8 ms·
That's a beautifully concise numbering system for sharing being used there. Now if only we had descriptions of chemistry that were this terse. Imagine if this
by heavenlyhash 11y ago
That's a beautifully concise numbering system for sharing being used there.
Now if only we had descriptions of chemistry that were this terse. Imagine if this kind of problem solving, collaboration, simulation, and instant verification were the norm for synthetic chem. One of the comments -- "[Let's] use gencols to rub the ship against gliders and *WSSs to see whether there is a useful collision to maybe build a puffer" -- just blew me away. If this were chemistry, that commentator would have been suggesting automatic nanomachine factory discovery.
(InChI appears to be close. But vast amounts of data are locked up in obtuse formats are either Assigned-Names-And-Numbers style formats which are useless to indexing and similarity searches, or formats that embed non-relative coordinates in 3d space, etc, in such a way that computing a deterministic ID for sharing is practically a nonstarter.)
- david-given 11y agoIt does help that Game of Life physics is somewhat simpler than Real Life physics. Of course, Real Life physics is a little less apt to collapse into a seething mass of undifferentiated matter of you poke it in the wrong place. This is the slowest spaceship known, right? (Which isn't a machine made out of other parts?)
- NoMoreNicksLeft 11y ago> It does help that Game of Life physics is somewhat simpler than Real Life physics. Are we sure of that yet? > Real Life physics is a little less apt to collapse into a seething mass of undifferentiated matter of you poke it in the wrong place. Are we sure of that yet?
- eru 11y agoWe are sure that Game of Life physics is simpler than Real Life _chemistry_. There, fixed that for you.
- Rhapso 11y agoIt also helps that we GoL comes with the capacity to instantiate the universe in any configuration we wish, rather than being forced to coerce it into that state from scratch.
- eru 11y agoNot from scratch, but from inside!
- onnoonno 11y agoInside? Tell me what the outside is, then :)
- eru 11y agoOutside the Game of Life is easy to tell. Outside the universe ain't. But even though, I can confidently say that we are definitely inside.
- onnoonno 11y agoBut does it make sense to even talk about inside and outside then when talking about the universe?
- Rhapso 11y agoIt makes about as much as uncountable infinite numbers. I can say everything in the universe is within a countably infinite distance of me. Thus, anything an uncountable infinite distance from me is outside the universe. Not a very tangible idea, but not useless of purpose of reasoning about the affairs of things.
- eru 11y agoIt's a bit of an abuse of notation. Talking about the inside definitely makes sense. (Talking about the outside is a bit like talking about the empty set.)
- dalke 11y agoYes, GoL physics is simpler than Real Life physics. RL follows quantum mechanics. As far as we know, its state cannot be recorded perfectly. GoL is a Turing Machine. Its state can be recorded perfectly. RL follows relativity. There is no equivalent in GoL. Hashlife gives a method to compute GoL boards faster than processing each cell, and gives an exact answer. There is no equivalent for RL. At best there are probabilistic predictions. (There might be a 1E-50000 chance that the Sun won't rise tomorrow because all of the atoms in the Sun fuse at the same time and it blows up.)
- grkvlt 11y ago> RL follows relativity. There is no equivalent in GoL Of course there is an equivalent of relativity! There's a fixed, ultimate speed-limit (i.e. c) of once-cell/time-step. It is not possible to transmit information faster than this in GoL.
- Dylan16807 11y agoYou can have C without relativity. There are no relative reference frames in GoL. Reactions only work at specific absolute speeds, and most of them only work at absolute speed 0.
- goldenkey 11y agoRelativity can exist in an absolute environment like GoL if you consider the momentum of the quantum vacuum virtual particles. Look it up :-)
- goldenkey 11y agoSeriously guys. Downvotes for talking about digital physics? Sad me. https://en.wikipedia.org/wiki/Superfluid_vacuum_theory#Relation_to_other_concepts_and_theories https://en.wikipedia.org/wiki/Superfluid_vacuum_theory#Relat... "Relativistic quantum field theory"
- 11y ago
- lmm 11y agoYes. Real Life physics has been proven to be either nonlocal or nondeterministic (Bell inequalities). Life physics is both local and deterministic.
- Rangi42 11y ago"A seething mass of undifferentiated matter" describes runaway exothermic reactions fairly well. It also helps that Games of Life can be saved and reloaded. If your lab bench explodes, too bad, start over from scratch (assuming you're uninjured).
- heavenlyhash 11y agoOh, of course, simulations without perfect replays would be an abomination! Not even worth mentioning! -- What are we, heathens who can't even manage the basics of reproducible builds? (cough)
- kordless 11y agoHypothesis: We don't have perfect replays because there are multiple players.
- creshal 11y ago> Now if only we had descriptions of chemistry that were this terse. Chemistry is dealing with a lot, lot more of concepts than the study of the Game of Life. Brevity only works when you have few enough information that you can map it to only concise words. (Entropy strikes again, even if it's information entropy for a change.)
- pervycreeper 11y agoIUPAC names are needlessly verbose and insufficiently descriptive.
- zrm 11y ago> (Entropy strikes again, even if it's information entropy for a change.) Information entropy and physics entropy are actually the same thing. You can measure heat capacity in bits.
