We address semiotic features of genetic coding, primarily the mechanisms for distinguishing between triplets. It implies that the minimal elements that allow codon recognition and amino acid coding should be identified. Half a century ago, linguist Roman Jakobson and microbiologist François Jacob revealed functional similarities between nucleotides in the genetic code and phonemes in natural language. Developing this analogy, we introduce the concept of a semiotic nucleotide. Unlike “material” nucleotides, its characteristics are limited to the function of differentiation within the processing of genetic information.

We demonstrate that, similarly to phonemes, nucleotides are also non-elementary entities and can be repre- sented as a set of two differential features: a) the number of rings and b) the number of hydrogen bonds. This makes it possible to convert semiotic nucleotides into double-byte units of digital information. Proceeding from this assumption, we suggest a new vision of such phenomena as the heterogeneity of the genetic code in terms of coding types, to reveal the code-distinguishing potential of positions within triplets, and represent wobbling as a specific reading regime. All these phenomena relate to the peculiarity of the triplet’s third position, where complete or partial neutralization of distinguishing features is possible.

The article introduces the concept of the logonomic sign as an elaboration on Hodge and Kress’s promising yet under-examined ideas about logonomic systems. Logonomic signs are defined as socially devised signs that constrain multimodal semiosis by restricting who is able to produce what signs under what circumstances. Based on the Peircean categories, the functioning of logonomic signs is modeled as a three-phase process of (1) logonomic understanding (production of the meaning that is the Initial Interpretant of a logonomic sign), (2) logonomic actualization (production of the actual semiotic event that is the Dynamical Interpretant of a logonomic sign), and (3) logonomic reproduction ([re]production of the semiotic Habit that is the Final Interpretant of a logonomic sign). Based on Kull’s theory of evolution of semiotic systems, logonomic signs are theorized as mechanisms of retention and standardization of semiotic Habits. The mechanism of reproduction of logonomic signs is modeled as a sign in which past logonomic semioses function as Objects by being iconically represented by similar current logonomic semioses functioning as Representamens, and in which future logonomic semioses are produced as Interpretants. The methodological potential of the proposed concept is discussed in the context of the integrative transdisciplinary capacity of semiotics in social research.

В статье рассматриваются различные варианты институционального строительства имперских структур, так или иначе отождествляемых с классической империей Рима. Обзор охватывает собственно римскую традицию и формирование последовательных версий имперско-республиканского комплекса. Различаются два способа использования институциональных структур: прямое и непосредственное наследование с преимущественно вертикальным переносом свойств и опосредованное восприятие с преимущественно горизонтальным переносом.

Рассматривается продолжение модифицированного существования римской традиции в виде теократической симфонии Царствия ромеев (Βασιλεία Ῥωμαίων) в Восточном Средиземноморье и хризалиды (теократии с феодализованной горизонталью и иерархической вертикалью) Христианской республики (Respublica Christiana) в Западной Европе. Отмечаются три попытки восстановить полноту имперской структуры еще в рамках западноевропейской хризалиды: удачную Карла Великого, не вполне удачную в виде Священной Римской империи и совсем неудачные усилия Плантагенетов заложить империю на западе Христианской республики в ходе Столетней войны.

Разбираются дальнейшие варианты уже опосредованного воспроизводства классических римских порядков в Соединенном Королевстве, а затем в США, а также в Первой Французской империи. Затрагиваются и другие ориентированные на римское наследие имперские проекты. Обсуждается опыт европейской интеграции и использование ЕС республиканских и имперских аспектов римского комплекса, использование институциональных образцов Христианской республики и Каролингской империи. Особое внимание уделяется имперской составляющей отечественной политической традиции. Показано, что во всех рассматриваемых случаях имперская компонента сочетается с иными порядками – от патримониальных и монархических до современных (корпоративных, консоциативных, федеративных и т.п.). Использование римского наследия осуществляется в виде прямого воспроизводства, опосредованной реставрации, частичного копирования, имитации и даже симуляции.

Evolutionary computation (EC) is an evidence of the successful implementation of principles of living organism functioning into computer science. Nowadays, it is getting more and more clear that the reverse transfer of computational results to synthetic biology is very promising in increasing the effectiveness of existing and development of new experimental techniques. We consider specific experimental situation of evolutionary search for a multi-domain macromolecule structure. Our aim here is to compare different experimental techniques with different selection rules through detailed theoretical analysis of the appropriate numerical algorithms. Since the main difference between these algorithms is the population size, we will specifically focus on the effect of this parameter on the search time.

In vitro evolution ("evolution in a test tube", directed evolution) is a modern technology used in bioengineering that mimics the process of natural selection to direct proteins or nucleic acids to acquire a specific function. One of the most promising directions in the development of modern technologies for the evolution of macromolecules in vitro is the use of microdroplet devices based on the principles of microfluidics. A significant increase in the efficiency and cost reduction of in vitro evolution approaches can be achieved through the development and analysis of new heuristic evolutionary algorithms. This goal is achieved by numerical tests on computer models of real molecular genetic experiments (in silico experiments). This work was inspired by our recent key observation that many heuristic evolutionary algorithms can be associated with new engineering solutions for the modules of such microfluidic devices. Here, we have proposed and simulated new approaches to in vitro evolution with the prospect of their implementation in experimental microfluidic setups. In this report, we have demonstrated in our in silico experiments that some algorithms that have proven themselves in evolutionary computing turn out to be significantly more efficient than those algorithms that model the routine approaches of modern microdroplet microfluidics. Prospects for the implementation of such promising algorithms in new experimental approaches are discussed.

