2552: The Last Molecule

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The Last Molecule

Title text: Biology is really struggling; they're barely at 93% and they keep finding more ants.

Explanation

This explanation may be incomplete or incorrect: Created by a CONFUSED PARTIAL BIOCHEMIST - Please change this comment when editing this page. Do NOT delete this tag too soon. If you can address this issue, please edit the page! Thanks.

This comic jokingly proposes a situation in which chemists have discovered and catalogued every single possible molecule. Thus they declare they have "completed chemistry."

In real life the number of ways to arrange atoms into molecules grows combinatorially with the number of atoms in a molecule. Since molecules can be arbitrarily large, the number of possible combinations is much much larger than the number of particles in the observable universe, making the full cataloging of all molecules impossible. Thus, a "final molecule" cannot be reached. In addition, chemistry is the study of the interaction and changing states of atoms and molecules, not simply the cataloging of all specimens of molecule. Even if we did have a list of every molecule, there are a far greater number of ways to continue studying them, so the field would still be nowhere near completed.

This is reminiscent of biology's focus in previous centuries on simply cataloging the species on Earth.

Further, the goal of science is not to "complete" a field, but to understand it better and better. No scientific field is considered fully understood. As readers are aware of this, part of the humor comes from the very high percentages given to the different fields. Putting Biology at 93% and Physics at 98% is patently absurd.

If biology were simply a matter of cataloging species, we might not even be at 10%. As mentioned in the comic, we can't even give a definitive answer to changing-target questions like how many kinds of ants there are, let alone microscopic organisms. When J.B.S Haldane, founder of the field of population genetics, was asked what could be inferred about the creator from the creation, he reportedly said, "He has an inordinate fondness for beetles". Insects aside, fundamental and important problems such as what genes promote which traits, the nature of cognition, and the mechanism behind several diseases remain complete mysteries. We know less about our own ocean floor than we do about the surface of Mars. Needless to say, Biology is nowhere close to 93% solved.

The title text in particular makes fun of Biology lagging behind due to the inherent difficulty of cataloging all species. Species are being constantly created and recategorized, so even if it were possible to know exactly what animals were alive on Earth at any one time, and which could interbreed, there would still be no agreement on the number of species they constituted, and that's without even getting into historic species, such as the contentious question of whether neanderthals are considered a subspecies of homo sapiens, or a whole separate species.

As for Physics, all the elementary particles of the Standard Model of particle physics have been experimentally detected, culminating in the 2012 detection of the Higgs Boson. But questions such as "what is dark matter?", "how do we unify the four fundamental forces?", "how do we make nuclear fusion possible on earth?", "is the speed of light symmetrical?", and "how many dimensions does the universe have?" make it clear that the field still has a long, long way to go.

Transcript

This transcript is incomplete. Please help editing it! Thanks.

[Ponytail is presenting on a stage. To the top-center of the slide which Ponytail is pointing to, there is a circled "100% complete" under "Chemistry", then to the left is "Biology" which is at "93% complete" and to the right is "Physics" which is at "98% complete". The bottom of the slide shows the structural formula of a molecule which is captioned "The Last One", along with a few smaller captions around it drawn as squiggles.]

Ponytail: With the discovery of the last molecule, I'm pleased to announce that chemistry is finally complete.

Ponytail: Best of luck to our competitors in their race for second place.

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Discussion

Unsuccessfully tried to search for a match to the image of the chemical compound. Did find this, which is difficult to use on a cellphone: OSRA: Optical Structure Recognition: https://cactus.nci.nih.gov/cgi-bin/osra/index.cgi 1 not72.70.211.172 07:43, 9 December 2021 (UTC)

I've tried to search for SMILES of the molecule, but also got nothing: https://pubchem.ncbi.nlm.nih.gov/#query=C1(C2CC(CCC)C(CC)C2(CCCC))C%3DCC(C(%3DCCC(%3DC)CC)C(C)C)%3DC1 162.158.222.137

Let's name it Excacidin ;) 256.256.256.256 (talk) 07:19, 10 December 2021 (UTC)

Here is updated SMILES taking into account comments below: N1(C2OC(CO)C(O)C2(OCCC))C=NC(C(=NCC(=O)O)N)=N1 162.158.222.123 16:44, 14 December 2021 (UTC)

I truly don't understand the God part of the current explanation. 172.68.110.121 07:55, 9 December 2021 (UTC)

There is an article at Smithonian Magazine that sums it up quite nicely: Of the 550 gigatons of biomass carbon on Earth, animals make up about 2 gigatons, with insects comprising half of that and fish taking up another 0.7 gigatons. Everything else, including mammals, birds, nematodes and mollusks are roughly 0.3 gigatons, with humans weighing in at 0.06 gigatons.

