The cashew nut is essential for physical and emotional well-being. It is an energetic diet and the best food medication for many illnesses. Nuts protects from malignant growth, coronary illness, circulatory strain, and various degenerative infirmities connected to aging. It can be used for several medicinal purposes. Every part of cashew has some important medicinal properties. Cashew kernel contains proteins, carbohydrates, vitamins, and fats which help gain energy. Cashew nuts are used for many purposes like blood sugar, weight loss, (...) cancer, cold and flu, aging, urinary disorders, digestive disorders, and bone relaxation. In comparing cashew with other nuts, Cashew kernels have good properties, including proteins, carbohydrates, fibers, and minerals, then almond, hazelnut, and walnuts. Cashew kernels contain the highest number of proteins (21%) when compared with Almonds (20.8%), Hazelnuts (15.6%), and Macadamia Nuts (60.9%). Cashew contain large amount of carbohydrate (22%) compared to other nuts like almonds, walnuts, etc. There are some strong benefits of Cashew for health. They boost the immune system, act as an antioxidant, remove gallstones, and beneficial for anemia. They are good sources of healthy fats that are necessary for our body to absorb fat-soluble vitamins. Its bark is known as the antihypertensive and glucose-lowering part. It has beneficial effect on the eyes and skin. This is rich in vitamin C, so it can be used for skin problems like acne, flawless freckles, skin lines and protects from aging. (shrink)

A number of experiences have demonstrated how digital solutions are effective in improving quality of life (QoL) and health outcomes for older adults. Smart Health Age-Friendly Environments (SHAFE) is a new concept introduced in Europe since 2017 that combines the concept of Age-Friendly Environments with Information Technologies, supported by health and community care to improve the health and disease management of older adults and during the life-course. This chapter aims to provide an initial overview of the experiences available not only (...) in Europe, based on the research work of the participants of the International Interdisciplinary Network on Health and Well-being in an Age-Friendly Digital World (NET4Age-Friendly), which could be of interest to preventive, health and social authorities. The chapter reports good practices, pain points, and bottlenecks that may require a collaborative, interdisciplinary research approach to facilitate the transformations towards smart, sustainable, health and age-friendly cities and communities. (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)

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)

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)

The purpose of this paper is to present a critique of the current view that reduces cancer to a cellular problem caused by specific gene mutations and to propose, instead, that such a problem might become more intelligible, if it is understood as a phenomenon that results from the breakdown of the morphological plan or Gestalt of the organism. Such and organism, in Aristotelian terms, is characterized for presenting a specific morphe or logos (form) and for having a telos (end) (...) to fulfill. A malignant tumor represents an entity separated from both the organic logos and the organic telos. According to the basic postulates of Semiophysics – a blend of Aristotelian physics and Catastrophe Theory developed by René Thom – an organism is a source (original) form individuated by a dominant pregnance that corresponds to its morphogenetic field. Here it is suggested that cancer in aged individuals might result from the progressive exhaustion of developmental constraints that regulate the process of ontogeny, that it is expected to go from the fertilized non-differentiated zygote to the mature fully developed organism, because there is no further point ahead in the developmental pathway past the reproductive age. Cancer in young individuals (before their reproductive maturity) may then be consequence of the premature derangement of such fundamental developmental constraints. In all cases the result is the loss of morphological coherence within the organism. Thus representing a conflict between an organized morphology (the organism) and a part of such a morphology that drifts towards an amorphous state (the tumor). (shrink)

Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems (MACS). While taking the emergence of properties seriously, the notion of MACS enables at the same time the design (or “meta-design”) of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied (...) in the field of Artificial Life, the specificity of MACS essentially lies in the close relation between their emergent properties and functional properties. Second, we argue that to be a MACS a system does not need to display more than weak emergent properties. Third, since the notion of weak emergence is based on the possibility of simulation, whether computational or mechanistic via machines, we see MACS as good candidates to help design artificial self-architected systems (such as robotic swarms) but also harness and redesign living ones (such as synthetic bacterial films). (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)

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.

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)

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 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)

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)

As Allaire and Firsirotu (1984) pointed out over a decade ago, the concept of culture seemed to be sliding inexorably into a superficial explanatory pool that promised everything and nothing. However, since then, some sophisticated and interesting theoretical developments have prevented drowning in the pool of superficiality and hence theoretical redundancy. The purpose of this article is to build upon such theoretical developments and to introduce an approach that maintains that culture can be theorized in the same way as structure, (...) possessing irreducible powers and properties that predispose organizational actors towards specific courses of action. The morphogenetic approach is the methodological complement of transcendental realism, providing explanatory leverage on the conditions that maintain for cultural change or stability. (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)

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. -/- .

