Individuality, creativity and genetic information:a prelude to gene music
Nobuo Munakata


Metaphor, sequence and information


Metaphors of life and music are abound in many cultures and societies. Perhaps, both in life and music, there are some remains and residues which can not be fully captured and attained through language, and we try to overcome this by metaphors. As an experimental geneticist, I wondered if certain metaphor may be pursued not merely in speculative and transcendental parlance but through playful experimentation. To materialize this, it was encouraging to recognize that there are several common terms used in biology and in music, such as "sequence" and "motif". Sequence in music seems to have originated as melismatic ornamentation of liturgical chants, and expanded to progression patterns in Baroque, and, in the current era of digital music, it refers to the string of MIDI information to realize musical performance with synthesizers. From a simple-minded look, both genes (and the primary products, i.e. DNA, RNA and proteins) and music are made of linear strings of quantum units and thus represented as sequences of information.

Here, we encounter another common term "information" freely used in biological contexts these days. Theory of information defines it as communicative contents from a sender to a receiver. This concept of information is expandable to music theory like analyses of what communicated among composers, performers, and audiences. In passing, I want to mention here that some late 20th century composers like John Cage have done amazingly playful experimentation on moving and removing the boundaries and frames surrounding them (Kostelanetz, 1993). In biology, it seems worthwhile we further extend it to embrace anything physically transferred, transmitted, reproduced, marked, engraved, imprinted, and stored metaphorized as "archi-écriture" (Derrida, 1976). This could envelop both genes and neurons as two systems of the most elaborate ways of transference and storage of information. Though we are not dealing with the latters here, they undoubtedly represent the highest fruits of biological creativity. The origin and development of musical creativity exhibited by most songbirds, many crustaceans and some humans as an interplay of genetic and neuronal information are fascinating subjects of biomusicology and bio-aesthetics.



Individuality of individuals and species

A fundamental concept (except "life" which seems too broad and void in common usage) in biology is "individual". A basic image of life is that an individual is thrown into the surrounding world, "Unwelt" (von Uexüll, 1934), and trying to survive and reproduce. It may be difficult to define individuals in some cases, such as asexual bacteria or some root-growing plants, and its border of inside and outside is often blurred, but this could be left for specialists to argue. Also, though we often set aside individuals and deal with parts (in biochemistry and biophysics) or congregates (in ecology) of individuals in many branches of biology, it is impossible to totally forget about individuals, except perhaps when speculating about totally alien world in astrobiology.

An individual is a concrete and unified substance that occupies definite time and space in the world and its existence is demarcated by the event of birth and death. We may give it a proper name. What makes individuals special and like nothing else, what comprises this-life-ness, is individuality. In this sense, an individual is an ultimate and singular subject in biology and an irreplaceable hero in the world. It has been forcefully argued by Gheselin (1997) that, another major subject in biology, the species, is also endowed with individuality and could be regarded as an individual. A species is also a unified singular existence occupying certain time and space, non-abstract, neither category nor class, and are demarcated by the origin and extinction. Common definition of species, naturally inbreeding populations of organisms (Mendelian population) is sometimes not applicable, again for asexual organisms and others. But even normally asexual organisms may have some means of transmission of genetic materials as evidenced by the wide occurrences of restriction enzymes with various recognition sequences that prevent the invasion by foreign genes. Here again, exact demarcations of each species can be left for specialists. In sum, all organisms are perpetuated and penetrated with the duality of individuality.

The ways the duality of individuality are grounded and sustained depend on genetic information. The assortment of parental chromosomes and faithful reproduction of the genome guarantee the consistency and unity of individuals. Except in special cases, such as immune systems in mammals or somatic mutations leading to tumor, the genomic information is invariable during the lifetime of an organism. On the other hand, the consistency of species through generations of individuals is guaranteed by common gene pools from which particular combinations are chosen to bear the next generations.

In addition to individuals and species, there are several assortments of biological substances such as cells, organs, tissues, families, flocks, herds, schools, ethnics and races. But these are not endowed with the individuality in the primary sense, and any attempt to abuse the concept of biological individuality for rationalization and authorization of ethnic or religious groups, organizations, nations and alliances, should be strongly opposed.

The individuality concept also gives some founding to the bioethics and environmental ethics, here we need to place individuals into the relationships with "the others", but this is clearly an area out of this essay trying to introduce and endorse bio-aesthetics.

Nature of creativity recorded in genetic information

This duality of individuality corresponds to the duality of temporality in the history of life. Individuals go through embryogenesis, development and aging. The molecular mechanisms of development are the most exciting subject in contemporary biology. The genetic studies made with several model organisms have made tremendous advancements, and many once insurmountable problems, starting from emergence of different cell types from the essentially identical genes have been given elegant and convincing answers. Currently, applications of gene arrays are producing pictures of gene expression in detail, though these development gave us another set of problems of how these snap shots of gene activities could be integrated and interpreted. On the other hand, it needs be remembered that development is the faithful repetition of genetic programs termed as "repetitive fabrication" by Coen (1999) with possible interplay with environment and chances, and does not represent the creative process itself. It is also clear that we need various levels of comparisons of the genes defining the developmental processes to have glimpse of creative evolution (Bergson, 1907).

The speciation processes are not clearly known, and probably no unified theory or fixed rules seem to apply, except general patterns like branching-off of new species (Eldredge and Cracraft, 1980). It is also not an easy task to integrate the phylogeny (cladograms) of species and genes. In other words, we have no way to directly observe the creativity at work; the temporality of species is simply too vast in contrast to our temporality of individual life. However, the inference on what might have happened could be glanced by the comparisons of some genes and families in some lineage. Followings are some of the postulated processes underlying the genomic evolution.

