Complete chemical synthesis, assembly, and cloning of a mycoplasma genitalium genome.Daniel Gibson,Benders G.,A. Gwynedd,Cynthia Andrews-Pfannkoch,Evgeniya Denisova,Baden-Tillson A.,Zaveri Holly,Stockwell Jayshree,B. Timothy,Anushka Brownley,David Thomas,Algire W.,A. Mikkel,Chuck Merryman,Lei Young,VladimirNoskov,Glass N.,I. John,J. Craig Venter,Clyde Hutchison,Smith A. &O. Hamilton -2008 -Science 319 (5867):1215--1220.detailsWe have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate (...) assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)
Meaning and understanding in large language models.Vladimír Havlík -2024 -Synthese 205 (1):1-21.detailsCan a machine understand the meanings of natural language? Recent developments in the generative large language models (LLMs) of artificial intelligence have led to the belief that traditional philosophical assumptions about machine understanding of language need to be revised. This article critically evaluates the prevailing tendency to regard machine language performance as mere syntactic manipulation and the imitations of understanding, which is only partial and very shallow, without sufficient grounding in the world. The article analyses the views on possible ways (...) of grounding as a condition for successful understanding in LLMs and offers an alternative way in view of the prevailing belief that the success of understanding depends mainly on the referential grounding. An alternative conception seeks to show that semantic fragmentism offers a viable account of natural language understanding and explains how LLMs ground the meanings of linguistic expressions. Uncovering how meanings are grounded allows us to also explain why LLMs’ ability to understand is possible and so remarkably successful. (shrink)
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Appearance and Persistence as the Unity of Diachronic and Synchronic Concepts of Emergence.Vladimír Havlík -2020 -Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 51 (3):393-409.detailsRecent philosophical discourse on emergence has developed with particular concern for the distinction between weak and strong emergence and with the primary focus on detailed analysis of the concept of supervenience. However, in the last decade and as a new departure, attention has been devoted to the distinction between synchronic and diachronic emergence. In this philosophical context, there is an ongoing general belief that these two concepts are so different that it is impossible to establish for them a general unifying (...) framework. It is the purpose of this paper to support an alternative view, i.e. that these concepts are different but not mutually exclusive, and that attending to appearance and persistence can, in this context, lead to an acceptable unifying framework for these two, differing concepts of emergence. (shrink)
Autour des conférences de Nietzsche «Sur l’avenir de nos établissements d’enseignement».Arnaud Francois,Vladimir Milisavljevic,Cristiana Asavoaie,Anna Bonalume &Jose A. Errazuriz -2015 -Meta: Research in Hermeneutics, Phenomenology, and Practical Philosophy 7 (2):252-272.detailsThe text focuses on reflecting on the role of modern university in a man intellectual development, starting from Nietzsche’s ideas. By drawing up some of the main methodological and philosophical concepts of the German philosopher, the text highlights a series of aspects on the Humboldian nature of current universities – a state of tension under the political, economic and social factors. Thus, the classic concepts of Bildung and Kultur specific to the XIX-century University are analyzed in relation with the crisis (...) that marked the Prussian state of Bismarck period. Higher education being available to the masses is a current problem Nietzsche didn’t avoid to call „savageness” and „decline” of the higher educational system. The purpose of the text is to point out if Nietzsche’s ideas can be still applied nowadays. (shrink)
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David Miller a racionalita bez „dobrých důvodů“? Ke kritice Millerovy interpretace kritického racionalismu.Vladimír Havlík -2018 -Teorie Vědy / Theory of Science 40 (1):63-87.detailsDavid Miller v pracích Critical Rationalism a Out of Error se jako jeden z mála Popperových žáků snaží nejen o vysvětlení a obhájení Popperova kritického racionalismu, ale zároveň i o jeho další rozvinutí. Millerovo znovunastolení kritického racionalismu ovšem předpokládá, že k racionálnímu jednání není třeba žádných „dobrých důvodů“, ale jen argumentů. Uvedená stať se zaměřuje právě na tuto otázku existence tzv. „dobrých důvodů“ ve spojení s racionalitou a racionálním rozhodováním a ukazuje, že Millerův požadavek neexistence „dobrých důvodů“ je nejen příliš (...) radikální, ale i nepřijatelný z hlediska Popperova nebo Musgravova pojetí kritického racionalismu. (shrink)
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Simulace a instrumentální pojetí vědy.Vladimír Havlík -2016 -Teorie Vědy / Theory of Science 38 (2):131-157.detailsStať se zabývá diskusemi o epistemologicko-metodologické roli simulací v soudobé vědě. Soustředí se nejprve na aktuálnost těchto diskusí v současné metodologii vědy a následně na její návaznost na určitou myšlenkovou tradici z osmdesátých let 20. století, kdy diskuse kolem modelování vyvolaly řadu otázek zpochybňujících tradiční pojmové distinkce, především mezi experimentem a teorií. Stať se přiklání v rámci těchto diskusí k názorům, které řadí simulace k novým a specifickým nástrojům vědy, jež také vyžadují novou a specifickou metodologii a epistemologické postavení. Pro (...) podporu této názorové pozice jsou uvedeny některé aktuální analýzy konkrétních příkladů simulací a jejich specifického postavení v moderní vědě. (shrink)
