DC (3/20/98)- A Texas researcher has tuned in to music to describe
the structure of proteins and genes. She hopes the new approach may ease
the task of teaching the complexities of cellular biology.
"Over a decade ago, I heard a colleague on the music faculty talk about
composing. As he discussed how he went about selecting, modifying, and
organizing musical themes, I was struck by the parallels between musical
structure and the structure of proteins and the genes that encode them,"
said biologist Mary Anne Clark at Texas Wesleyan University in Fort Worth,
View: 3-D representation
of Bovine gamma crystallin protein
a musical representation of same midi file
She eventually linked up with computer music pioneer John Dunn at
Algorithmic Arts who had created a computer
program that transformed protein sequences into music. The two worked together
to refine the "sonification of proteins" into more sophisticated music
than earlier efforts had produced. Clark took into account higher-level
structural features of proteins, such as regions of helix formation and
other folding patterns. This added additional depth to the music.
The two were united in the goals of conveying something not only about
the primary amino acid sequence and the folding patterns of proteins but
also making audible the esthetic patterning of nature's deep structure.
The result is a sonic playback of protein structures disguised as a CD
of "art music."
This novel approach can help demonstrate the relationship between similar
structures in different organisms. For example, the music of the human
protein hemoglobin and that of the globin in a tuatara, an exotic three-eyed
lizard, are recognizably variations on a theme, she notes. Although the
similarities between the two sequences can be seen in their written records,
they are more impressive when heard. Clark uses amino acid solubilities
to assign pitches to specific amino acids in the sequences, so that even
when the absolute sequences vary, strings of adjacent amino acids that
have the same solubility relationships will produce similar musical phrases.
"The tuatara would seem to have little in common with humans," Clark
says, "but the similarities indicate that both proteins are variations
on a theme that was in existence before the divergence of the mammalian
and reptile lineages 200 million years ago. Other variations of beta-globin
can be found in Australian ghost bats, Brazilian tapirs, Kenyan clawed
frogs, Antarctic dragon fish, and Emperor penguins. Although the beta-globin
sequences aren't identical, they all would be recognizable as variations
on a theme if converted to music."
Clark hopes the audio CD she and Dunn are producing will be a valuable
teaching tool for students studying genetics or protein chemistry.
"I love to walk into the music building, which on my campus is next
door to the science building. Through the doors of the practice rooms,
I can hear fragments of 1000 years of written music, played or sung by
the current generation of music students, some with finesse, some with
hesitation, some with wild improvisation. I think that if somehow I could
walk into a living cell, I would hear something similar - the ribosomes
ticking away at the synthesis of proteins, playing out their amino acid
sequences, note by note, according to a genetic score that is reproduced
sometimes with utter fidelity, sometimes with a few unscheduled substitutions,
and sometimes with stunningly inventive flourishes. Every generation of
cells in every living organism plays the genetic score of its species.
However, while the history of music as we know it goes back some 1000 years,
the history of genetic music is at least 3.8 billion years in the making,"
UC Santa Cruz biologist David Deamer is a pioneer in the creative use
of DNA patterns to synthesize music. His system uses raw data derived from
the light absorption spectra of the four bases (adenine, cytosine, thymine,
guanine) that make up the DNA molecule is converted into sonic frequencies.
These are programmed and sent to a synthesizer, and then arranged into
four pitch collections (or four 'scales' based on the individual base molecules).