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)

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)

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)

In 2011, a 5,000-year-old “male” skeleton buried in a “female” way was discovered by an archaeological team just outside of modern-day Prague. This article queries the impulse to name such a discovery as evidence of transgender identity, and bodies, in an increasingly ancient past. To do so, it takes up the work of Denise Ferreira da Silva, Sylvia Wynter, and Hortense Spillers as a means to push back against the impetus to name such discoveries “transgender” in order to shore up (...) the legitimacy of contemporary trans identity. Each of these three thinkers offers a different vantage point for rethinking such naming practices that push the reader to consider how desires to name and place “transgender” in a distant past papers over the violence of plantation slavery, global imperialism, and the Enlightenment's shift toward scientific reason. This article argues not that such anthropological discoveries should not be considered transgender, but rather that the desire for them to be, or become, transgender does not legitimate contemporary transgender identity, and may instead treat certain iterations of transness as spatially and temporally universal. (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)

A World of Muscle, Bone & Organs: Research and Scholarship in Dance is an e-book exploring contemporary ideas and themes in the research and practice of dance. It contains 23 chapters written by researchers at the Centre for Dance Research (C-DaRE), Coventry University, and is divided into six sections: Spaces of Practice, Philosophy, Communities, Politics, Data and Thinking, and Epistemology.

Mitchell & Gronenborn propose that we account for the presence of multiple models of protein structure, each produced in different contexts, through the framework of integrative pluralism. I argue that two interpretations of this framework are available, neither of which captures the relationship between a model and the protein structure it represents or between multiple models of protein structure. Further, it inclines us toward concluding prematurely that models of protein structure are right in their contexts and makes extrapolation of findings (...) from one context to another seem unwarranted. Instead, protein structure determination ought to be understood as modestly monistic. There is one model for every protein in each physicochemical context, and models of the same protein produced in different contexts are compatible with one another. ‘Integrating’ multiple models amounts to extrapolating from one context to another; this is possible because the effect of context on protein folding is relatively weak and predictable. Modest monism better describes the practice of protein structure determination than integrative pluralism and enables greater attention to how context affects protein folding. (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)

In this experimental investigation the Aluminium 6063 is treated with Aluminium Oxide (Al2O3) and Chicken Bone Ash (CBA). This Aluminium metal matrix composite is mixed at certain compositions and observed with the mechanical properties. Two main mechanical properties which includes Surface roughness and corrosion behavior is mainly focused in this research work. In this Research work aluminium hybrid metal matrix composite (AHMMC) is fabricated through stir casting process. Al6063 shows good mechanical properties and corrosion behavior changes, when combined with (...) reinforcements, Al2O3 and Chicken Bone Ash (CBA). Stir casting is an efficient cycle for the manufacture of aluminum hybrid composites. There are numerous boundaries in this cycle, which influence the behavior of corrosion and mechanical properties of the composites. Stir casting is a fluid state technique for the manufacture of composite materials, in which a scattered stage is blended in with a liquid network metal by methods for mechanical mixing. Stir Casting is the least difficult and the most financially savvy strategy for fluid state manufacture. Finally in this research work, when the compositions of each and every reinforcement increase, simultaneously the surface roughness of the composite also get increases. (shrink)

Objectives: The most principal nutrition source of a bone is nutrient arteries. They are important at every stage of bone development. A nutrient artery enters a bone through the nutrient foramen, the largest hole on the outer surface of the bone. The foramen is important both morphologically and clinically. -/- Methods: A total of 414 adult human dry bones were investigated in this study to identify topographic and morphological features of nutrient foramina in the scapula, clavicle, (...) humerus, radius and ulna. Nutrient foramina were examined with a hand lens. Their dimensions and directions were determined with a 21-gauge needle, and thus major foramina were detected. Positions of nutrient foramina were noted according to surfaces of the bones, and to segments separated as proximal, middle and distal by calculating foraminal index. -/- Results: A single nutrient foramen was found in 71% of our samples. We observed that 94.2% of foramina in the clavicle, 89.3% of foramina in the humerus, 51.3% of foramina in the radius, and 67.7% of foramina in the ulna were located in the middle 1/3 segment of the bones. -/- Conclusion: Our findings were in line with the data in the literature. On account of pathologies associated with the nutrient foramen, our findings may be helpful for surgeons to design applications performed in the region. In addition, we think that our data by contributing to the literature may be a resource for clinicians due to the importance of the nutrient foramen for surgical procedures. (shrink)

