Applying mild methods of preparation, part of the ribosomes of rabbit reticulocytes are found in aggregates (later called polyribosomes) of up to six ribosomal units. Upon treatment with RNA-ase, they desintegrate into single ribosomes. The fast-sedimenting aggregates are found to be more active in protein synthesis in terms of incorporation of radioactive amino acids, whereas the single ribosomes are more receptive to stimulation by the artificial messenger RNA poly-U. The findings indicate that the linkage of ribosomes into aggregates (...) is due to the messenger RNA. They support a tape-reading mechanism of protein synthesis whereby growth of the peptide chain is accompanied by shifting the active site of the ribosome from one coding group of nucleotides of the messenger RNA to the next. (shrink)

The short paper introduces the concept of possible branches of double-stranded DNA (later sometimes called palindromes): Certain sequences of nucleotides may be followed, after a short unpaired stretch, by a complementary sequence in reversed order, such that each DNA strand can fold back on itself, and the DNA assumes a cruciform or tree-like structure. This is postulated to interact with regulatory proteins. -/- .

A classic analytic approach to biological phenomena seeks to refine definitions until classes are sufficiently homogenous to support prediction and explanation, but this approach founders on cases where a single process produces objects with similar forms but heterogeneous behaviors. I introduce object spaces as a tool to tackle this challenging diversity of biological objects in terms of causal processes with well-defined formal properties. Object spaces have three primary components: (1) a combinatorial biological process such as protein synthesis that (...) generates objects with parts that are modular, independent, and organized according to an invariant syntax; (2) a notion of “distance” that relates the objects according to rules of change over time as found in nature or useful for algorithms; (3) mapping functions defined on the space that map its objects to other spaces or apply an evaluative criterion to measure an important quality, such as parsimony or biochemical function. Once defined, an object space can be used to represent and simulate the dynamics of phenomena on multiple scales; it can also be used as a tool for predicting higher-order properties of the objects, including stitching together series of causal processes. Object spaces are the basis for a strategy of theorizing, discovery, and analysis in biology: as heuristic idealizations of biology, they help us transform inchoate, intractable problems into articulated, well-structured ones. Developing an object space is a research strategy with a long, successful history under many other names, and it offers a unifying but not overreaching approach to biological theory. (shrink)

Forty years’ experience as a bacterial geneticist has taught me that bacteria possess many cognitive, computational and evolutionary capabilities unimaginable in the first six decades of the twentieth century. Analysis of cellular processes such as metabolism, regulation of protein synthesis, and DNA repair established that bacteria continually monitor their external and internal environments and compute functional outputs based on information provided by their sensory apparatus. Studies of genetic recombination, lysogeny, antibiotic resistance and my own work on transposable elements (...) revealed multiple widespread bacterial systems for mobilizing and engineering DNA molecules. Examination of colony development and organization led me to appreciate how extensive multicellular collaboration is among the majority of bacterial species. Contemporary research in many laboratories on cell–cell signaling, symbiosis and pathogenesis show that bacteria utilise sophisticated mechanisms for intercellular communication and even have the ability to commandeer the basic cell biology of ‘higher’ plants and animals to meet their own needs. This remarkable series of observations requires us to revise basic ideas about biological information processing and recognise that even the smallest cells are sentient beings. Previous article in issue. (shrink)

I present a reconstruction of F.H.C. Crick's two 1957 hypotheses "Sequence Hypothesis" and "Central Dogma" in terms of a contemporary philosophical theory of causation. Analyzing in particular the experimental evidence that Crick cited, I argue that these hypotheses can be understood as claims about the actual difference-making cause in protein synthesis. As these hypotheses are only true if restricted to certain nucleic acids in certain organisms, I then examine the concept of causal specificity and its potential to counter (...) claims about causal parity of DNA and other cellular components. I first show that causal specificity is a special kind of invariance under interventions, namely invariance of generalizations that range over finite sets of discrete variables. Then, I show that this notion allows the articulation of a middle ground in the debate over causal parity. (shrink)