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Physicalism and the Status of Special Science Laws.Vladimír Havlík -2019 -Teorie Vědy / Theory of Science 41 (2):201-228.detailsPhysicalism as a metaphysical or ontological concept has maintained a dominant position since the second half of the last century to the present day. The claim that everything is physically constituted often accompanies microphysical reductionism, which assumes the existence of fundamental laws to which everything is reducible. In this context, a question regarding the status and possible autonomy of the laws of special sciences arises. The article focuses on the basic philosophical discussions between the strong, weak, and non-reductive physicalism that (...) treat the laws of special sciences in different ways, but none of which can be considered sufficiently convincing and successful. The article seeks to prove the existence of a universal mechanism that leads to the emergence of new and complex entities and regulations of their behaviour, thus justifying the autonomous status of special sciences and laws. (shrink)
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Сommunicative Discourse of Tattvasaṅgrāha by Śāntarakṣita.Vladimir P. Ivanov &Иванов Владимир Павлович -2024 -RUDN Journal of Philosophy 28 (1):57-68.detailsThe study provides an insight into the structural features of the famous VIII century Buddhist treatise Tattvasaṅgrāha by Śāntarakṣita with regard to the text’s main purpose ( prayojana ) as it is treated in Kamalaśīla’s commentary Pañjikā. Any text along with its referential (representational) function of conveying message - meaning to the addressee, or its expressive function, reflecting the author's attitude to what is communicated, also performs the ‘appellative’ function, encouraging the recipient of the message to act. This function which (...) could also be called praxiological was always significant in Indian text culture, since from the times of Veda-s it was embedded in its very core. This function is of paramount importance in the case of Indian religious and philosophical texts, whose main aim is to convince and transform the consciousness of their percipients. Along with linear models of message transfer, Sanskrit texts could demonstrate non-linear semantic structures, transmitting the main idea of the text indirectly. It is exactly how one should perceive the message of Śāntarakṣita’s Tattvasaṅgrāha according to the suggested by Śāntarakṣita’s prominent student Kamalaśīla in his Pañjikā -commentary to the treatise. He proposes to consider Tattvasaṅgrāha not as a thematically heterogeneous encyclopaedic or doxographic work, whose main objective is to refute different non-Buddhist views (as it is often treated by scholars now), but as a text, which by its very design exposes one of the most important Buddhist principles - the law of the dependent origination ( pratītyasamutpāda ). The themes, discussed in a number of the chapters of Tattvasaṅgrāha, indeed, appear to have direct correlation with the characteristics of pratītyasamutpāda given to it in Śālistamba-sūtra - an early Mahāyāna text, which explains this universal law. Kamalaśīla suggests looking at Tattvasaṅgrāha as at one big unit-sentence - mahāvākya, with the exposition of pratītyasamutpāda as its unitary purpose-meaning ( abhidheya ). In this context, the treatise functions as a praxiological tool for the ‘installing’ into the consciousness of the text’s addressee the knowledge of ‘true principles’ (tattva-s) of pratītyasamutpāda. This interpretation of the main message of the text raises also a question of the adequate translation of the name of the treatise into other languages, because, according to Kamalaśīla, ‘ Tattvasaṅgrāha’ means the ‘Assembly of Principles-(tattva’-s)’ which specify precisely pratītyasamutpāda (pratītyasamutpāda-viśeṣaṇāni tattvāni). (shrink)
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El Apocalipsis, un libro de resistencia social: aportes éticos y morales.Vladimir Merchán Jaimes,Guillermo León Herrera Gil &Elkin Alonso Gómez Salazar -2022 -Perseitas 11:224-245.detailsEl presente trabajo se propone rescatar la resistencia y la crítica al poder imperial romano del libro del Apocalipsis como una fuente fundamental para la teología moral cristiana, que lo convirtieron en un foco de luz que ilumina el camino de la conducta humana hacia un mundo mejor. Al mismo tiempo, ofrece pautas para la defensa de la vida en un entorno donde los totalitarismos políticos, económicos y religiosos atentan contra ella. Además, quiere destacar dicha resistencia y crítica como uno (...) de los factores generadores, y por tanto centrales, de la teología del Apocalipsis. Para ello se utilizarán los principios metodológicos de la lectura contextual que parten de la convicción según la cual el texto es una expresión de las vivencias comunitarias del hagiógrafo y de su actitud ante las circunstancias sociales que lo provocaron. El libro busca afectar el entorno, pero este también configura el contenido de la obra escrita. En un segundo momento, con el método se indaga qué de ese momento histórico puede iluminar el presente del lector. En el caso del Apocalipsis, se elegirán los textos en los que el autor presente los temas y actores principales de la trama, a saber: el ser supremo sentado en el trono, el cordero y el mal —simbolizado específicamente en el tercer jinete—, ya que en ellos se juega el mensaje del libro, la soberanía divina que humaniza o la soberanía diabólica deshumanizante. (shrink)