Objective: The present study aims to determine the number and position of the nutrient foramina (NF) of the human femur, tibia, and fibula and to observe the size, direction, and obliquity of the nutrient foramina. Methods: We observed 265 adult human, lower limb long bones in the Department of Anatomy of the Gaziantep University. The nutrient foramina were identified with naked eyes, and the obliquity was determined with a hypodermic needle. Gauge 20 and 24 needles were used for size determination. (...) Shape was observed with the naked eye and classified into oval and round types. The nutrient foramina location was determined by dividing total bone length into three segments, and the locations were validated by calculating foraminal index (FI). Results: Results showed that 79% of the long bones had a single nutrient foramen. More than 96% of the nutrient foramina were directed away from the knees. A total of 87% of the femoral foramina were located in the middle third, 72% of the tibial foramina were located in the proximal third, and 98% of the fibular nutrient foramina were located in the middle third of the specimens. Overall, no foramina were found on the distal third of the studied bones. Conclusion: Our study findings are in accordance to the findings from several research studies. The assessment of pathological conditions associated with the findings of foramen nutricium in our study may help clinicians and surgeons in planning treatments for applications to be performed in this region. However, it is thought that literature will be a source for basic and clinical sciences by providing reference values. (shrink)

Abstract: Sickle cell disease (SCD) comprises an inherited blood disorder that is life long and affects many people globally. Despite progress in therapy, SCA is a considerable cause of mortality and morbidity. This study was designed to measure the immunological and inflammatory parameters of patients with sickle cell disease (SCD) and to found if there is any role of it in the pathogenicity of the disease. This study included A total of 32 patients, their ages ranged from 16 to 55 (...) years patients with Sickle cell disease who have been evaluated during vaso occlusive crisis and had been followed up till they attained steady state, and there are 32 normal control subjects matched with patients in age and sex. In general there was elevation in all parameters the study were included in patients than control and particularly in crisis, despite the IgM value which was insignificantly decrease, but the statically significant elevation reported only in CRP, IgG, IgA. (shrink)

Good sciences have good metaphors. Indeed, good sciences are good because they have good metaphors. AI could use more good metaphors. In this editorial, I would like to propose a new metaphor to help us understand intelligence. Of course, whether the metaphor is any good or not depends on whether it actually does help us. (What I am going to propose is not something opposed to computationalism -- the hypothesis that cognition is computation. Noncomputational metaphors are in vogue these days, (...) and to date they have all been equally plausible and equally successful. And, just to be explicit, I do not mean “IQ” by “intelligence.” I am using “intelligence” in the way AI uses it: as a semi-techical term referring to a general property of all intelligent systems, animal (including humans), or machine, alike.). (shrink)

Macromolecular protein complexes catalyze essential physiological processes that sustain life. Various interactions between protein subunits could increase the effective mass of certain peptide groups, thereby compartmentalizing protein α-helices. Here, we study the differential effects of applied massive barriers upon the soliton-assisted energy transport within proteins. We demonstrate that excentric barriers, localized onto a single spine in the protein α-helix, reflect or trap three-spine solitons as effectively as concentric barriers with comparable total mass. Furthermore, wider protein solitons, whose energy is (...) lower, require heavier massive barriers for soliton reflection or trapping. Regulation of energy transport, delivery and utilization at protein active sites could thus be achieved through control of the soliton width, or of the effective mass of the protein subunits. (shrink)

In this work I propose a theory of evolution as a process of unfolding. This theory is based on four logically concatenated principles. The principle of evolutionary order establishes that the more complex cannot be generated from the simpler. The principle of origin establishes that there must be a maximum complexity that originates the others by logical deduction. Finally, the principle of unfolding and the principle of actualization guarantee the development of the evolutionary process from the simplest to the most (...) complex. These logical principles determine the existence of a virtual ideological matrix that contains the sequence of the preformed and folded morphogenetic fields. In this manner, the evolutionary process consists of the sequential unfolding and actualization of these fields, which is motorized by a process of teleologization carried out by the opening consciousness of the forms included in the fields of the ideological matrix. This theory leads to a radical change of perspective regarding the materialist worldview, and places life at the center of the evolutionary process as an activity carried out by a consciousness that seeks to fulfill a purpose by actualizing its own potentialities. (shrink)

