Skip to content →

Author: lievenlb

The symmetries of Covid-19

A natural question these days might be: “what are the rotational symmetries of the Covid-19 virus?”



Most illustrations show a highly symmetric object, suggesting it might have icosahedral symmetry. In fact, many viruses do have icosahedral symmetry as a result of the ‘genetic economy principle’ proposed by Watson and Crick in 1956, resulting in the Caspar-Klug classification of viral capsids.

But then, perhaps this icosahedral illusion is a result of design decisions illustrators made turning scientific data into pictures. Veronica Falconieri Hays wrote a beautiful article describing the effort going into this: How I built a 3d-model of the coronavirus for Scientific American. Here’s her final picture



And yes, icosahedral symmetry was one of her design decisions:

The M proteins form pairs, and it is estimated that there are 16–25 M proteins per spike on the surface of the virus. I ended up modeling 10 M protein pairs (so 20 M proteins) per spike in my model. Some researchers hypothesize that the M proteins form a lattice within the envelope (interacting with an underlying lattice of N proteins; see below). I decided to use an icosahedral sphere to create a regular distribution of the M protein dimers to hint at this hypothesis.

The spikes (or S-proteins) are the tentacles in these pictures, and one of the few hard figures on Corona is that ‘on average’ there are 74 of them.

This fact is enough to rule out icosahedral symmetry.

If the icosahedral rotation group (of order $60$, isomorphic to $A_5$) acts on the $74$ spikes, then each orbit consists of $60$ spikes unless that spike lies on a twofold, threefold or fivefold rotation axis, in which cases the number of spikes in its orbit are respectively $30$, $20$ or $12$. So, we can’t get a total number of $74$ spikes!

However, just looking at the number of spikes we cannot rule out octahedral symmetry!

The octahedral rotation group (of order $24$, isomorphic to $S_4$) will have orbits of size $24$ unless the spike lies on a twofold, threefold or fourfold rotation axis, giving orbits of size $12$, $8$ and $6$ respectively (the midpoints of edges, the vertices and the midpoints of faces of the octahedron), and

\[
74 = 24+24+12+8+6 \]

The most symmetric arrangement of spikes would be to subdivide each of the $8$ triangular faces of the octahedron into $6$ triangles with vertices the midpoint of the face, a vertex and a midpoint of an edge, and then to position the spikes on the axis through the vertices and midpoints of these smaller triangles.

Googling around I found very few references to symmetries of Covid-19, probably because it has an helical RNA-coil, which seems not to go well with Caspar-Klug type polyhedral viral capsids.

Here’s an exception: A structural model for the Coronavirus nucleocapsid by Federico Coscio, Alejandro D. Nadra, and Diego U. Ferreiro.



They propose a truncated octahedron as capsid (in transparent brown) with interior a continuous coil packing of blue and cyan helices. The virus membrane with the spikes and M proteins is drawn in blue.

If you have better info or references on the (conjectural) symmetries of Covid-19, please leave a comment.

One Comment

Richard Borcherds on Witt and the Leech lattice

A rare benefit of the Covid-situation is that Richard Borcherds decided to set up a YouTube channel with recordings of his online lectures.

Plenty of gems to be discovered there, including a talk on Monstrous Moonshine, and a talk he gave for the Archimedeans about the Sporadic Groups.

As part of his History of Science-course he addressed the question whether Witt discovered the Leech lattice.

A while ago I’ve blogged about that very same question here:

The summary of these posts being that I thought it was rather unlikely for Witt to have discovered the Leech lattice.

However, using the same sources, Borcherds rates a more than 90% probability for Witt to have indeed discovered the Leech lattice in 1940.

His evidence for this is:

  • Witt said he discovered it.
  • His construction (in his 1972 colloquium talk) is unlike any other construction of the Leech lattice.
  • Witt was the expert on Steiner systems, and the system S(5,8,24) is crucial in Leech’s construction of his lattice.

Leave a Comment

Sylvester’s synthemes

I was running a bachelor course on representations of finite groups and a master course on simple (mainly sporadic) groups until Corona closed us down. Perhaps these blog-posts can be useful to some.

A curious fact, with ripple effect on Mathieu sporadic groups, is that the symmetric group $S_6$ has an automorphism $\phi$, different from an automorphism by conjugation.

In the course notes the standard approach was given, based on the $5$-Sylow subgroups of $S_5$.

Here’s the idea. Let $S_6$ act by permuting $6$ elements and consider the subgroup $S_5$ fixing say $6$. If such an odd automorphism $\phi$ would exist, then the subgroup $\phi(S_5)$ cannot fix one of the six elements (for then it would be conjugated to $S_5$), so it must act transitively on the six elements.

The alternating group $A_5$ is the rotation symmetry group of the icosahedron



Any $5$-Sylow subgroup of $A_5$ is the cyclic group $C_5$ generated by a rotation among one of the six body-diagonals of the icosahedron. As $A_5$ is normal in $S_5$, also $S_5$ has six $5$-Sylows.