Terms loaded with informational connotations are often employed to refer to genes and their dynamics. Indeed, genes are usually perceived by biologists as basically ‘the carriers of hereditary information.’ Nevertheless, a number of researchers consider such talk as inadequate and ‘just metaphorical,’ thus expressing a skepticism about the use of the term ‘information’ and its derivatives in biology as a natural science. First, because the meaning of that term in biology is not as precise as it is, for instance, in (...) the mathematical theory of communication. Second, because it seems to refer to a purported semantic property of genes without theoretically clarifying if any genuinely intrinsic semantics is involved. Biosemiotics, a field that attempts to analyze biological systems as semiotic systems, makes it possible to advance in the understanding of the concept of information in biology. From the perspective of Peircean biosemiotics, we develop here an account of genes as signs, including a detailed analysis of two fundamental processes in the genetic information system (transcription and protein synthesis) that have not been made so far in this field of research. Furthermore, we propose here an account of information based on Peircean semiotics and apply it to our analysis of transcription and protein synthesis. (shrink)

We propose a novel paradigmatic approach to sentient reality as a whole, with specific application to Information-guided DNA dynamics, leading to a triadic genomic configuration , which accommodates besides the parental hereditar legacy, a transcendental originating highly complex guiding matrix able to control the specific way the protein-synthesis is performed. The Self’s own “Soul Genome”, transcending the zero point energy interdimensional barrier, couples to the zygote’s quantum-governed energetic configuration by way of resonant bands of subtle energy superposition effects (...) at the instance of fertilization, triggered by a Zinc-spark related biophotonic bridge. Thus, unique secondary torsion parameters in the DNA strands determine the way the basic protein-generating template is read, supplying the new entity’s psycho-cognitive particularities along purposeful developmental vectors. (shrink)

Assembly of minimal genomes revealed many genes encoding unknown functions. Three overlooked functional categories account for some of them. Cells are prone to make errors and age. As a first key function, discrimination between proper and changed entities is indispensable. Discrimination requires management of information, an authentic, yet abstract, cur- rency of reality. For example proteins age, sometimes very fast. The cell must identify, then get rid of old proteins without destroying young ones. Implementing discrimination in cells leads to the (...) second set of functions, usually ignored. Being abstract, information must nevertheless be embodied into material entities, with unavoidable idiosyncratic properties. This brings about novel unmet needs. Hence, the buildup of cells elicits specific but awkward material implementations, ‘kludges’ that become essential under particular settings, while difficult to identify. Finally, a third functional category char- acterizes the need for growth, with metabolic implementations allowing the cell to put together the growth of its cytoplasm, membranes, and genome, spanning different spatial dimensions. Solving this metabolic quandary, critical for engineering novel synthetic biology chassis, uncovered an unexpected role for CTP synthetase as the coordinator of nonhomothetic growth. Because a significant number of SynBio constructs aim at creating cell factories we expect that they will be attacked by viruses (it is not by chance that the function of the CRISPR system was identified in industrial settings). Substantiating the role of CTP, natural selection has dealt with this hurdle via synthesis of the antimetabolite 30-deoxy-30,40-didehydro- CTP, recruited for antiviral immunity in all domains of life. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to (...) enhance accessibility to results of protein research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Handbook entry on "Synthesis," surveying the roles played by synthesis in Husserl, important precursors in the history of philosophy, and the legacy of the term in Heidegger and Merleau-Ponty.

