Related papers: Expanding the Grammar of Biology
Chargaff once said that "I saw before me in dark contours the beginning of a grammar of Biology". In linguistics, "grammar" is the set of natural language rules, but we do not know for sure what Chargaff meant by "grammar" of Biology.…
The importance of statistical patterns of language has been debated over decades. Although Zipf's law is perhaps the most popular case, recently, Menzerath's law has begun to be involved. Menzerath's law manifests in language, music and…
Parametric approaches to grammatical diversity range from Chomsky's 1981 classical Principles & Parameters model to minimalist reinterpretations: in some proposals of the latter framework, parameters need not be an extensional list given at…
Yuri Manin's approach to Zipf's law (Kolmogorov complexity as energy) is applied to investigation of biological evolution. Model of constructive statistical mechanics where complexity is a contribution to energy is proposed to model…
This paper presents the study of a DNA replication model grounded in the biochemical kinetics of DNA polymerases, which copy each DNA strand into a complementary strand, except for rare point-like mutations caused by nucleotide substitution…
The central dogma of molecular biology, formulated more than five decades ago, compartmentalized information exchange in the cell into the DNA, RNA and protein domains. This formalization has served as an implicit thematic distinguisher for…
Chargaff's second parity rule for short oligonucleotides states that the frequency of any short nucleotide sequence on a strand is approximately equal to the frequency of its reverse complement on the same strand. Recent studies have shown…
The article represents a new class of hidden symmetries in long sequences of oligonucleotides of single stranded DNA from their representative set. These symmetries are an addition to symmetries described by the second parity rule of…
The application of Genetic Programming to the discovery of empirical laws is often impaired by the huge size of the search space, and consequently by the computer resources needed. In many cases, the extreme demand for memory and CPU is due…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
The ambitious and ultimate research purpose in Systems Biology is the understanding and modelling of the cell's system. Although a vast number of models have been developed in order to extract biological knowledge from complex systems…
Despite widespread calls for the incorporation of mathematical modeling into the undergraduate biology curriculum, there is lack of a common understanding around the definition of modeling, which inhibits progress. In this paper, we extend…
Research in quantitative evolutionary genomics and systems biology led to the discovery of several universal regularities connecting genomic and molecular phenomic variables. These universals include the log-normal distribution of the…
The frequency distributions of DNA k-mers are shaped by fundamental biological processes and offer a window into genome structure and evolution. Inspired by analogies to natural language, prior studies have attempted to model genomic k-mer…
It is often stated that there are no laws in biology, where everything is contingent and could have been otherwise, being solely the result of historical accidents. Furthermore, the customary introduction of fundamental biological entities…
Linguistic laws, the common statistical patterns of human language, have been investigated by quantitative linguists for nearly a century. Recently, biologists from a range of disciplines have started to explore the prevalence of these laws…
A three-dimensional model of the genetic vocabulary is proposed in terms of determinative degree, an introduced characteristic of nucleotide, which reflects absolute difference between purin and pyrimidin bases in one DNA strand. In the…
In 1987, Yomdin proved a lemma on smooth parametrizations of semialgebraic sets as part of his solution of Shub's entropy conjecture for $C^\infty$ maps. The statement was further refined by Gromov, producing what is now known as the…
Motivated by the concept of degeneracy in biology (Edelman, Gally 2001), we establish a first connection between the Multiplicity Principle (Ehresmann, Vanbremeersch 2007) and mathematical statistics. Specifically, we exhibit two families…
A symmetry is a `change without change'. As simple as it sounds, this concept is the fundamental cornerstone that unifies all branches of theoretical physics. Virtually all physical laws -- ranging from classical mechanics and…