just started in a computational chemistry lab so I'll probably get some details wrong, but for small systems, you can use a method called CCSD(T) for up to ~20 atoms, but it scales O(N^7). I've been mainly using DFT for the systems I've been simulating, which scales O(N^3). I've been running a system with about 50 atoms with a decent basis set (how the orbitals are modelled), and it takes about 30 minutes for each optimization step with 24 cores and 48 GB of RAM.

DFT works in many cases, but in some cases it doesn't estimate the energy right, due to how it bypasses some correlation calculations. Bonds are extremely sensitive to energy calculations, so you need to get super close to the actual energy in order to get useful results.

Anyways, someone with more experience here could probably add more, but that's what I've picked up so far.

[vessenes]

Cool details, thanks. To help me understand your life, what would be like a one year and a five year research goal for you? I never spent time in lab sciences so it’s kind of a black box for me.

[smj-edison]

Disclaimer: I'm only a freshman, so there's still a ton I don't know :)

Right now the lab is having me get comfortable using software like Gaussian and ORCA by simulating a bifurcating reaction. This is a reaction that, depending on the catalyst's momentum, will change what site it bonds to (it makes either a 6-membered or 7-membered ring). I'm finding the intermediate states (where the molecule is most stable) and transition states (the tipping point), and then running trajectories to see which output is more likely.

Once I've finished simulating that, I should be comfortable enough with the process to jump on the bigger project, which is machine learning interatomic potential (MLIP) model distillation. There's a lot of exciting work around speeding up DFT methods by using machine learning (note this is not generative AI, it's merely predicting the molecule energy based on atomic positions). So my one year goal is to get on that project and start contributing.

My five year goal is to, well, graduate. But then I'll probably do a PhD in computational chemistry, since I'm really interested in ways to speed up and scale existing methods. My big dream is to simulate large biological systems while still having bond formation and breaking, to automatically elucidate biochemical pathways, but there's still a lot of steps in-between.

[WillAdams]

Good luck!

I assume you are familiar with:

https://matt.might.net/articles/phd-school-in-pictures/

I hope and pray that your research helps to make the world a better place and that the rest of us can use your knowledge to help to make the world a place which merits your research.

[smj-edison]

Thank you for the kind words! I've been wanting to do this research precisely because of firsthand experience with how hard chronic illness can be, and I'm hoping to attack it with a systems approach.

I haven't seen that website before, but it sounds pretty accurate from what I've heard. It's insane how high of a mountain needs to be climbed just to catch up to the state-of-the-art, and how much work is needed to push through to figure out something truly new.

Here's to making the world a better place!

[not-a-llm]

do you think quantum computers would help simulating this? I've seen contradictory opinions from the experts - it can in theory but not really in practice (even assuming sufficiently large quantum computers will be built)

[smj-edison]

I'm only a freshman, so I don't feel very qualified to comment on that :) I hope so though!

[nixonaddiction]

yea im doing my masters in dft research so ik abt this. depends what u want 2 simulate! chemists more do molecular dynamics type stuff and will use experimental data for fitting data etc. like uh what surface of a metal water will react with from thermodynamics or something. (that isnt my field lol i just know a lot of catalysis guys.)

truly ab initio methods involve figuring out electronic properties from scratch like ionization energy or bandstructure. the real issue is that we dont have exact relations for the exchange and correlation terms. we can know the kinetic energy and charge screening, but we dont know how the electrons are interacting with each other. generally the xc term is treated as a function of electron density or its gradient (see: lda, gga, meta-gga) but there are so many different ways to approximate that. different models are good for different applications also, like transition metals vs organics. and then theres the issue of basis sets (most people use gaussian basis sets that have been tuned over many years but theres also plane waves and finite element methods) which can also change results. and even once u have a decent approximation of density you can try perturbative methods (GW family, delta scf i count also) to try and improve the approximation. i am rambling and typing this on my phone. essentially yes, but often calculations are a little inaccurate. but more accuracy has a higher computational cost, which makes it hard to run larger simulations. tradeoffs of engineering. hope this was coherent.

[OgsyedIE]

To complete accuracy, we cannot yet manage one proton.

[ordersofmag]

If you want to get pedantic we can't simulate anything with complete accuracy in the absence of a theory that encompasses all the known forces. Which we don't have. (Damn you gravity. Can't you just get along with the others)

To a useful level of accuracy we can certainly simulate water. And we can do the same for a single proton for some definitions of useful (but not other definitions).

[terminalbraid]

That's a fundamentally different problem and a terribly unfair comparison.

[moring]

Am I right with my assumption that by "fundamentally different problem", you mean we lack a good simulation model, but that the number of degrees of freedom would actually be manageable?

[terminalbraid]

To simulate a proton you need to solve a strongly coupled highly relativistic SU(3) gauge theory (naturally non-abelian i.e. the force carrier field itself carries charge and is self-interacting at tree order) problem with constituents that have masses orders of magnitude below the relevant energy scales (i.e. you have many matter AND force particles that can pop in and out of existence and they all strongly interact with one another).

To simulate a water molecule you do so with a weakly coupled SU(1) gauge theory (light does not interact with itself at tree order) problem where the masses of all constituents are orders of magnitude above the relevant energy scales (you can think of it as the electrons and nuclei and particles coming in and out of existence are contained in a renormalization scheme).

We have "good simulation models" of both, but the former is extraordinarily complicated compared to the latter for the reasons stated above.

[wombatpm]

Physical Chemistry (I think it was Chem 361 at UofI) took most of the semester to get to the point where we could derive the shape of the hydrogen orbitals. Probably the best lecture of that class.

[oh_my_goodness]

The subject in chemistry isn't theory. It's what actually happens in nature. Even immense levels of theory just don't close the gap.