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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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IV. Ecosmomics: An Independent, UniVersal, Source Code-Script of Generative Complex Network Systems

2. The Innate Affinity of Genomes, Protenomes and Language

Jolma, Arttu, et al. DNA-dependent Formation of Transcription Factor Pairs Alters Their Binding Specificity. Nature. 527/384, 2015. A Karolinska Institute, Sweden group and colleagues, led by Jussi Talpale, report a unique parsing of nucleotide genetics by treating them much as a linguistic script. The achievement was noted in a Science Daily item for November 15, 2015 (Google SD and article keywords) entitled Complex Grammar of the Genomic Language. A gene regulatory code is thus composed by “DNA words,” which can be seen to combine and compound just as lexicons and sentences.

Kay, Lily. A Book of Life?: How the Genome Became an Information System and DNA a Language. Perspectives in Biology and Medicine. 41/4, 1998. The late philosopher of science discerns intrinsic congruities between the verbal and genetic codes.

Kay, Lily. Who Wrote the Book of Life? Stanford, CA: Stanford University Press, 2000. A premier history of science study of how a linguistic metaphor came to represent the genetic code. The author goes on to note a correspondence between molecular genetics, language and the Chinese divination system, the I Ching.

As with (linguist Roman) Jakobson, the answer was affirmative (to the question of one basic code) and pointed to a universe fundamentally different from that portrayed in Jacques Monod’s Chance and Necessity. Rather than viewing DNA-based life as a product of chance, it would be chance subject to the structures and patterns of the I Ching. And rather than being a gypsy living on the edge of an alien world, as Monod decried, a human being would enjoy a deep sense of security that emerged from being planted physically and spiritually in an internal natural order. (318)

Lackova, Ludmila, et al. Arbitrariness is not Enough: Towards a Functional Approach to the Genetic Code. Theory in Biosciences. Online May, 2017. Palacky University, Olomouc, Czech Republic linguists Lackova, Vladimir Matlach, and Dan Faltynek build a case for a semiotic definition of genomic conveyance. By this view, similar to written and oral communications, nucleotides and proteins are all about signs, symbols, interpretation and transcription. Apropos, from our home page a slide presentation, Cosmic Genesis in the 21st Century, that I gave at Palacky University in 2005 can be accessed.

Arbitrariness in the genetic code is one of the main reasons for a linguistic approach to molecular biology: the genetic code is usually understood as an arbitrary relation between amino acids and nucleobases. However, from a semiotic point of view, arbitrariness should not be the only condition for definition of a code, consequently it is not completely correct to talk about “code” in this case. Semiotically, a code should be always associated with a function and we propose to define the genetic code not only relationally (in basis of relation between nucleobases and amino acids) but also in terms of function (function of a protein as meaning of the code). In fact, if the function of a protein represents the meaning of the genetic code (the sign’s object), then it is crucial to reconsider the notion of its expression (the sign) as well. In our contribution, we will show that the actual model of the genetic code is not the only possible and we will propose a more appropriate model from a semiotic point of view. (Abstract)

Lackova, Ludmilla. Folding of a Peptide Continuum: Semiotic Approach to Protein Folding. Semiotica. 233/77, 2020. The Palacky University, Olomouc, CR linguist continues her studies of innate affinities across genetic, metabolic and onto communicative codes, which each seem to have a common textual nature. What then might be their phenomenal message as we first grade readers try to interpret, translate and understand?

In this paper I attempt to study the notion of “folding of a semiotic continuum” in a direction of a possible application to the biological processes (protein folding). The process of obtaining protein structures is compared to the folding of a semiotic continuum. Consequently, peptide chain is presented as a continuous line potential to be formed (folded) in order to create functional units. The functional units are protein structures having a certain usage in the cell or organism (semiotic agents). Moreover, protein folding is analyzed in terms of tension between syntax and semantics. (Abstract)

Lee, Ji-Hoon, et al. A DNA Assembly Model of Sentence Generation. BioSystems. Online, June, 2011. Seoul National University, Kyungpook National University, and University of Arkansas, bioinformatic scientists add to the evidence that these widely separated generative sources of life and culture share deep affinities with regard to their grammatical structures. Since the inklings of Roman Jakobson and Jean Piaget in the 1970s and earlier that genome and “languagome” (just coined) are deeply similar, this emergent evolutionary correspondence has been steadily proven, which this whole section seeks to document.

Recent results of corpus-based linguistics demonstrate that context-appropriate sentences can be generated by a stochastic constraint satisfaction process. Exploiting the similarity of constraint satisfaction and DNA self-assembly, we explore a DNA assembly model of sentence generation. The words and phrases in a language corpus are encoded as DNA molecules to build a language model of the corpus. Given a seed word, the new sentences are constructed by a parallel DNA assembly process based on the probability distribution of the word and phrase molecules. Here, we present our DNA code word design and report on successful demonstration of their feasibility in wet DNA experiments of a small scale. (Abstract)

Li, Zhi, et al. Extracting DNA Words Based on the Sequence Features. Theoretical Biology and Medical Modelling. 13/2, 2016. Shanxi Medical University, Taiyuan, China researchers carry out a formal interpretation of genetic systems by way of linguistic and textual terms. Nucleotide strings appear as a language with words, sentences, vocabularies, so that genomes are akin to a written book. This deep correspondence is braced by a novel algorithm that traces salient aspects of non-uniform distributions and integrity. Its validity is checked by applying to a select English volume, The Holy Bible (see quotes). How fortuitous, for here is evidence of a direct relation between religious scripture and a naturome code, God’s word and works.