More lowbrow, such a subgroup is generated by a permutation of the form $(1,2,a,b,c)$, of which there are six. Good old Sylow tells us that these $5$-Sylow subgroups are conjugated, giving a monomorphism
\[
S_5 \rightarrow Sym(\{ 5-Sylows \})\simeq S_6 \]
and its image $H$ is a subgroup of $S_6$ of index $6$ (and isomorphic to $S_5$) which acts transitively on six elements.

Left multiplication gives an action of $S_6$ on the six cosets $S_6/H =\{ \sigma H~:~\sigma \in S_6 \}$, that is a groupmorphism
\[
\phi : S_6 \rightarrow Sym(\{ \sigma H \}) = S_6 \]
which is our odd automorphism (actually it is even, of order two). A calculation shows that $\phi$ sends permutations of cycle shape $2.1^4$ to shape $2^3$, so can’t be given by conjugation (which preserves cycle shapes).

An alternative approach is given by Noah Snyder in an old post at the Secret Blogging Seminar.

Here, we like to identify the six points $\{ a,b,c,d,e,f \}$ with the six points $\{ 0,1,2,3,4,\infty \}$ of the projective line $\mathbb{P}^1(\mathbb{F}_5)$ over the finite field $\mathbb{F}_5$.

There are $6!$ different ways to do this set-theoretically, but lots of them are the same up to an automorphism of $\mathbb{P}^1(\mathbb{F}_5)$, that is an element of $PGL_2(\mathbb{F}_5)$ acting via Mobius transformations on $\mathbb{P}^1(\mathbb{F}_5)$.

$PGL_2(\mathbb{F}_5)$ acts $3$-transitively on $\mathbb{P}^1(\mathbb{F}_5)$ so we can fix three elements in each class, say $a=0,b=1$ and $f=\infty$, leaving six different ways to label the points of the projective line
\[
\begin{array}{c|cccccc}
& a & b & c & d & e & f \\
\hline
1 & 0 & 1 & 2 & 3 & 4 & \infty \\
2 & 0 & 1 & 2 & 4 & 3 & \infty \\
3 & 0 & 1 & 3 & 2 & 4 & \infty \\
4 & 0 & 1 & 3 & 4 & 2 & \infty \\
5 & 0 & 1 & 4 & 2 & 3 & \infty \\
6 & 0 & 1 & 4 & 3 & 2 & \infty
\end{array}
\]
A permutation of the six elements $\{ a,b,c,d,e,f \}$ will result in a permutation of the six classes of $\mathbb{P}^1(\mathbb{F}_5)$-labelings giving the odd automorphism
\[
\phi : S_6 = Sym(\{ a,b,c,d,e,f \}) \rightarrow Sym(\{ 1,2,3,4,5,6 \}) = S_6 \]
An example: the involution $(a,b)$ swaps the points $0$ and $1$ in $\mathbb{P}^1(\mathbb{F}_5)$, which can be corrected via the Mobius-automorphism $t \mapsto 1-t$. But this automorphism has an effect on the remaining points
\[
2 \leftrightarrow 4 \qquad 3 \leftrightarrow 3 \qquad \infty \leftrightarrow \infty \]
So the six different $\mathbb{P}^1(\mathbb{F}_5)$ labelings are permuted as
\[
\phi((a,b))=(1,6)(2,5)(3,4) \]
showing (again) that $\phi$ is not a conjugation-automorphism.

Yet another, and in fact the original, approach by James Sylvester uses the strange terminology of duads, synthemes and synthematic totals.

  • A duad is a $2$-element subset of $\{ 1,2,3,4,5,6 \}$ (there are $15$ of them).
  • A syntheme is a partition of $\{ 1,2,3,4,5,6 \}$ into three duads (there are $15$ of them).
  • A (synthematic) total is a partition of the $15$ duads into $5$ synthemes, and they are harder to count.

There’s a nice blog-post by Peter Cameron on this, as well as his paper From $M_{12}$ to $M_{24}$ (after Graham Higman). As my master-students have to work their own way through this paper I will not spoil their fun in trying to deduce that

  • Two totals have exactly one syntheme in common, so synthemes are ‘duads of totals’.
  • Three synthemes lying in disjoint pairs of totals must consist of synthemes containing a fixed duad, so duads are ‘synthemes of totals’.
  • Duads come from disjoint synthemes of totals in this way if and only if they share a point, so points are ‘totals of totals’

My hint to the students was “Google for John Baez+six”, hoping they’ll discover Baez’ marvellous post Some thoughts on the number $6$, and in particular, the image (due to Greg Egan) in that post



which makes everything visually clear.

The duads are the $15$ red vertices, the synthemes the $15$ blue vertices, connected by edges when a duad is contained in a syntheme. One obtains the Tutte-Coxeter graph.

The $6$ concentric rings around the picture are the $6$ synthematic totals. A band of color appears in one of these rings near some syntheme if that syntheme is part of that synthematic total.

If $\{ t_1,t_2,t_3,t_4,t_5,t_6 \}$ are the six totals, then any permutation $\sigma$ of $\{ 1,2,3,4,5,6 \}$ induces a permutation $\phi(\sigma)$ of the totals, giving the odd automorphism
\[
\phi : S_6 = Sym(\{ 1,2,3,4,5,6 \}) \rightarrow Sym(\{ t_1,t_2,t_3,t_4,t_5,t_6 \}) = S_6 \]

Leave a Comment