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

For most of their respective existences, reliabilism and evidentialism (that is, process reliabilism and mentalist evidentialism) have been rivals. They are generally viewed as incompatible, even antithetical, theories of justification.1 But a few people are beginning to re-think this notion. Perhaps an ideal theory would be a hybrid of the two, combining the best elements of each theory. Juan Comesana (forthcoming) takes this point of view and constructs a position called “Evidentialist Reliabilism.” He tries to show how each theory can (...) profit by borrowing elements from the other. Comesana concentrates on reliabilism’s problems and how it might be improved by infusions from evidentialism. This paper follows a similar tack. My emphasis, however, is the reverse of Comesana’s. I highlight problems for evidentialism and show how it could benefit by incorporating reliabilist themes. I am not sanguine that evidentialists will see it my way. They might even view my proposals as an insidious attempt to convert evidentialists to reliabilism. Well, I won’t debate the best way to formulate this paper’s recipe. At any rate, it began with the idea (which anteceded my reading of Comesana) of creating a synthesis of reliabilism and evidentialism. It retains significant strands of that idea, although the synthesis theme does not pervade the entire paper. What is mentalist evidentialism? Its original formulation was succinct. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (...) (GO). PRO relates to UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Talk at University of Turin, 'Kant, oltre Kant, May 5th 2023. --- -/- It is useful, while keeping in mind a holistic approach, to concentrate on a common theme in Kant’s text, which it will turn out is the quintessential element of his novel ‘way of thinking’, as he himself put it in preface of the second edition of the Critique of Pure Reason. This common theme is the idea of synthesis, which is what holds together, and is the (...) entryway to, all the other familiar aspects of Kant’s thought: his concept of self-consciousness or how mind is involved in cognition, his ideas about the role of the imagination, his theory of knowledge and his metaphysics of experience, and not unimportantly, its relation to what is probably the most Kantian element here: the categories of the understanding as the first principles of knowledge. But the meaning of synthesis and its role in its various facets, though frequently the subject of discussion in papers and monographs alike, is hardly understood in contemporary Kant scholarship. Most readings of the text of the Deduction, the part in which Kant elucidates his concept of synthesis, exhibit a shallow, mechanical understanding of it. -/- A compounding factor is that synthesis can’t really be understood independently of the other aforementioned elements of Kant’s thought. Grasping the meaning of synthesis implies coming to grips with his concept of self-consciousness and the way both self-consciousness and the categories are intricately and intimately involved. Most interpretations consider these aspects too much as if they were indeed separable faculties or entities that serve separable functions, undercutting an important feature of Kant’s metaphysics: the possibility of a priori unified cognition, for which an indivisible self-legislating subject is responsible. Rather, they are expressions of various aspects of a singular function of the mind as the ground of possible unified knowledge. -/- One striking example of such a superficial reading of the text is the way the relation between figurative synthesis and intellectual synthesis—or in the case of the A-Deduction the threefold synthesis—is standardly interpreted, as if the two are independent or quasi-independent functions of different faculties of the mind, the imagination and the understanding. In this paper, I focus on the relation between figurative and intellectual synthesis, while arguing that failing to understand this properly, indeed the relation between the imagination and the understanding, leads to a vicious regress in the explanation of the ground of knowledge, for which a priori synthesis is specifically designed. In other words, failing to see the intimate relation between the imagination and the understanding, the very identity that lies at their root, risks losing sight of the primary aim of Kant’s thought: the possibility of a priori unified knowledge. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD (...) as a post-translational modification reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a (...) class='Hi'>PRotein Ontology (PRO) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

A response to Lindsay Craig's essay, The So-Called Extended Synthesis and Population Genetics.

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides (...) a framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and (...) modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Evolutionary theory is undergoing an intense period of discussion and reevaluation. This, contrary to the misleading claims of creationists and other pseudoscientists, is no harbinger of a crisis but rather the opposite: the field is expanding dramatically in terms of both empirical discoveries and new ideas. In this essay I briefly trace the conceptual history of evolutionary theory from Darwinism to neo-Darwinism, and from the Modern Synthesis to what I refer to as the Extended Synthesis, a more inclusive (...) conceptual framework containing among others evo–devo, an expanded theory of heredity, elements of complexity theory, ideas about evolvability, and a reevaluation of levels of selection. I argue that evolutionary biology has never seen a paradigm shift, in the philosophical sense of the term, except when it moved from natural theology to empirical science in the middle of the 19th century. The Extended Synthesis, accordingly, is an expansion of the Modern Synthesis of the 1930s and 1940s, and one that—like its predecessor—will probably take decades to complete. (shrink)

This synthesis of 5 prominent conflict management paradigms uses power differential as the single most contributing variable to their process and outcome of conflict. Efforts of scholars to integrate or synthesize conflict paradigms have been unsuccessful or clumsy by the scholars’ own assessments. The 5 selected paradigms represent an interdisciplinary set of normative and descriptive paradigms from different social contexts and intellectual frameworks. The 5 share the common traits of rival goals, three levels of socially constructed power differential, and (...) outcomes relative to the total value of the rival goal. An inverse relationship between power differential and the total value of conflict outcomes is supported by all 5 paradigms and empirical data. Explanatory metatheory is the methodology used for synthesis. An increase in power differential results in a decrease in total value of the rival goal. Power differential is constructed using Max Weber’s ideal-type method. The power differentials are abstracted from the paradigms themselves. Empirical work form secondary sources and case studies complete the analysis. (shrink)

In this essay, I evaluate four central metaethical readings of Spinoza’s moral philosophy in the literature: unqualified anti-realism, qualified anti-realism, qualified realism, and unqualified realism. More specifically, I discuss the metaethical readings of Charles Jarrett (unqualified anti-realism), Matthew Kisner (qualified anti-realism), Jon Miller (qualified realism), and Andrew Youpa (unqualified realism), each of which captures core aspects of this debate. My conclusions are that (1) Spinoza is neither an unqualified anti-realist nor an unqualified realist and (2) Spinoza’s ethical framework represents a (...) qualified synthesis of realist (naturalistic) and anti-realist (affective) features. (shrink)