(1) Adaptive co-option of existent or duplicated genes. From my specialty, it is likely the plethora of mechanisms of DNA repair, such as spore repair specializing in the repair of solar-UV induced lesion in bacterial spores, are adaptive employment of some existing genes to particular environmental assaults inductive particular types of DNA damage (Nicholson et al., 2000). From another aspect, this is considered as the consolidation of environmental information into genes, or internalization of environment.

(2) Networks or "rhizome" (Deleuze and Guattari, 1980) of cellular responses to signals and stimuli, and cellular differentiation and developmental pathways, are composed of modular elements, genetic toolkits, such as complexes of transcription factors and signal transduction pathways. Small changes in cis-regulatory elements in promoter sequences of some key selector or switch genes could effectively lead the new deployments and modulations in the developmental processes sometimes resulting in the functional and morphological changes and diversification (Carrol et al., 2001).

(3) Expansion and diversification of family genes. The first multicellular organisms of which "complete" genomic sequence was unraveled was a nematode worm, Caenorhabditis elegans. One astonishing findings was the existence of large families of genes, such as nuclear hormone receptor genes. Almost 300 genes have been identified in the family and the majority of which have no phylogenic (orthologic) relationships to those identified in other animals (Sluder et al., 1999). It seemed such lineage specific expansions of family genes are common, and the expansion is accompanied with sufficient diversification warranting the maintenance of large family members.

Above lists are undoubtedly spotty both due to my limited interest and understanding and the early stages of phylogenomics. No general conclusion should be drawn from this sketch. But an emerging impression is that no simple and definite rule or laws could be erected with regard to evolutional creative processes. We may posit such term like "historically contingent tinkering" to describe this. Tinkering based on what you already have (genetic toolkits), but contingent meaning that the tinkerer has no preconception what to make (Jacob, 1977). Only after the drama has been played out to a certain stage, you could look back to see if there was any plot and trod the way it has taken.

Thus, creativity has no definite rule or no all encompassing law regarding organismic structure and function; it is every time already there yet every time new and, divergent out of normalcy despite of faithful trials of repetition, the change without aims. In short, there is no royal road or fixed schedule of creation.

Various associations of genetic information

Now, if we identify and determine the sequence of a gene, we take some routine undertakings in research, such as identifying the start and end of each transcript, splicing patterns, protein coding regions, and promoter sequences, the results of which can be piled into maps and catalogues, and many long and winding stories could be written for each gene in each organism. But beyond this database knowledge, in order to understand the history, phylogeny and biological meanings of the genes, comparative approach may still be the only way to take. Though often brilliantly illuminating, sequence comparisons are rather ambiguous undertakings, only validated by the concept of lineage. Often interesting inferences are made based borderline "gray" similarity, in contrast, perfect conservation or total randomness are less likely to be useful inferring phylogenetic relationships and functional conservation and changes. The logic of "similarity" defies simple, objective and mechanistic logic.

As a corollary to this, we need to take various strategies and different ways to represent and capture the meanings of the sequences. Various ways to depict proteins are known, such as shaded circles, ellipses and polygons, ribbon and sheets, or balls and sticks. To extend visual to aural display may not be farfetched considering the imminent advancement of digital multimedia. Often, I am distracted by cheap and emotional ("soupy and soapy") music played along with videos of genetics in educational media. Considering what we are dealing with are not easy extensions of traditional wisdom, customs or imaginations, easy cliché in the use of music seems disgusting and dangerous.

A pioneer in artificial intelligence, Marvin Minsky (1981) made an encouraging comment for various unorthodox ways of representations and displays, here I consider "a thing or idea" to imply genetic information: "A thing or idea seems meaningful only when we have different ways to represent it -different perspective and different associations". In gene sequences, 40 billion years of history of creative evolution are recorded together with the future potentials of the biosphere and we need to make them meaningful and to learn for our pursuit of creative life.


References:
Richard Kostelanetz (1993) John Cage, Writer: Selected Texts (Cooper Square Press, New York).
Jack Derrida (1967) De la Grammatologie (English translation by G. C. Spivak, The John Hopkins University Press, Baltimore, 1976)
Jakob von Uexkül and Georg Kriszat (1934) Streifzüge durch die Umwelten von Tieren und Menschen Bedeutungslehre (Japanese translation by T. Hidaka and Y. Noda, Shisakusha, Tokyo, 1973).
Michael T. Ghiselin (1997) Metaphysics and the Origin of Species (State University of New York Press, Albany).
Henri Bergson (1907) L'evolution créatrice (English translation by A. Mitchell, Dover Publications, New York, 1998).
Niles Eldredge and Joel Cracraft (1980) Phylogenetic patterns and the evolutionary process (Columbia University Press, New York).
Gilles Deleuze and Félix Guattari (1980) Rhizome, extrait de Mille Plateaux (Japanese translation by K. Toyohashi, Asahi Shuppansha, Tokyo, 1987).
Enrico Coen (1999) The Arts of Genes (Oxford University Press, Oxford).
Wayne L. Nicholson, Nobuo Munakata, Gerda Horneck, Henry J. Melosh and Peter Setlow (2000) Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments. Microbiology and Molecular Biology Reviews 64: 548-572.
Sean B. Carroll, Jennifer K. Grenier and Scott D. Weatherbee (2001) From DNA to Diversity (Blackwell Science, Massachusetts).
Ann E. Sluder, Siuyien Wong Mathews, David Hough, Viravuth P. Yin, and Claude V. Maina (1999) The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. Genome Research 9:103-120.
Francois Jacob (1977) Evolution and tinkering. Science 196:1161-1166.
Marvin Minsky (1981) Music, mind, and meaning. pp. 639-655 in C. Roads (Ed.), The music machine (The MIT Press, Cambridge).

End of essay as 2002/07/12.