Shanxi Medical University, Taiyuan, China researchers carry out a formal interpretation of genetic systems by way of linguistic and textual terms. Nucleotide strings appear as a language with words, sentences, vocabularies, so that genomes are akin to a written book. This deep correspondence is braced by a novel algorithm that traces salient aspects of non-uniform distributions and integrity. Its validity is checked by applying to a select English volume, The Holy Bible (see quotes). How fortuitous, for here is evidence of a direct relation between religious scripture and a naturome code, God’s word and works.

List, Johann-Mattis, et al. Networks of Lexical Borrowing and Lateral Gene Transfer in Language and Genome Evolution. BioEssays. Online December, 2013. From our late vantage, Philipps-University Marburg, Heinrich-Heine University Düsseldorf, linguists and biologists achieve a keen observation about the historical study and affinity of these disparate programs. The course of linguistics has mostly been reconstructed in terms of vertical “trees,” which is also how eukaryote cellular life proceeds. But language history is actually seen to take horizontal, net-like pathways through sharings, akin to how microbial prokaryotes trade genetic materials. So a further, novel correspondence can be elucidated between genome and languagome. See also in BioEssays 36/1, 2014 Horizontal Gene Acquisitions by Eukaryotes as Drivers of Adaptive Evolution by Gerald Schonknecht, et al, whence such parallel traffic occurs for these nucleated cells.

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution. (List Abstract)

In contrast to vertical gene transfer from parent to offspring, horizontal (or lateral) gene transfer moves genetic information between different species. Bacteria and archaea often adapt through horizontal gene transfer. Recent analyses indicate that eukaryotic genomes, too, have acquired numerous genes via horizontal transfer from prokaryotes and other lineages. Based on this we raise the hypothesis that horizontally acquired genes may have contributed more to adaptive evolution of eukaryotes than previously assumed. Current candidate sets of horizontally acquired eukaryotic genes may just be the tip of an iceberg. We have recently shown that adaptation of the thermoacidophilic red alga Galdieria sulphuraria to its hot, acid, toxic-metal laden, volcanic environment was facilitated by the acquisition of numerous genes from extremophile bacteria and archaea. Other recently published examples of horizontal acquisitions involved in adaptation include ice-binding proteins in marine algae, enzymes for carotenoid biosynthesis in aphids, and genes involved in fungal metabolism. (Schonknecht Abstract)

List, Johann-Mattis, et al. Unity and Disunity in Evolutionary Sciences: Process-Based Analogies Open Common Research Avenues for Biology and Linguistics. Biology Direct. Online August, 2016. University of Pierre and Marie Curie, Paris theorists including Eric Bapteste survey the long together and apart interplay between genetics and languages. While parallels seem innately evident, their actual discernment has proven elusive until these late days of algorithmic network complexities. As this section reports, a cross-fertilization of analytic techniques such as homolog identification, sequence alignment, and protein literacy is much underway. And may we again report that from cosmic and galactic webs to neural net connectomics, from uniVerse to human epitome, the one, same iconic scriptome recurs and informs in kind.

We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift). (Results)

Livnat, Adi. Simplification, Innateness, and the Absorption of Meaning from Context. arXiv:1605.03440. Reviewed more in Systems Evolution, the University of Haifa theorist continues his project (search) to achieve a better explanation of life’s evolution by way of algorithmic computations, innate network propensities, genome – language affinities, neural net deep learning, and more.

Markos, Anton and Dan Faltynek. Language Metaphors of Life. Biosemiotics. Online August 14, 2010. Charles University (Prague) scientist, and Palacky University (Olomouc, Czech Republic, where I once gave a keynote, see home page) philosopher argue that not only is communication the essence of livingness, it involves constant “readings” by all manner of creatures. Verily a greater, textual nature is revealed that evolved, emergent beings, now we phenomenal humans, are invited to read.

We believe that linguistic processes are present at all levels of life’s organization in the biosphere. Ecosystems, for example, do not build their homes – oikos – for ever; they maintain them by incessant communications games, reading included. We tend to read like our contemporaries, and from this common ground there often emerges something new unique; understanding the text is a unique performance of the reader. The same holds, we believe, for the members of any living species – in a species-specific way.

Moghaddasi, Hanieh, et al. Distinguishing Functional DNA Words. Nature Scientific Reports. 7/41543, 2017. With Khosrow Khalifeh and Amir Darooneh (search), University of Zanjan, Iran biophysicists discuss similar algorithmic ways to parse genetic and written textualities, whence both are seen as an extension of statistical mechanics and Tsallis entropy. In an evolutionary perspective such archetypal, generative inscriptions strongly imply a common, exemplary source. OK

Functional DNA sub-sequences and genome elements are spatially clustered through the genome just as keywords in literary texts. Therefore, some of the methods for ranking words in texts can also be used to compare different DNA sub-sequences. In analogy with the literary texts, here we claim that the distribution of distances between the successive sub-sequences (words) is q-exponential which is the distribution function in non-extensive statistical mechanics. (Abstract)

DNA sequences as one-dimensional arrays of four nucleotides (A, C, T and G) can be considered as texts so that they can be analyzed from a linguistic point of view to discover their different linguistic features. It is believed that there is a meaningful relation between linguistic interpretation of sub-sequences and their biological significances. Here, the important matter is how to define the alphabets and words, for example nucleotides may be assumed as letters and sequences of n consecutive nucleuotides (n-tuples) as words. Some genome elements like exons, introns and others can also play the role of words. (1)

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