In the beginning of the 20th century the groundbreaking work of Ramon y Cajal firmly established the neuron doctrine, according to which neurons are the basic structural and functional units of the nervous system. Von Weldeyer coined the term “neuron” in 1891, but the huge leap forward in neuroscience was due to Cajal’s meticulous microscopic observations of brain sections stained with an improved version of Golgi’s la reazione nera (black reaction). The latter improvement of Golgi’s technique made it possible to (...) visualize the arborizations of single neurons that were “colored brownish black even to their finest branchlets, standing out with unsurpassable clarity upon a transparent yellow background. All was sharp as a sketch with Chinese ink”. The high quality of both the visualization of individual nerve cells and the work performed on studying the anatomy of the central nervous system lead Ramon y Cajal to the conclusion that axons output the nervous impulses to the dendrites or the soma of other target neurons. (shrink)

Biochemical kinds such as proteins pose interesting problems for philosophers of science, as they can be studied from the points of view of both biology and chemistry. The relationship between the biological functions of biochemical kinds and the microstructures that they are related to is the key question. This leads us to a more general discussion about ontological reductionism, microstructuralism, and multiple realization at the biology-chemistry interface. On the face of it, biochemical kinds seem to pose a challenge for ontological (...) reductionism and hence motivate a dual theory of chemical and biological kinds, a type of pluralism about natural kinds. But it will be argued that the challenge, which is based on multiple realization, can be addressed. The upshot is that there are reasonable prospects for ontological reductionism about biochemical kinds, which corroborates natural kind monism. (shrink)

Today a change is imperative in approaching global problems: what is needed is not arm-twisting and power politics, but searching for ways of co-evolution in the complex social and geopolitical systems of the world. The modern theory of self-organization of complex systems provides us with an understanding of the possible forms of coexistence of heterogeneous social and geopolitical structures at different stages of development regarding the different paths of their sustainable co-evolutionary development. The theory argues that the evolutionary channel to (...) the observed increasing complexity is extremely narrow and only certain discrete spectra of relatively stable self-maintained structures are feasible in complex systems. There exists a restricted set of ways of assembling a complex evolutionary whole from diverse parts. The law of nonlinear synthesis of complex structures reads: the integration of structures in more complex ones occurs due to the establishment of a common tempo of their evolution. On the basis of the theory, we can see not only desirable but also attainable futures. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for (...) different purposes and the separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

Wittgenstein held that Russell’s multiple relation theory of judgment fails to explain an atomic judgment’s representation of entities as combined. He demonstrated this failure as follows. Under the multiple relation theory, an atomic judgment is a complex whose relating relation is judgment, the universal, and whose terms include the entities the judgment represents as combined. Taking such a complex we may arrive through the substitution of constituents at a complex whose relating relation is again judgment but whose terms do not (...) include entities which are logically suited for combination. This second judgment complex will not represent any of its terms as combined, for entities that are logically uncombinable are unrepresentable as combined. Russell’s theory does not, however, explain how the original judgment differs from the complex arrived at by the substitution of constituents such that the former but not the latter represents certain of its terms as combined. (shrink)