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A hybrid genetic algorithm, list-based simulated annealing algorithm, and different heuristic algorithms for travelling salesman problem.Vladimir Ilin,Dragan Simić,Svetislav D. Simić,Svetlana Simić,Nenad Saulić &José Luis Calvo-Rolle -2023 -Logic Journal of the IGPL 31 (4):602-617.detailsThe travelling salesman problem (TSP) belongs to the class of NP-hard problems, in which an optimal solution to the problem cannot be obtained within a reasonable computational time for large-sized problems. To address TSP, we propose a hybrid algorithm, called GA-TCTIA-LBSA, in which a genetic algorithm (GA), tour construction and tour improvement algorithms (TCTIAs) and a list-based simulated annealing (LBSA) algorithm are used. The TCTIAs are introduced to generate a first population, and after that, a search is continued with the (...) GA. The problem of premature convergence of the GA to local optimum is tackled by a method called social disaster technique. Afterwards, the LBSA is applied to generate a new population based on one of two proposed operators called packing and judgement day. The proposed algorithm is implemented in the MATLAB environment, and its two variants, called GA-TCTIA-LBSA packing and GA-TCTIA-LBSA judgement day, are tested on symmetric and asymmetric instances from TSPLIB. The overall results demonstrate that the proposed GA-TCTIA-LBSAs offer promising results, particularly for small-sized instances. (shrink)
The naturalness of artificial intelligence from the evolutionary perspective.Vladimír Havlík -2019 -AI and Society 34 (4):889-898.detailsCurrent discussions on artificial intelligence, in both the theoretical and practical realms, contain a fundamental lack of clarity regarding the nature of artificial intelligence, perhaps due to the fact that the distinction between natural and artificial appears, at first sight, both intuitive and evident. Is AI something unnatural, non-human and therefore dangerous to humanity, or is it only a continuation of man’s natural tendency towards creativity? It is not surprising that from the philosophical point of view, this distinction is the (...) basic question that fundamentally affects all other considerations and conclusions pertaining to artificial intelligence. In this article, I would like to explain this difference and draw attention to some conclusions, which may result from a naturalistic perspective with regard to recent philosophical posthumanism. For this purpose, I present several examples of the natural–artificial distinction in the different fields of the philosophy of science and then discuss their implications for the problem of intelligence. Based on Dennett’s conception of intentionality and the naturalistic perspective, I demonstrate that besides the traditional conception, there is a non-anthropocentric evolutionary view in which the natural–artificial distinction disappears and it is possible to see a united process of intelligence creation. (shrink)
The Logical Legacy of Nikolai Vasiliev and Modern Logic.Dmitry Zaitsev &Vladimir Markin (eds.) -2017 - Cham: Springer Verlag.detailsThis volume offers a wide range of both reconstructions of Nikolai Vasiliev’s original logical ideas and their implementations in the modern logic and philosophy. A collection of works put together through the international workshop "Nikolai Vasiliev’s Logical Legacy and the Modern Logic," this book also covers foundations of logic in the light of Vasiliev’s contradictory ontology. Chapters range from a look at the Heuristic and Conceptual Background of Vasiliev's Imaginary Logic to Generalized Vasiliev-style Propositions. It includes works which cover Imaginary (...) and Non-Aristotelian Logics, Inconsistent Set Theory and the Expansion of Mathematical Thinking, Plurivalent Logic, and the Impact of Vasiliev's Imaginary Logic on Epistemic Logic. The Russian logician, Vasiliev, was widely recognized as one of the forerunners of modern non-classical logic. His "imaginary logic" developed in some of his work at the beginning of 20th century is often considered to be one of the first systems of paraconsistent and multi-valued logic. The novelty of his logical project has opened up prospects for modern logic as well as for non-classical science in general. This volume contains a selection of papers written by modern specialists in the field and deals with various aspects of Vasiliev's logical ideas. The logical legacy of Nikolai Vasiliev can serve as a promising source for developing an impressive range of philosophical interpretations, as it marries promising technical innovations with challenging philosophical insights. (shrink)
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Vladimir Solovyov’s “Three Speeches on Dostoevsky.” Then and Now.Vladimir N. Porus -2022 -Russian Studies in Philosophy 60 (1):60-73.detailsThis article discusses the connection between the ideas of Fyodor M. Dostoevsky andVladimir S. Solovyov on the need for cultural and moral transformation of those who would claim to participate in...
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Letter fromVladimir V. Mironov to Aleksandr V. Mikhailovsky.Vladimir V. Mironov -2021 -Russian Studies in Philosophy 59 (3):243-245.detailsMy dear Aleksandr!I have finally found some quiet time for a slow and attentive read of your article “The Beginning of the Black Notebooks.”1 I very much liked the article, especially for your trul...
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