About half of all known living species on earth are insects. Therefore if there was a god who created all life, it would be reasonable to assume he likes them. Bischoff (talk) 08:26, 9 December 2021 (UTC)

1 Ton = 10^3 kg = 1 Mg → 1 gigaton = 1 Pg (note, not pentagram!) --Slashme (talk) 02:27, 10 December 2021 (UTC)

Chemistry. I love chemistry :-) There is a concept called "Chemical Space" that I learned about in school. https://en.wikipedia.org/wiki/Chemical_space may help, in short: Chemical space is a huge but finite space of all possible atom arrangements in molecules. 162.158.91.106 07:59, 9 December 2021 (UTC)

I've heard the claim, that we know less about our own ocean floor than we do about the surface of Mars several times before. Is there actually a credible source for this and how do we even quantify how much we know about either area? Bischoff (talk) 08:26, 9 December 2021 (UTC)

This essay might shed some light on the question. [Just How Little Do We Know about the Ocean Floor?] From a geographical perspective, our maps of the ocean floor are much less detailed than those covering Mars. (5km resolution for ocean floor, 100m resolution for Mars - radar doesn't work underwater). 162.158.107.18 09:25, 9 December 2021 (UTC)

The current explanation says that there are an infinite number of chemicals. Is that true? Source? Explanation how that is possible? Obviously the number of possible molecules is huge, but is it actually a literal, mathematical infinite? Given a finite observable universe, with presumably a finite number of atoms in it. There appear to be a finite number of elements which are stable for any appreciable amount of time and capable of forming molecules. It seems like there might be practical limitations to the size of a molecule, so that you can't keep making bigger and bigger ones just by adding more atoms/subunits? If you just keep adding carbon atoms to a diamond will you eventually reach a point where forces such as gravitation become a factor and the molecular bonds fail? I can imagine that long chain molecules light years long might reach point where other forces overwhelm the bond strength? 108.162.246.76 09:10, 9 December 2021 (UTC)

For obvious reasons, as long as you limit the number of atoms involved the number of possible "molecules" is - in a mathematical sense - finite. (As there is only a finite number of reasonable stable elements.) But already simple things like polymers can bind millions of atoms in a single molecule. Together with the possible variations intrinsic to such polymers a simple "material" like phenolic resin [[1]] is a mixture of more different chemical compounds (in a strict sense) than mankind can ever describe. For all practical application this compexity is not relevant, so no one really cares about.

Additionally there is no clear boundary between typical molecules and other types of condensed matter, like crystals. Same applies to biochemistry. Does chemistry include bio-molecules? If yes, the chemistry guy have to include all the gene sequencing in their to-do list.

What is this practical applications? This is XKCD! I am curious about what are the limits on molecular size (if there are any). You often learn things by looking at the boundaries or extremes, even if those boundaries are (or appear) unatainable in practice. I wish What If was still going, seems like an interesting question for Randal. 108.162.245.13 19:42, 19 December 2021 (UTC)

"how fast does light travel in one direction?" is not a good example for incompleteness in physics, because this question was settled by Michelson and Morley in the 19th century (answer: it travels with the speed of light)

It's not clear to me either what was meant here - seems out of place.

We know how fast light travels when it goes somewhere and comes back – that's c – but we don't know how fast it goes when only traveling in one direction. For example, light going at c/2 in one direction and returning instantaneously in the other would still match our observations. We also can't reliably synchronize clocks over a distance because we'd either have to do it with a speed-of-light delay, or separate two clocks and find that relativity changed the timings. Of course, Occam's razor indicates that a consistent speed is more likely, but that's not proof. 172.70.126.87 12:42, 9 December 2021 (UTC)

Observing two points (nominal source and nominal destination) from a third point perpendicularly off the mid-point between thoss two points, at an arbitrary distance, you ought to see if there's slowness or instaneity involved (at least make a comparison between bidirectional traversal). This does not remove a response bias in the signal from either end as sent towards the recorder at the observation point, but as the stand-off is increased it makes both observation paths nearer and nearer to parallel and so significantly removes the quantifiable initial 'sideways bias' that may exist.