In this chapter I advance a moderately conceptualist interpretation of Kant’s account of the threefold synthesis in the A-Deduction. Often the first version of TD, the A-Deduction, is thought to be less conceptualist than the later B-version from 1787 (e.g. Heidegger 1991, 1995). Certainly, it seems that in the B-Deduction Kant puts more emphasis on the role of the understanding in determining the manifold of representations in intuition than he does in the A-Deduction. It also appears that in the (...) A-Deduction the seemingly pre-conceptual aspects of a priori synthesis, namely those of the synthesis of apprehension and the imagination, are more prominently featured than in the B-Deduction. And the fact that in the A-Deduction judgement does not appear to play any significant role reinforces the view that the A-Deduction is less strongly conceptualist. I believe that Kant is a conceptualist also in the A-Deduction (as much as in the B-Deduction) in the sense that all syntheses, which are expounded in the second section of the A-Deduction, must be seen as involving the categories or the understanding as the seat of the categories. However, despite some apparent strong modal claims regarding apperception in the A-Deduction, I argue that Kant is a moderate conceptualist in the sense that he allows for the real possibility that some representations are apprehended that are not subsumed or subsumable under the categories, or determined or determinable by the understanding as the seat of the categories. Not all representations must be synthesised and hence be conceptualised (by means of the categories), nor are all representations necessarily conceptualisable (by means of the categories). Often it is argued that the application of the categories must be seen as separate from or prior to conceptualisation (that is, employment of concepts in a judgement), so that the categories must be considered to apply to representations at least to the extent that the productive imagination or recognitive synthesis is involved, even if no empirical concepts are applied in an actual judgement. But it is difficult to see how categories can apply outside the context of an actual judgement in which ipso facto empirical concepts are employed, because, after all, categories are nothing but logical functions of judgement (e.g. B143). More in particular, I shall argue for the claims that (1) appearances to the contrary, all three levels of syntheses in the A-Deduction, including the synthesis of recognition, are interdependent and are not to be seen as operating singly or independently of each other, and hence of the categories; (2) ‘mere’ apprehension, or ‘mere’ intuition, is not dependent on the understanding and the application or possible application of the categories; and that (3) ‘mere’ apprehension does not even invoke a priori synthesis of apprehension and hence is as such fully lawless in terms of Kantian a priori laws. In this context, I also address Kant’s argument in the A-Deduction about the role of the imagination in the production of spatial objects and explain his apt use of the example of cinnabar to show that the kind of association that is at issue here concerns the possibility of knowledge, not the possibility of mere association, as is often assumed. (shrink)

In an intriguing but neglected passage in the Transcendental Deduction, Kant appears to link the synthetic activity of the understanding in experience with the phenomenon of attention (B156-7n). In this paper, we take up this hint, and draw upon Kant's remarks about attention in the Anthropology to shed light on the vexed question of what, exactly, the understanding's role in experience is for Kant. We argue that reading Kant's claims about synthesis in this light allows us to combine two (...) aspects of Kant's views that many commentators have thought are in tension with one another: on the one hand, Kant's apparent commitment to naïve realism about perception and, on the other, his apparent commitment to the necessity of synthetic activity by the understanding for any kind of cognitive contact with external objects. (shrink)

In this paper, I propose a novel interpretation of the role of the understanding in generating the unity of space and time. On the account I propose, we must distinguish between the unity that belongs to determinate spaces and times – which is a result of category-guided synthesis and which is Kant’s primary focus in §26 of the B-Deduction, including the famous B160–1n – and the unity that belongs to space and time themselves as all-encompassing structures. Non-conceptualist readers of (...) Kant have argued that this latter unity cannot be the product of categorial synthesis. While they are correct that this unity is not the product of any particular act of category-guided synthesis, I argue that conceptualists are right to nevertheless attribute this unity to the understanding. I argue that it is a result of what we can think of as the ‘original’ synthesis of understanding and sensibility themselves – it is a synthesis, moreover, in which the whole is logically prior to the parts. (shrink)

The two principal models of design in methodological circles in architecture—analysis/synthesis and conjecture/analysis—have their roots in philosophy of science, in different conceptions of scientific method. This paper explores the philosophical origins of these models and the reasons for rejecting analysis/synthesis in favour of conjecture/analysis, the latter being derived from Karl Popper’s view of scientific method. I discuss a fundamental problem with Popper’s view, however, and indicate a framework for conjecture/analysis to avoid this problem.

The modern synthesis in evolutionary biology is taken to be that period in which a consensus developed among biologists about the major causes of evolution, a consensus that informed research in evolutionary biology for at least a half century. As such, it is a particularly fruitful period to consider when reflecting on the meaning and role of chance in evolutionary explanation. Biologists of this period make reference to “chance” and loose cognates of “chance,” such as: “random,” “contingent,” “accidental,” “haphazard,” (...) or “stochastic.” Of course, what an author might mean by “chance” in any specific context varies. -/- In the following, we first offer a historiographical note on the synthesis. Second, we introduce five ways in which synthesis authors spoke about chance. We do not take these to be an exhaustive taxonomy of all possible ways in which chance meaningfully figures in explanations in evolutionary biology. These are simply five common uses of the term by biologists at this period. They will serve to organize our summary of the collected references to chance and the analysis and discussion of the following questions: • What did synthesis authors understand by chance? • How did these authors see chance operating in evolution? • Did their appeals to chance increase or decrease over time during the synthesis? That is, was there a “hardening” of the synthesis, as Gould claimed (1983)? (shrink)