Historically, hypotheses failed in most cases to correctly forecast the workings of complex biological systems. Francis Crick’s adaptor hypothesis, however, stands out as an exceptional case of a confirmed abstract prediction. This hypothesis presciently anticipated the existence of RNA adaptors that function as bridges between amino acids and the chemically different nucleic acid template for proteins. Crick conjectured that the adaptors are enzymatically charged with cognate amino acids, they bind to complementary protein-coding nucleic acid, and their liberated amino acids (...) are incorporated into growing protein chains. Independently from and concomitantly with Crick’s hypothesis, Mahlon Hoagland and Paul Zamecnik conducted experiments with no guiding theory that culminated in discoveries of the actual adaptors, transfer RNA (tRNA) molecules, and their amino acids charging enzymes. This paper traces the parallel histories of Crick’s adaptor hypothesis and of the experimental discovery of tRNA and compares their relative impacts on the scientific community. Remarkably, despite the brilliance of Crick’s confirmed prognostication, it had marginal impact on practicing scientists. Conversely, Hoagland and Zamecnik’s experimental discoveries and their evidence-based model of protein synthesis had immediate and enduring impact. I discuss possible explanations for the different impacts of the theoretical prediction and experimental identifications of the same entities. (shrink)

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles (...) which stand in the way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (shrink)

The problem with reductionism in biology is not the reduction, but the implicit attitude of determinism that usually accompanies it. Methodological reductionism is supported by deterministic beliefs, but making such a connection is problematic when it is based on an idea of determinism as fixed predictability. Conflating determinism with predictability gives rise to inaccurate models that overlook the dynamic complexity of our world, as well as ignore our epistemic limitations when we try to model it. Furthermore, the assumption of a (...) strictly deterministic framework is unnecessarily hindering to biology. By removing the dogma of determinism, biological methods, including reductive methods, can be expanded to include stochastic models and probabilistic interpretations. Thus, the dogma of reductionism can be saved once its ties with determinism are severed. In this paper, I analyze two problems that have faced molecular biology for the last 50 years—protein folding and cancer. Both cases demonstrate the long influence of reductionism and determinism on molecular biology, as well as how abandoning determinism has opened the door to more probabilistic and unconstrained reductive methods in biology. (shrink)

Chemical kinds (e.g. gold) are generally treated as having timelessly fixed identities. Biological kinds (e.g. goldfinches) are generally treated as evolved and/or evolving entities. So what kind of kind is a biochemical kind? This paper defends the thesis that biochemical molecules are clustered chemical kinds, some of which–namely, evolutionarily conserved units–are also biological kinds.On this thesis, a number of difficulties that have recently occupied philosophers concerned with proteins and kinds are shown to be resolved or dissolved.

Parents are usually appreciated as possessing legitimate moral authority to compel children to make at least modest sacrifices in the service of widely shared values of moral decency. This essay argues that such authority justifies allowing parents to authorize a child to serve as an organ or tissue donor in certain circumstances, such as to authorize bone marrow donations to save a sibling with whom the potential donor shares a deep emotional bond. The approach explored here suggests, however, that (...) at least under some conditions, parents have legitimate authority to authorize donations forbidden by current guidelines. (shrink)

In recent years, technology has evolved significantly to intervene in the treatment of diseases through diagnosis online before going to the specialist doctor, where it become possible for the patient to know the name of his illness, the specialist doctor who can treat him and the multiple treatment methods through specially designed systems called expert systems. The expert system is based on the principle of asking the user gradual questions about the symptoms he feels, leading him to the result of (...) diagnosing the illness, dealing with it quickly, and tips for permanent treatment. These systems may also help both trainee physicians and physiotherapists. This research paper is a living example of these effective applications, explaining in a simplified manner some of ankle diseases, how to deal with them and methods of physical therapy. The ankle is a small region in the leg. It is two joints, the first consist of three bones (tibia, fibula and talus underneath) which is called true ankle joint. The other is called subtalar joint have two bones: talus on top and calcaneus on the bottom. This tarsus between the end of the leg and the start of the foot facilitates the movement up-down and left-right with no problems in normal case, although, it needs a special case as Physiotherapist when gets injury. We have identified seven ankle diseases: Ankle Sprain, Fracture (of Fibula), Rheumatoid Arthritis, Rheumatoid Fever, Gout, and Osteoarthritis (Degenerative Joint) using SL5 Object Expert System Language in the work of the expert system. (shrink)