I leave it as an excercise to the reader to produce the reasons why this might not practically work to quash all such 'inbuilt universal asymmetry', but it's a good start! 172.70.90.141 13:21, 9 December 2021 (UTC)

I genuinely don't understand the confusion being proposed here; in practice it's trivial to synchronize a single photon emitter with a single photon detector (such as a PMT) and confirm the speed of light across a single path, with no return trip involved. As far as I know there is know precidence in QM to suspect bidirectional travel could be a special case.

I like Veritasium as much as the next guy, but I don't think that this one is a serious debate like the other examples. If you're going to consider something like this a great unsolved mystery in physics, I'm sure there are countless other questions just like this for almost every topic in physics and not everything can be a great unsolved mystery.172.70.134.23 17:37, 9 December 2021 (UTC)

To quote Randall Munroe in https://what-if.xkcd.com/114/, "The whole universe is matter, as far as we can tell. No one is sure why there is more matter than antimatter, since the laws of physics are pretty symmetrical, and there's no reason to expect there to be more of one than the other. Although when it comes down to it, there's no reason to expect anything at all." Antimatter aside, this shows that the laws of the universe are sometimes asymmetrical. I also like the point that "when it comes down to it, there's no reason to expect anything." Why should we expect the speed of light to be symmetrical? There's no real reason to. Beret (talk) 14:53, 9 December 2021 (UTC)

On the contrary, without any such thing as the æther (the fundament through which we would be passing) there is no reason to expect the speed of light (in any given frame of reference) to be asymmetrical. Relativistic frame-dragging and other distortions due to (or resulting in!) accelerative forces will act accordingly, but not change c itself, in proper calculations, as a function to direction. 172.70.86.12 16:02, 9 December 2021 (UTC)

https://en.wikipedia.org/wiki/One-way_speed_of_light In any case, the point is that there is no reason to expect light speed to be symmetrical, either. Asymmetry in this case is not due to frame dragging, it would be some fundamental feature of photons or the universe. There is currently no experimental way to test this. Beret (talk) 17:00, 9 December 2021 (UTC)

Maybe we can cite one of some famous declarations of physicist saying the physics is almost done (taken from this site) :

The British scientist William Cecil Dampier recalled his apprenticeship at Cambridge in the 1890s: “It seemed as though the main framework had been put together once for all, and that little remained to be done but to measure physical constants to the increased accuracy represented by another decimal place.” British physicist J. J. Thomson: “All that was left was to alter a decimal or two in some physical constant.” American physicist Albert A. Michelson: “Our future discoveries must be looked for in the sixth place of decimals.”

My physics professor from freshman year: "If you're ever in a room with physicists who say that the physics of Earth are done, and there's nothing else left to calculate, ask them "what about turbulence?". You'll be sure to get some dirty looks."108.162.246.122 21:08, 9 December 2021 (UTC)

--Marceluda (talk) 15:32, 9 December 2021 (UTC)

I'd argue that fusion on earth is an engineering problem, not a matter of physics completeness (yeah, engineering is just applied physics and math just theoretical physics and biology what happens when you close two physicists in a room for too long, but still). Also, the problem of the symmetry of light speed is, from the present understanding of physics, a matter of metaphysics. 172.68.94.143 13:42, 10 December 2021 (UTC)

Having worked in fusion research, I'd say it's still a physics problem because we don't yet know if it's physically possible for a burning plasma to be confined for long enough on a small enough scale to create a viable power plant. It's not necessarily just a question of designing the right machine, if you see what I mean. And if it was, I'd like to think we'd find a few hundred billion of dollars of funding and just get it done. IMO the reason it's not a funding priority is that we can't be sure it would work with _any_ amount of money. That said, while it's potentially a question of great value to humanity, I don't think it's significant in terms of the completeness of physics as a field. --192·168·0·1 (talk) 15:18, 10 December 2021 (UTC)

To rant further about fusion funding, we don't know whether we can win any given war either but that doesn't stop us spending trillions of dollars on them. Maybe if we called fusion research "the war on paying for electricity / wrecking the environment" maybe we'd get it sorted. --192·168·0·1 (talk) 15:23, 10 December 2021 (UTC)