Infants apparently start to understand their experience via the linked concepts of numerical identity and spatio-temporally continuous objects during the forth month of life. As described by Piaget and Klein, this development requires them to synthesise their experience in a new ways: in particular they must start to acknowledge that the main target of their anger at frustration and the main target of their gratitude and love are the same person, who is unique and irreplaceable. This seems to have an (...) immediate consequence in the onset of separation distress and stranger anxiety, and apparently has far-reaching psychological consequences later. (shrink)

The Modern Synthesis (MS) is the current paradigm in evolutionary biology. It was actually built by expanding on the conceptual foundations laid out by its predecessors, Darwinism and neo-Darwinism. For sometime now there has been talk of a new Extended Evolutionary Synthesis (EES), and this article begins to outline why we may need such an extension, and how it may come about. As philosopher Karl Popper has noticed, the current evolutionary theory is a theory of genes, and we (...) still lack a theory of forms. The field began, in fact, as a theory of forms in Darwin’s days, and the major goal that an EES will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes. (shrink)

Recent debates between proponents of the modern evolutionary synthesis (the standard model in evolutionary biology) and those of a possible extended synthesis are a good example of the fascinating tangle among empirical, theoretical, and conceptual or philosophical matters that is the practice of evolutionary biology. In this essay, we briefly discuss two case studies from this debate, highlighting the relevance of philosophical thinking to evolutionary biologists in the hope of spurring further constructive cross-pollination between the two fields.

The conference paper follows Lacanian and Freudian discussions concerning (obsessional) neurosis to locate the development of alt-right meme culture expression in a dialectic of political affect. The internet meme response to the MAGA hat kid scandal of January 2019 is analyzed under the scope of recent transformations in media culture and illuminates the psychoanalytical foundation of political reactionism as a counterproductive mechanism of identity politics, namely, the desire for identity legitimization.

To approach the issue of the recent proposal of an Extended Evolutionary Synthesis (EES) put forth by Massimo Pigliucci and Gerd Müller, I suggest to consider the EES as a metascientific view: a description of what’s new in how evolutionary biology is carried out, not only a description of recently learned aspects of evolution. Knowing ‘what is it to do research’ in evolutionary biology, today versus yesterday, can aid training, research and career choices, establishment of relationships and collaborations, decision (...) of funding and research policies, in order to make the field advance for the better. After reviewing the concepts associated to the EES proposal (categorized for convenience as mechanisms, measures, fields, perspectives and applications), I show their transience, and sketch out ongoing disagreements about the EES. Then I examine the deep difficulties, i.e., the enormity and complexity of the covered field, affecting the achievement of trusted metascientific views; the insufficiency of conceptual analysis to capture the substance of scientific research; the entanglement between empirical and metascientific concepts, between multiple chronologies, and between descriptive and normative intentions; and the ineliminable stakeholding of any reviewer involved in the reviewed field. I propose that disciplines such as scientometrics, ethnography, sociology, economics and history, combined with conceptual analysis, inspire a more rigorous approach to the evolutionary biology scientific community, more grounded and shared, confirming or transforming claims for ‘synthesis’ while preserving their maintenance goals. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data (...) set has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the (...) extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to ‘extend’ the Modern Synthesis-derived ‘standard evolutionary theory’ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES—published by Laland and collaborators in 2015—in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework. (shrink)

