A Matter of Sound

 ... is the title (in its print edition) of an article in the January 2022 issue of Physics World, the magazine of the UK Institute of Physics. It appears on the Physics World website under the title Sonifying science: from an amino acid scale to a spider silk symphony.

The notion underlying the article is that vibrations or movements at molecular levels can be represented as sounds and, therefore, in the form of music. And, equally, vice versa - a musical form can be used to predict a structure at a molecular level. The main substance of the article applies this notion to the amino acid structure of the proteins that occur in living things.

...we developed a systematic way of translating a protein’s sequence of amino acids into a musical sequence, using the physical properties of the molecules to determine the sounds (ACS Nano 13 7471). The system translates the 20 types of amino acids (figure 1) into a 20-tone scale. Any protein’s long sequence of amino acids then becomes a sequence of notes. The sounds are transposed in order to bring them within the audible range for humans (20 Hz–20 kHz), without affecting the structural features by following the concept of transpositional equivalence. Indeed, the tones and their relationships are based on the actual vibrational frequencies of each amino acid molecule itself, providing a physical basis for protein sonification.

It is worth listening to the "amino acid scale" embedded in the original online article. It is impressively musical to the ear, though we would not recognise it as a scale in the conventional sense. The musical representation of the Lysozyme enzyme, also embedded in the article, is considerably less pleasing to the ear.

It would be very easy to make more of this idea in philosophical terms than the idea itself really justifies. Nevertheless, it is interesting to reflect on the suggestion that the structure and behaviour of key molecules that make up living things can be understood in a form of music, albeit a form that noticeably differs from our usual understanding to musical form (for example, it being based on a 20-tone scale rather than a 12-tone scale). It suggests an aesthetic form that might be seen in those molecules, and in the life based upon them, something that a classical metaphysics would denote by the term "beauty". Whether or not the specific musical form suggested by the authors of this article proves to withstand the scrutiny over time of scientific peers, there remains the suggestion implied in it that the molecules at the heart of living things are capable of being represented by an aesthetic form.

A couple of further points. Whilst each amino acid in a protein is represented by its own tone, the higher order structure of the protein - its folding and the sequencing of different amino acids in the chain of the protein - are expressed as rhythm and note volume. The musical representation is therefore, in principle, able to express increasing complexity in protein molecules.

The article also refers to work done on different coronaviruses, including the virus causing the current COVID-19 pandemic. We have heard much about the "spike protein" of this virus, and the way in which it binds to a receptor in our human cells, leading to the infection of the cell by the virus and the subsequent reproduction of the virus. 

Previously, researchers looked at biochemical mechanisms when studying how spike proteins, which give coronaviruses their distinct crown-like appearance, interact with human cells. Instead, we used atomistic simulations and AI to study the mechanical aspects of how the spike proteins move, change shape and vibrate.

The authors of the article were able to establish a correlation between how infectious and dangerous a virus might be and two particular features of the vibrational motions of the spike protein molecules in coronaviruses. This offers a potential technique for quickly screening emerging virus variants to assess their potential risks; and the possibility of treating coronaviruses by finding a molecule that will bind on to the spike proteins so that their vibrations are limited or cancelled out altogether.