- creshal 11y ago…huh. That's neat.
- duaneb 11y agoThe terseness vanishes when considering the complexities of interactions and possible classifications. In fact, I'd say that the above terseness is only possible because it's about half of ALL the interesting effects possible in the game of life.
- theophrastus 11y agoif InChI doesn't do it for you, i suppose SMILES[1] isn't sufficient either? By-the-bye, you're not ever going to be able to "concisely" encode 3d (or even 2d coordinate) structures, because there isn't just one such. They're a thermally sampled average of structures. [1] https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system https://en.wikipedia.org/wiki/Simplified_molecular-input_lin...
- dalke 11y agoheavenlyhash wants three things: 1) pass structure information around so it can be simulated or reproduced, 2) a deterministic ID for sharing and linking chemical information, and 3) viable methods for determining identity and similarity from the cloud of all chemical configurations. SMILES is better at #1 than InChI, but not as good as a 3D structure representation. But the 3D structure isn't as compact, and offers few advantages for structure identity for small molecules where the 3D configuration is more easily predicted from geometry. InChI is better for #2 than SMILES because different tools generate a different canonical structure, and because general purpose text search engines like Google don't do so well with SMILES as InChI keys. Fingerprints, either binary or count, are more often used for the similarity aspect of #3, than n-gram solutions using the SMILES directly (like LINGO), or any method based on InChI. Also common are 3D shape and electrostatics comparison methods, with attempts to sample configuration space. And for certain chemical structures other approximations are even more important. DNA similarity is based on very different principles than used for small molecules.
- theophrastus 11y agoIn my humble experience "1)" and "2)" are sufficiently overlapping as to be indistinguishable. Whereas "3)...identity" only demands that the same system be used for both the search compound and the database ("cloud"). For that, a particular implementation of "canonical SMILES" is perfectly respectable. But it's a notably different world once one gets into "3)...similarity". With that you've opened a vast library of doctoral theses, commercial promises, and ingenuity, (and essentially my entire career). And yes, as you suggest, DNA similarity is a wholly different beast.
- dalke 11y agoInChI is not designed as, nor can used for, what you propose. Last I checked, conversion from an InChI to a structure format was not a supported option, and only exists for testing purposes. Which is not to say that people don't use for that. (Also, last I checked, there are inputs which cause InChI to segfault. And there's no spec for how to interpret InChIs other than to run the reference code.) The InChI normalization step may also change the chemistry. For example, it may put things into a preferred tautomer form or charge state. This is essential for its goal of linking disparate records, but it is not chemistry preserving, and can be worse than passing an SD file to your nanomachine factory. It was designed as "deterministic ID for sharing", yes, but not for sharing structure information but rather information related to the structure. The most "concise" solution is to record the positions of the nuclei and the total charge. Then any quantum mechanics program will be able to reconstruct (to the desired level of approximation) the electron density of the molecule. This is the one you reject. For good reasons. As you say, you want a nomenclature that can help with identity and similarity, and electron density is a very slow way to do that. But such nomenclature is driven by human concepts. Fundamentally, there are different reaction rates depending on the relative orientation of two molecules. We see this in molecular beam experiments. For example, from 1979, http://www.sciencedirect.com/science/article/pii/0009261479803851 http://www.sciencedirect.com/science/article/pii/00092614798... "Molecular beam reaction of K atoms with sideways oriented CF3I". InChI doesn't have a special name for "sideways oriented CF3I", even though a complete, concise system would have to be able to provide a name for it. Instead, we've come up with concise approximations - a SMILES string, a bitstring fingerprint, etc. - which are tractable for the purposes you want, so long as we stay within relatively normal chemistry. But it's still humans who categorize things into, say, "aromatic" or "chiral", so our approximate nomenclature has to partially encode how humans think of chemistry. The Game of Life is much simpler than the Reality of Life.
- heavenlyhash 11y agoAll of this is true. The word "close" was chosen very, very deliberately. Though the Game of Life is surely simpler than the Reality of Life... if one were to flat out name the core concept as "godel numbers for chemical formations", it's certainly possible, don't you think? InChI isn't it, I agree; just wanted to toss the seed of the idea out there, with an example that's a lot "closer" to the target semiotics than a bunch of unnormalized floating point coordinates drifting around in xml. "good enough is the enemy of good" can apply in spades here, so I appreciate your thorough analysis of specific weak points in InChI.
- scythe 11y agoTopologically, encoding a 2D structure into a 1D line of text is dramatically simpler than encoding a 3D structure into a 1D line of text. To motivate this simply, recall that no graph whose minors include K5 or K3,3 can be drawn in the plane, whereas any graph can be drawn in 3D. It gets even simpler because all GoL graphs are confined to a grid. tl;dr: easier problem is easier!
- dclowd9901 11y ago3D software development does it with tuples all day long.
- theoh 11y agoGiven that what's being shared is a very small bitmap, wouldn't hex would be more concise?
- dnautics 11y agoChemistry isn't even fully expressible using naive graph structures (atoms = vertices, bonds = edges), for example, eta-2 metal-pi bonds where the chemical bond is between an atom and another bond.