Evolutionary computing (EC) is an area of computer sciences and applied mathematics cov- ering heuristic optimization algorithms inspired by evolution in Nature. EC extensively study all the variety of methods which were originally based on the principles of selectionism. As a result, many new algorithms and approaches, significantly more efficient than classical selectionist schemes, were found. This is especially true for some families of special prob- lems. There are strong arguments to believe that EC approaches are quite suitable for modeling and numerical analysis of those methods of synthetic biology and biotechnology that are known as in vitro evolution. Therefore, it is natural to expect that the new algorithms and approaches developed in EC can be effectively applied in experiments on the directed evolution of biological macromolecules. According to the John Holland’s Schema theorem, the effective evolutionary search in genetic algorithms (GA) is provided by identifying short schemata of high fitness which in the further search recombine into the larger building blocks (BBs) with higher and higher fitness. The multimodularity of functional biological macromole- cules and the preservation of already found modules in the evolutionary search have a clear analogy with the BBs in EC. It seems reasonable to try to transfer and introduce the methods of EC, preserving BBs and essentially accelerating the search, into experiments on in vitro evolution. We extend the key instrument of the Holland’s theory, the Royal Roads fitness function, to problems of the in vitro evolution (Biological Royal Staircase, BioRS, functions). The specific version of BioRS developed in this publication arises from the realities of exper- imental evolutionary search for (DNA-) RNA-devices (aptazymes). Our numerical tests showed that for problems with the BioRS functions, simple heuristic algorithms, which turned out to be very effective for preserving BBs in GA, can be very effective in in vitro evo- lution approaches. We are convinced that such algorithms can be implemented in modern methods of in vitro evolution to achieve significant savings in time and resources and a sig- nificant increase in the efficiency of evolutionary search.

We address the possibilities of the description of the genetic code as a sign system. We make a differentiation between language and speech, that is, between a system of abstract syntagmatic and paradigmatic relations, and its actual manifestation. This can also be represented as a dichotomy of biochemical substance and semiotic form. As the minimal unit of the alphabet, we consider the distinctive features of nuclei acids (number of bonds and type of the base—purine or pyrimidine). Positions within triplets (first, second, or third) are considered as grammatical categories and each of them is endowed with its codon-forming functions regardless of which nucleotide it is filled with. The distinction between alphabet (nucleotides), vocabulary (amino acids), and grammatical categories allows us to identify the formation rules for the significant units of the genetic code (doublets and triplets) and explicate their compositional semantics (correspondence rules between codons and amino acids). The grammar of the genetic code may be represented as a system of operations or one-side dependencies, regulated by left or right contexts of the nucleotide in the central positions. The principle of context sensitivity allows us to describe cases when biochemically the same sequence of nucleotides, depending on their location, acquires a different meaning and performs a different function.

Успехи языкознания ХХ века были достигнуты за счет разграничения языка, системы и речи, т. е. магифестации системы. Фонема определяется исключительно негативно: как минимальный набор дифференциальных признаков. Уравнение основных единиц генетического кода с буквами латинского алфавита оправдано только как привычный способ нотации. Между тем единственным, кто сравнивал нуклеотиды с фонемами, был Ф. Жакоб, вероятно, под влиянием Р. Якобсона (1971). Экстраполяция методов фонологии на генетический код приводит к разграничению между нуклеотидом как биохимическим элементом и нуклеотидом как внутрисистемной (абстрактной) семиотической единицей генетического кода. Последний характеризуется только двумя дифференциальными признаками – количеством водородных связей и принадлежностью к группе пуринов или пиримидинов. Только эти две особенности имеют существенное значение для процессов кодирования – дифференциации аминокислот. Аналогии между фонемами и нуклеотидами как минимальными элементами соответствующих семиотических систем могут быть продолжены. Парадигматические и синтагматические закономерности, хорошо описанные в фонологических системах, имеют место в процессах экспрессии генов (вырожденность кода, сильные и слабые позиции, комплементарность, вобблинг).

The paper discusses the possible development of Lotman’s idea of the semiosphere, expanding it by introducing the concept of semio-poiesis as applied to the emergence of the genetic code. The birth of life, which involves controlling complex information processes, leads to the first semiotic relations expressed in genetic coding. Semio-poiesis, recursive auto-referential processing of a semiotic system, becomes a form of organization of the bio-world when notions of meaning and aiming are introduced into it. The increasing complexity of the genetic code, semio-poiesis, is manifested as the establishment of regularly reproduced connections between signifieds and signifiers; and the emergence of operations, allowing to generate meaningful, hierarchically organized entities (codons) and describing relationships within the system (gene expression). The notion of semio-poiesis can clarify the characteristics of semiosis as an intrinsic dynamic process of the self-organization and self-development of the semiosphere, what Lotman designated as the “self-growing Logos”.

We discuss the influence of linguistic metaphors on understanding genetic information processing and reveal the semantic roots and heuristic value of metaphors related to the genetic reading. They are derived from the equa-tion of life with a book; thus, genetic information processing is understood as some operations on text. Some essential gene expression features are shared with human reading: a faculty can identify the biochemical sequenc-es based on their functions in an abstract system and distinguish between type and its context-dependent tokens. The genetic information can be considered as a dual biochemical and semiotic entity, and as a complement to biochemical methods also a semiotic apparatus can be applied.