Objective: Atlas is located at a critical point close to the vital centers of the medulla oblongata, which can be compressed by the dislocation of the atlantoaxial complex or instability of the atlantooccipital joint. This study aimed to determine in detail the morphometric and morphological characteristics of the atlas to guide the reduction of the risk of complications and increase the success rate in various surgical approaches for the craniovertebral junction. -/- Methods: In this study, 17 atlas vertebrae whose measurement (...) parameters were pronounced and unknown gender, age, and ethnic characteristics were examined. -/- Results: Totally 16 parameters, 11 of which were bilateral and 5 were unilateral, were examined on the atlas. Also, no accessory foramen transversarium was found in these atlas vertebrae. Of the 23 foramina transversaria that were prominent and not broken, 7 were found to be round-shaped (30.43%), and 16 were oval-shaped (69.57%). -/- Conclusion: It is deducted that the results obtained in this study will help to have information about the morphometry and morphology of atlas vertebrae. Although information such as age, gender, and ethnic origin is not known about the bones evaluated, it is the advantage of this study that a large number of parameters are evaluated and compared with previous publications. Nevertheless, it seems that there is a need for studies in which much more cases are assessed, and information such as age, gender, and ethnic origin is known. (shrink)

The following bare-bones story introduces the idea of a cumulative hierarchy of pure sets: 'Sets are arranged in stages. Every set is found at some stage. At any stage S: for any sets found before S, we find a set whose members are exactly those sets. We find nothing else at S.' Surprisingly, this story already guarantees that the sets are arranged in well-ordered levels, and suffices for quasi-categoricity. I show this by presenting Level Theory, a simplification of set theories (...) due to Scott, Montague, Derrick, and Potter. (shrink)

Consciousness has been the bone of contention for philosophers throughout centuries. Indian philosophy largely adopted lived experience as the starting point for its explorations of consciousness. For this reason, from the very beginning, experience was an integral way of grasping consciousness, whose validity as a tool was considered self-evident. Thus, in Indian philosophy, the question was not to move from the brain to mind but to understand experience of an individual and how such an experience is determined through mental (...) structures (and secondarily, the preoccupation with the brain and its relation to the mind). In contrast, cognitive science (the study of mind and cognition through 1 interdisciplinary methods, with emphasis on computational methods) found its debates soaked in discussion which primarily involved the brain and mind. Experience was not considered a primary source of information and its validity had to be established to consider it a source of information of mind. With the rise of physicalism and realization that mental states are correlative to brain states, the body was virtually neglected from involvement in understanding the mind and the attempts to reduce mind to the brain were rampant. The inability to explain subjective experience of an individual through neuroscientific findings alone has urged philosophers to explore other ways of understanding the ontology of mind. Over the last few years, embodied cognition and enactive approach have brought back the body as a central participant in this debate, providing fertile grounds to explain the relation of brain, body and mind. This paper proposes that we understand the brain as a complex system from which the mind emerges. This emergence is marked by the development of novel property of self-consciousness in human beings. The mind is a process which is embedded throughout the body and thus, the body acts as an actualizing medium for the individual. Thus, the brain is a necessary condition for the mind to be while the mind is embedded throughout the body. The brain and mind are in reciprocal causal relationship with one another, as is the body and environment with one another. In this paper, embodied cognition is understood through principles of Merleau Ponty's idea of embodiment, than through Andy Clark and Francis Varela's alone. (shrink)

Much of the current research in regenerative medicine concentrates on stem-cell therapy that exploits the regenerative capacities of stem cells when injected into different types of human tissues. Although new therapeutic paths have been opened up by induced pluripotent cells and human mesenchymal cells, the rate of success is still low and mainly due to the difficulties of managing cell proliferation and differentiation, giving rise to non-controlled stem cell differentiation that ultimately leads to cancer. Despite being still far from becoming (...) a reality, these studies highlight the role of physical and biological constraints (e.g., cues and morphogenetic fields) placed by tissue microenvironment on stem cell fate. This asks for a clarification of the coupling of stem cells and microenvironmental factors in regenerative medicine. We argue that extracellular matrix and stem cells have a causal reciprocal and asymmetric relationship in that the 3D organization and composition of the extracellular matrix establish a spatial, temporal, and mechanical control over the fate of stem cells, which enable them to interact and control (as well as be controlled by) the cellular components and soluble factors of microenvironment. Such an account clarifies the notions of stemness and stem cell regeneration consistently with that of microenvironment. (shrink)

