Related papers: Origin and evolution of the genetic code: The univ…
The pace of progress in the fields of Evolutionary Computation and Machine Learning is currently limited -- in the former field, by the improbability of making advantageous extensions to evolutionary algorithms when their capacity for…
Based on statistical analysis of the complete genome sequences, a remote relationship has been observed between the evolution of the genetic code and the three domain tree of life. The existence of such a remote relationship need to be…
In the crystal basis model of the genetic code, it is deduced that the sum of usage probabilities of the codons with C and A in the third position for the quartets and/or sextets is independent of the biological species for vertebrates. A…
Much evolutionary information is stored in the fluctuations of protein length distributions. The genome size and non-coding DNA content can be calculated based only on the protein length distributions. So there is intrinsic relationship…
The origin of diversification and coexistence of genes and species have been traditionally studied in isolated biological levels. Ecological and evolutionary views have focused on the mechanisms that enable or constrain species coexistence,…
I consider the many ways in which evolved information-flows are restricted and metabolic resources protected and hidden -- the thesis of living phenomena as evolutionary cryptosystems. I present the information theory of secrecy systems and…
Code evolution is a family of techniques that rely on large language models to search through possible computer programs by evolving or mutating existing code. Many proposed code evolution pipelines show impressive performance but are often…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
Information theoretic analysis of large evolved programs produced by running genetic programming for up to a million generations has shown even functions as smooth and well behaved as floating point addition and multiplication loose entropy…
The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of…
Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly…
The dynamics of adaptation is difficult to predict because it is highly stochastic even in large populations. The uncertainty emerges from number fluctuations, called genetic drift, arising in the small number of particularly fit…
Biological evolution provides a creative fount of complex and subtle adaptations, often surprising the scientists who discover them. However, because evolution is an algorithmic process that transcends the substrate in which it occurs,…
The standard model of particle physics contains N_gen=3 generations of quarks and leptons, i.e., two sets of three particles in each sector, with the two sets differing by 1 unit of charge in each. All 12 "predicted" particles are now…
The problem of compression in standard information theory consists of assigning codes as short as possible to numbers. Here we consider the problem of optimal coding -- under an arbitrary coding scheme -- and show that it predicts Zipf's…
The digital transformation of automation places new demands on data acquisition and processing in industrial processes. Logical relationships between acquired data and cyclic process sequences must be correctly interpreted and evaluated. To…
The development of a large non-coding fraction in eukaryotic DNA and the phenomenon of the code-bloat in the field of evolutionary computations show a striking similarity. This seems to suggest that (in the presence of mechanisms of code…
The premise of genetic analysis is that a causal link exists between phenotypic and allelic variation. Yet it has long been documented that mutant phenotypes are not a simple result of a single DNA lesion, but rather are due to interactions…
Many biological phenomena or social events critically depend on how information evolves in complex networks. However, a general theory to characterize information evolution is yet absent. Consequently, numerous unknowns remain about the…