Regarding the final molecule, using the above mentioned cactus website optical recognition I got: *[C@H](*CC[C@H](C)[C@H](C1CC1C[C@H](CC)CCC)C2[C@H](*)[C@@H]2C)CC3C*(CCC)C(CCC)[C@H]3CCCCC, which isn't recognized as a molecule. Anyone have any better ideas on if there is a similar known molecule? Stickfigurefan (talk) 17:16, 10 December 2021 (UTC)

Regarding the completeness of chemistry, I see no reason why a DNA molecule can't be longer than observable universe (it definitely wouldn't collapse into black hole ; obviously, tugging on it would break it somewhere). Regarding the completeness of biology, what organism would such molecule encode? While, mathematically speaking, observable universe is finite, I would consider this idea alone to ensure chemistry and biology can't ever be complete. -- Hkmaly (talk) 23:35, 10 December 2021 (UTC)

Should we really use "citation needed" for a quotation, where we might actually want a citation? We're only supposed to use that ironically here. Barmar (talk) 17:46, 10 December 2021 (UTC)

Why citation needed?

I saw a citation needed about the Higgs Boson. Is it needed for humor? The higgs boson isn't obvious.--172.70.34.191 19:14, 10 December 2021 (UTC)

Circular reasoning

I think something could be added about how determining how "complete" is a discipline already requires a complete knowledge of that discipline, even if we limit this to the inappropriate "number of known entities" approach. Some plausible estimates are naturally possible and a historic example seems to be more in line with the current explanation. A good fit seems to be how in physics the proton, neutron and electron model seemed at some point quite complete and was less crowded than the current one, still not sure how much of this understanding is a myth or how to put it in the explanation, so I prefer to leave it to someone else. For biology Wikipedia has Biological dark matter and the more theoretical Shadow biosphere, in case the number of unstudied multicellular organisms isn't sobering enough. 172.70.98.153 02:07, 12 December 2021 (UTC)

Serious hypothesis for the molecule's structure

I'm not sure why everyone keeps interpreting the picture as only containing carbon atoms. The leftmost moiety is clearly an O²-substituted furanosyl group; exactly which furanose it is is uncertain, since the stereochemistry is not indicated at all. It could be D-ribofuranose, D-arabinofuranose, D-xylofuranose, D-lyxofuranose, or any of their L-enantiomers.

The central ring best matches the pattern of a 1,2,4-triazole, just looking at the bond patterns. It is consistent with how I've seen them in other compounds. Similarly, the rightmost group is clearly the -COOH of a carboxylic acid.

Probably the most ambiguous group is the one second from the right. Based on the bond patterns alone, it would be consistent with an amidine, which is probably the possibility most likely to occur in real compounds. However, N′-monosubstituted amidines seem pretty rare based on a cursory search, and most likely tautomerize quickly into N-monosubstituted amidines. I don't have any other idea of what it could be, though.

I strongly suspect that the furanose is D-ribofuranose. The leftmost three groups can be seen as a modification of adenosine, which is one of the nucleosides found in DNA. In addition, the majority of this molecule exactly matches the antiviral drug taribavirin, which is used against hepatitis C and influenza. In fact, the drug may very well have been the inspiration for this molecule. The only two differences are an O²-propyl substitution on the ribofuranose, and an N′-(carboxymethyl) substitution on the amidine.

Assuming this interpretation of the molecule's structure is correct, its preferred IUPAC name (PIN) is "[(amino{1-[(2R,3S,4R,6R)-4-hydroxy-5-(hydroxymethyl)-3-propoxyoxolan-2-yl]-1H-1,2,4-triazol-3-yl}methylidene)amino]acetic acid". LegionMammal978 (talk) 05:29, 12 December 2021 (UTC)

E. O. Wilson found a lot of ants

Coincidentally, world-renowned myrmecologist E. O. Wilson — who personally discovered more than 400 species of ants — died on 2021-12-26. Reading the comic in January 2022, I initially took "they keep finding more ants" as a posthumous homage to Wilson... but as this comic was apparently published 2021-12-09, I guess that would have required a time machine on Munroe's part. Just a coincidence, then. 172.70.230.153 16:10, 3 January 2022 (UTC)