Change is the fundamental idea of evolution. Explaining the extraordinary biological change we see written in the history of genomes and fossil beds is the primary occupation of the evolutionary biologist. Yet it is a surprising fact that for the majority of evolutionary research, we have rarely studied how evolution typically unfolds in nature, in changing ecological environments, over space and time. While ecology played a major role in the eventual acceptance of the population genetic viewpoint of evolution in the (...) synthetic era (circa 1918-1956), it held a lesser role in the development of evolutionary theory until the 1980s, when we began to systematically study the evolutionary dynamics of natural populations in space and time. As a result, early evolutionary theory was initially constructed in an abstract vacuum that was unrepresentative of evolution in nature. The subtle synthesis between ecology with evolutionary biology (eco-evo synthesis) over the past 40 years has progressed our knowledge of natural selection dynamics as they are found in nature, thus revealing how natural selection varies in strength, direction, form, and, more surprisingly, level of biological organization. Natural selection can no longer be reduced to lower levels of biological organization (i.e., individuals, selfish genes) over shorter timescales but should be expanded to include adaptation at higher levels and over longer timescales. Long-term and/or emergent evolutionary phenomena, such as multilevel selection or evolvability, have thus become tenable concepts within an evolutionary biology that embraces ecology and spatiotemporal change. Evolutionary biology is currently suspended at an intermediate stage of scientific progress that calls for the organization of all the recent knowledge revealed by the eco-evo synthesis into a coherent and unified theoretical framework. This is where philosophers of biology can be of particular use, acting as a bridge between the subdisciplines of biology and inventing new theoretical strategies to organize and accommodate the recent knowledge. Philosophers have recommended transitioning away from outdated philosophies that were originally derived from physics within the philosophical zeitgeist of logical positivism (i.e., monism, reductionism, and monocausation) and toward a distinct philosophy of biology that can capture the natural complexity of multifaceted biological systems within diverse ecosystems—one that embraces the emerging philosophies of pluralism, emergence, and multicausality. Therefore, I see recent advances in ecology, evolutionary biology, and the philosophy of biology as laying the groundwork for another major biological synthesis, what I refer to as the Second Synthesis because, in many respects, it is analogous to the aims and outcomes of the first major biological synthesis (but is notably distinct from the inorganic and contrived progressive movement known as the extended evolutionary synthesis). With the general development of a distinctive philosophy of science, biology has rightfully emerged as an autonomous science. Thus, while the first synthesis legitimized biology, the Second Synthesis autonomized biology and afforded biology its own philosophy, allowing biology to finally realize its full scientific potential. (shrink)

Protein α-helices provide an ordered biological environment that is conducive to soliton-assisted energy transport. The nonlinear interaction between amide I excitons and phonon deformations induced in the hydrogen-bonded lattice of peptide groups leads to self-trapping of the amide I energy, thereby creating a localized quasiparticle (soliton) that persists at zero temperature. The presence of thermal noise, however, could destabilize the protein soliton and dissipate its energy within a finite lifetime. In this work, we have computationally solved the system (...) of stochastic differential equations that govern the quantum dynamics of protein solitons at physiological temperature, T=310 K, for either a single isolated α-helix spine of hydrogen bonded peptide groups or the full protein α-helix comprised of three parallel α-helix spines. The simulated stochastic dynamics revealed that although the thermal noise is detrimental for the single isolated α-helix spine, the cooperative action of three amide I exciton quanta in the full protein α-helix ensures soliton lifetime of over 30 ps, during which the amide I energy could be transported along the entire extent of an 18-nm-long α-helix. Thus, macromolecular protein complexes, which are built up of protein α-helices could harness soliton-assisted energy transport at physiological temperature. Because the hydrolysis of a single adenosine triphosphate molecule is able to initiate three amide I exciton quanta, it is feasible that multiquantal protein solitons subserve a variety of specialized physiological functions in living systems. (shrink)

The article aims to substantiate the philosophy of synthesis, which is built on the basis of analysis, but gives it a constructive direction. The turning point from analysis to synthesis is the problematization of the elements identified in the analysis, their criticism, replacement, or rearrangement, leading to the construction of alternative concepts and propositions that expand the field of the thinkable and innovate the categorical apparatus of philosophy. This article provides examples of philosophical synthesis at different levels: (...) alternative terms and concepts (“infinition”), postulates (the “diamond rule” in ethics), and disciplines (“horrology” as the study of the self-destructive mechanisms of civilization). Next, we consider the transition from the philosophy of synthesis to the synthesis of philosophy itself with contemporary scientific and technical practices. Technology of the 21st century is no longer instrumental/utilitarian, but a fundamental technology ("onto–technology"), which, thanks to science’s penetration into the micro- and macrocosm, can change the foundational parameters of being, thereby acquiring a philosophical dimension. Accordingly, philosophy as a study of the most general principles of the universe becomes a practical requirement in any “world-forming,” synthesizing acts of technology, including the design of computer games and multi-populated virtual worlds (e.g., “Second Life”), that involve a new ontology, logic, ethics, and axiology. The vocation of philosophy in the 21st century is not just to comprehend our unique world, but to lay the foundations for new world-forming practices, to initiate and design the ontology of possible worlds, and to pave the way for alternative forms of synthetic life and artificial intelligence. Contrary to Hegel, philosophy is no longer the “owl of Minerva” taking flight at dusk, but a skylark proclaiming the dawn of a new creative day. -/- . (shrink)

