Complexity

Abstract

Protein segments that contain few of the possible twenty amino acids, sometimes in tandem repeat arrays, are referred to as containing “simple” or “low complexity” sequence. Many proteins of the malaria parasite, P. falciparum, are longer than their homologs in other species by virtue of their content of such low complexity segments that have no known function; these are interspersed among segments of higher complexity to which function can often be ascribed. If there is low complexity at the protein level then there is low complexity at the corresponding nucleic acid level (often seen as a departure from equifrequency of the four bases). Thus, low complexity may have been selected primarily at the nucleic acid level and low complexity at the protein level may be secondary. The amino acids in low complexity segments may be mere placeholders. The amino acid composition of low complexity segments should then be more reflective than that of high complexity segments on forces operating at the nucleic acid level – such as GC-pressure, AG-pressure, AC-pressure, and fold pressure. Consistent with this, for amino acid-determining first and second codon positions, low complexity segments show significant contributions to downward GC-pressure (decreased percentage of G+C) and to upward AG-pressure (increased percentage of A+G). When not countermanded by high contributions to AG-pressure, which locally decrease fold potential, low complexity segments can also contribute to fold potential. Thus they can influence recombination within a gene. Short tandem repeat sequences under AC-pressure violate PR2 and are extruded asymmetrically as stem-loops from DNA duplexes. This may favor specialized forms of somatic recombination, but probably does not affect meiotic pairing of chromosomes. These observations have implications for our understanding of malaria, infectious mononucleosis, and brain diseases in which protein aggregates accumulate.

All perception and all response, all behaviour and all classes of behaviour, all learning and all genetics, all neurophysiology and all endocrinology, all organization and all evolution – one entire subject matter – must be regarded as communicational in nature, and therefore subject to the great generalizations or ‘laws’ which apply to communicational phenomena. We therefore are warned to expect to find in our data those principles of order which fundamental communication theory would propose.

Gregory Bateson (1964) [1]