English Abstract: The manuscript describes a new scientific discipline called Octology, which should unify morphogenetic linguistics and neurobiology to investigate the development of the words, cognition and behavior. -/- Russian Abstract: В книге даётся описание научной дисциплины Октологии, призванной объединять морфогенетическую лингвистику и нейробиологию для исследования словообразования, понимания и поведения. -/- German Abstract: Der Begriff Oktologie (Engl. octology) wurde von Dr. Andrej Poleev in seinem gleichnamigen Aufsatz, der am 8. März 2010 erschienen ist, im Umlauf gebracht, und bezeichnet eine (...) wissenschaftliche Disziplin, welche die morphogenetische Linguistk und Neurobiologie vereint, um die Zusammenhänge zwischen Wahrnehmung, Verhalten und Wortbildung zu erforschen. Die Sprache ist das Mittel zwischenmenschlicher Verständigung, und der Sprache ist dieses Buch gewidmet. Wie entsteht Sprache? Welche sprachliche Formen gab es, gibt es heute, und wird es noch geben? In welchem Verhältnis steht Kultur zur Sprache? Was sind neurobiologische Grundlagen des Denkens und der Verbalisierung mentaler Inhalte? Mit diesen und anderen Fragen befasst sich neue Wissenschaft, die im Jahr 2010 gegründet wurde, um interdisziplinär die Zusammenhänge zwischen Wahrnehmung, Wortbildung und Verhalten zu erforschen. (shrink)

Upon separation of the protein from the nucleic acid component of tobacco mosaic virus by phenol, using a fast and gentle procedure, the nucleic acid is infective in assays on tobacco leaves. A series of qualitative and quantitative control experiments demonstrates that the biological activity cannot depend on residual proteins in the preparation, but is a property of isolated nucleic acid which is thus the genetic material of the virus.

The overarching argument of Currie’s Rock, Bone, and Ruin is that we should be optimistic rather than pessimistic about what the historical sciences can tell us, even about the deep past. To adopt either of these two positions is to take a stance on how the historical sciences tend to perform—on whether they tend to do well, or poorly, when it comes to informing us about the past.

While Darwin is commonly supposed to have demonstrated the inapplicability of the Aristotelian ontology of species to biological science, recent developments, especially in the wake of the Human Genome Project, have given rise to a new golden age of classification in which ontological ideas -- as for example in the Gene Ontology, the Cell Ontology, the Protein Ontology, and so forth -- are once again playing an important role. In regard to species, on the other hand, matters are more complex. (...) We provide a brief overview of recent proposals concerning the ontology of species, dealing with species as sets, classes and as collections, the views of Ernst Meyr, and mereological views. (shrink)