Biological order provided by α-helical secondary protein structures is an important resource exploitable by living organisms for increasing the efficiency of energy transport. In particular, self-trapping of amide I energy quanta by the induced phonon deformation of the hydrogen-bonded lattice of peptide groups is capable of generating either pinned or moving solitary waves following the Davydov quasiparticle/soliton model. The effect of applied in-phase Gaussian pulses of amide I energy, however, was found to be strongly dependent on the site of (...) application. Moving solitons were only launched when the amide I energy was applied at one of the α-helix ends, whereas pinned solitons were produced in the α-helix interior. In this paper, we describe a general mechanism that launches moving solitons in the interior of the α-helix through phase-modulated Gaussian pulses of amide I energy. We also compare the predicted soliton velocity based on effective soliton mass and the observed soliton velocity in computer simulations for different parameter values of the isotropy of the exciton-phonon interaction. The presented results demonstrate the capacity for explicit control of soliton velocity in protein α-helices, and further support the plausibility of gradual optimization of quantum dynamics for achieving specialized protein functions through natural selection. (shrink)

The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of generalized Davydov equations that govern the quantum dynamics of multiple amide I exciton quanta propagating along the hydrogen-bonded peptide groups in α-helices. Computational simulations have confirmed the generation of moving Davydov solitons by applied pulses of amide I energy for protein α-helices of varying length. The stability (...) and mobility of these solitons depended on the uniformity of dipole-dipole coupling between amide I oscillators, and the isotropy of the exciton-phonon interaction. Davydov solitons were also able to quantum tunnel through massive barriers, or to quantum interfere at collision sites. The results presented here support a nontrivial role of quantum effects in biological systems that lies beyond the mechanistic support of covalent bonds as binding agents of macromolecular structures. Quantum tunneling and interference of Davydov solitons provide catalytically active macromolecular protein complexes with a physical mechanism allowing highly efficient transport, delivery, and utilization of free energy, besides the evolutionary mandate of biological order that supports the existence of such genuine quantum phenomena, and may indeed demarcate the quantum boundaries of life. (shrink)

Abstract: A novel quadric-dentate demi-macrocycle of the type [C14H30N2O2] (ClO4)2¯ was synthesized by 1:2 condensation reaction at high dilution process. The desired demi-macrocycle was characterized by spectral methods such as UV-visible, IR, 1HNMR and elemental analysis. The results obtained were in close conformity with properties and proposed structure.

The development of student's skills in the conduct of research, both qualitative and quantitative, is envisioned in the K to12 curriculum. This study uses qualitative research to show students' perceptions and understanding of a particular issue. Similarly, it describes apparent cultures postulated within the students' chosen themes. Finally, it determines the development of cultural knowledge in the context of Merleau-Ponty's phenomenology of perception among Grade 11 students at a Senior High School near Laguna Lake in the City of San Pedro, (...) Laguna, Philippines, during the school year 2016-2017. Semi-structured interviews, focus group discussions, and triangulation was used to obtain students' cultural understanding and share their experiences undertaking diverse qualitative research using purposive sampling. The data was analyzed using phenomenological analysis. Students' perceptions and streams of consciousness include street children, child labor fishermen, and school violence. Cultural understanding encompasses (a) the economic and psychological implications of family, (2) camaraderie, pakikisama and pakikiisa, and (3) education as a survival strategy. Senior High School students' research experiences connect underpinnings of cultural understanding. (shrink)

Phthalic anhydride and 3-Nitro Phthalic anhydride were reacted with 2-aminomethyl benzimidazole in pyridine to give 2- (5-substituted phthalimidomethyl) bezimidazoles. These benzimidazoles were refluxed with chloroacetyl chloride in dry benzene followed by reaction with different secondary amines to give 1-(N-substituted amino acetyl)-2-(5-substituted phthalimidomethyl) benzimidazoles. Antiviral activity of these compounds was studied against Ranikhet Disease Virus (RDV) and Vaccinia Virus (VV). Some of these compounds have been found to be active against RDV.

3, 5 dinitro benzoic acid hydrazide was prepared by the hydrazinolysis of the corresponding ethyl ester. Condensation of this hydrazide with different aromatic acids in presence of POCl3 gave 2-3, 5 dinitropheny1-5-substituted pheny1 1, 3, 4-oxadiazoles. All the final compounds were tested against Ranikhet Disease Virus (RDV). However no compound showed antiviral activity against RDV.