Contemporary organisms commonly use the genetically encoded 20 amino acids to synthesize proteins. However, earlier protein synthesis was plausibly much simpler and utilized a subset of the standard proteinogenic amino acids. We reconstructed ancestral nucleoside diphosphate kinases (NDKs) by combining the computational inference of ancestral sequence and a whole gene synthesis technique. One of the reconstructed NDKs, Arc1, is an extremely thermally stable protein with the unfolding midpoint temperature of 114℃ and the magnitude of its specific activity is comparable with those of extant NDK. Arc1 lacks cysteine and therefore consists of 19 amino acid letters. To address simpler constituents for primitive proteins, we comprehensively reduce the size of the amino acid alphabet in Arc1 to reduced sets. We found that many but not all of the reduced-set amino acids were consistent with those plausibly abundant in primitive environment. We also found that the remaining inconsistent amino acids were important for activity but not for stability. Our results are compatible with the hypothesis that amino acids available in the prebiotic environment were first used for creating stable protein structures and their functions were later improved by recruiting other amino acids.
“It from Biobit” is an adaptation of “It from Qubit” which is the title of a running international research project on quantum fields (including condensed-matter physics), quantum gravity and quantum information, supported by Simons Foundation. The latter is also an adaptation of J.A.Wheeler’s “It from bit” (1990). “It” refers to everything physical (and everything biological and cultural in our case).
Evolutionary molecular engineering has provided various tools to explore the functionality of the possible world in biopolymer sequence spaces. It also has provided the evolvability view point of life, regarding the origins of life as the emergence of “encoded digital information” in our Universe. Because this encoded digital nature was based on the specific interaction between biomolecules, it did not reach the level of the ideal symbol (bit) manipulation. We would like to call this biomolecular information processing the “Biobit” manipulation. The Biobit molecular information network, however, invented homo sapience and the bit manipulation (including language, logic, math…) and then invented the concept of Qubit, through the biological and cultural evolution.
“It from Qubit” project inspired us the evolution of matter (quantum many-particle system, e.g. molecule) may be called as Qubit evolution, that is, complexity of an evolved molecule may be measured by the entanglement entropy in the molecule. Adenine has a greater Qubit (more entangled) than hydrogen molecule. Specific interaction of complementary bases thus evolved was a basis of Biobit manipulation in the RNA world. A Biobit code is largely physicochemically related to its meaning (structure and function), in contrast to an arbitrary correspondence in the conventional bit code. In this article we discuss informational evolution of our Universe in three stages, Qubit/Biobit/bit evolution, laying emphasis on the emergence of Biobit.