Why Are Viral Capsids Icosahedral? | Hacker News Reader

Why Are Viral Capsids Icosahedral?

asimov.press

80 pointssurprisetalk33 comments

We used to joke in my biophysics grad program that basically everything was determined by its surface area to volume ratio.

"First, assume a spherical chicken."

> even though evolution is contingent at a local level (such as a specific protein sequence or the shape of a flower), it is remarkably predictable at a global level (such as the very existence of proteins and flowers across many species)

to be fair... flowers are a very recent invention that appeared only after the dinosaurs got wiped out and clean slate allowed co-evolution of flowers and pollinators to occur

Flowering plants (angiosperms) appeared during the Cretaceous before dinosaurs got wiped out, and there is fossil evidence of insects pollinating non-flowering plants (gymnosperms) like ferns and confers even earlier than that: https://repository.si.edu/server/api/core/bitstreams/152b12d...

The header illustration brought to my mind, for some reason, the tomato bushy stunt virus depiction by the late Irving Geis: https://pdb101.rcsb.org/sci-art/geis-archive/gallery/geis-05...

>an estimated 70 percent of viral capsids known to date are icosahedral, shaped like tiny soccer balls.

Soccer balls are not icosahedra. The archetypal soccer ball is a truncated icosahedron: https://en.wikipedia.org/wiki/Truncated_icosahedron

And that archetypal soccer ball design is called the Telstar and named for a communications satellite, fun fact. I think before 1968 the volleyball shape was more popular https://en.wikipedia.org/wiki/Adidas_Telstar

do you know what the modifier "like" means in the sentence you quoted, or are you just being annoyingly pedantic

There are a few pictures of truncated icosahedra in the article, alongside several other shapes that are not icosahedra. The point is that they have icosahedral symmetry. The L is important.

I was going to comment pedantically that soccer balls were dodecahedrons not icosahedrons, but in reading the article, I came to realize that truncated icosahedrons are the same as truncated dodecahedrons.

This was such a delightful realization I felt the need to comment anyway.

that is indeed a delightful realisation! akin to when I noticed that a cube and an octahedron both had a cross section that was a regular hexagon.

Hmm. I'm sorry, but truncated dodecahedra are different from truncated icosahedra.

Truncated dodecahedra are made from twelve 10-gon and twenty triangular faces. Truncated icosahedra are made from twenty hexagonal and twelve pentagonal faces.

eh but also organic chemistry only does well 30 and 60 degrees

Not in 3D.

https://upload.wikimedia.org/wikipedia/commons/thumb/c/c2/Il...

That image just demonstrates what was mentioned in the article, that the sphere cannot be covered only with regular hexagons, but a part of them must be replaced with regular pentagons, so the angles that are multiples of 30 degrees are not sufficient.

So the previous poster was right.

An angle projected on a plane is not the same as a 3D angle.

Also see the structure of diamond (109 degs).

Not in 3D Euclidean space. I'm pretty sure 3D Hyperbolic space allows it just fine.

The universe seems perfectly happy to have, for example, 5-member rings tho.

See buckyballs as a trivial refutation of your point.

Are buckyballs organic?

Yes! Not sure why you're asking- things don't have to be created by biological processes to be organic (this concept is totally unrelated to "organic" in the supermarket).

Formally, yes. "Organic chemistry" is not too far off a synonym for "chemistry with carbon involved".

"Not too far off" = "exactly defined as".

I wasn't sure if there were any weird edge cases, but yeah.

I mean, I don't think diamonds are considered "organic"; same for graphite. But that's where the term "organic" itself starts to break down as a category.

I was also thinking carbonates in a geologic context.

Wikipedia: "Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials (i.e. matter in its various forms that contain carbon atoms)."

It doesn't break down at all. Diamonds are organic structures, in the classical definition of that term. (Assuming they weren't treated with insecticides in the mine... /s)

I don't think wikipedia is the best reference here, and I think you're also misinterpreting them; not all carbon-containing substances (including diamond) are considered organic. There is no true classical definition of the term- it's actually a fairly nebulous concept. Ultimately you're just arguing about definitions which is not particularly interesting.

CO, CO2, carbonate salts like Na2CO3, or CaCO3, and cyanides like HCN, NaCN, and KCN are usually considered inorganic compounds instead of organic compounds, despite containing carbons. But the vast majority of carbon-containing compounds are considered organic, and there are no organic compounds that don't contain carbon.

> there are no organic compounds that don't contain carbon

It's very much nitpicking and an edge case but now you've got me wondering if some silicone hydrocarbon analogs might not qualify. Noting that we have plausible theories about the feasibility of silicone based life.

> we have plausible theories about the feasibility of silicone based life.

... Do we? Last I heard those weren't really viable due to some combination of being too stable or too unstable in all the available solvents.

Maybe I'm out of date then. They looked plausible when I read about them years ago.

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