Description courte (Électre, 2019) : Une étude d'un des principaux axes de réflexion du philosophe des sciences et de la nature Raymond Ruyer (1902-1987). À la lumière des découvertes de l'embryogenèse et en s'appuyant par ailleurs sur la théorie de l'information, il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. -/- Short Descriptor (Electre 2019): A study of one of the main axes of reflection of the French philosopher of science and of nature Raymond Ruyer (1902-1987). Relying on (...) the discoveries about embryogenesis, and also with the use of information theory, Ruyer proposed an interpretation of the main unifying concepts of mechanistic cybernetics. -/- Cet ouvrage propose une étude fouillée d'un des principaux axes de réflexion du philosophe des sciences et de la nature français Raymond Ruyer (1902–1987) : la cybernétique. Après avoir proposé une philosophie structuraliste, Ruyer la modifia à la lumière des découvertes de l'embryogenèse, puis il proposa une interprétation des concepts unificateurs de la cybernétique mécaniste. Réfléchissant sur cette dernière et sur la théorie de l'information, en particulier sur l'origine de l'information, il défendit que cette cybernétique n'était qu'une lecture inversée de la vraie cybernétique, qui nous donnerait de lire dans l'expérience même les traces du pouvoir morphogénétique, appréhendé comme un champ axiologique. Dans un texte résumant son propre parcours, Ruyer affirma finalement que la critique de la théorie de l'information « peut donner […] l'espoir d'aboutir à quelque chose comme une nouvelle théologie. » Les idées directrices de Ruyer sont tout particulièrement contextualisées ici à partir de la question du développement des formes en biologie, et de celles de la génétique, de la genèse stochastique de l'ordre, et de l'identification mentale ou physique de l'information. Il se termine en départageant ce qui est théologique et axiologique dans ce projet de métaphysique qui, bien que resté inachevé, n'en représente pas moins le plus impressionnant conçu en France au siècle dernier. – This book offers an in-depth study of one of the main axes in the reflection of French philosopher of science and nature Raymond Ruyer. In a text summarising his own development, Ruyer stated about the philosophical critique of information theory that it "is what can give the most long-lasting hope of getting to something like a new theology." After propounding a structuralist philosophy, and distinguishing between form and structure, to then modify it in the light of discoveries in embryogenesis, Ruyer offered a re-evaluation of the unifying concepts of mechanistic cybernetics. Thinking about it and about information theory, he defended the idea that this cybernetics was in reality an inverted reading of the real one, which would allow us to read in experience itself traces of the morphogenetic power, apprehended as the axiological field. On some transversal points, the development of forms in biology and genetics, the stochastic genesis of order, the identification of information with either psychological and mental, or physical reality, behaviour, and the access to meaning, this work exposes the main ideas of Ruyer while situating them in the context of the breadth of others' contributions. It ends by determining what is theological and axiological in this project for a metaphysics which, although unfinished, is nevertheless the most impressive effort done in France in the last century. – Available on i6doc dot com (ISBN 978-2-930517-56-8 ; pdf 978-2-930517-57-5). (shrink)

The tears of Odysseus -- History : music gives voice to the ineffable -- Tears, chills, and broken bones -- The music itself -- Explaining strong emotional responses to music I -- Explaining strong emotional responses to music II -- The sublime, revisited -- Conclusion : values.

In the last few years, the idea of human being has been enlarged from the individual closeness to morphogenetic openness. Concurrently with discovers and researches into invisible worlds that live with human beings – microbes, fungi, bacteria, etc. – a debate has opened up that agrees with recent positions in the field of ontology. The human being is capable of poietic openness and is defined by relations. Anyway, an absence of a rigorous conceptualisation of the individualising process remains latent (...) to the discourse. A classic principle of individualisation is probably incomplete. This paper brings into dialogue individualisation with singularisation through the manifestation process of expression in accordance with recent theoretical enactments of hybridisation processes. (shrink)

The question which this paper examines is that of the correct scope of the claim that extra-linguistic factors (such as gender and social status) can block the proper workings of natural language. The claim that this is possible has been put forward under the apt label of silencing in the context of Austinian speech act theory. The ‘silencing’ label is apt insofar as when one’s ability to exploit the inherent dynamic of language is ‘blocked’ by one’s gender or social status (...) then one might justly be said to be silenced. The notion that factors independent of any person’s linguistic competence might block her ability to exploit the inherent dynamic of language is of considerable social as well as theoretical significance. I shall defend the claim that factors independent of a person’s linguistic competence can indeed block her ability to do things with words but I will show that the cases that have been previously considered to be cases of illocutionary failure are instances of rhetic or locutionary act failure instead. I shall refine the silencing claim as previously advanced in the debate in at least one fundamental respect. I also show that considering the metaphysics of speech acts clarifies many of the issues previously appearing as thorny bones of contention between those who hold that the only notion of silencing that is coherent is that of physically preventing someone from speaking or writing and those who hold the opposite sort of claim sketched above. (shrink)

While many different mechanisms contribute to the generation of spatial order in biological development, the formation of morphogenetic fields which in turn direct cell responses giving rise to pattern and form are of major importance and essential for embryogenesis and regeneration. Most likely the fields represent concentration patterns of substances produced by molecular kinetics. Short range autocatalytic activation in conjunction with longer range “lateral” inhibition or depletion effects is capable of generating such patterns (Gierer and Meinhardt, 1972). Non-linear reactions (...) are required, and mathematical criteria were derived to design molecular models capable of pattern generation. The classical embryological feature of proportion regulation can be incorporated into the models. The conditions are mathematically necessary for the simplest two-factor case, and are likely to be a fair approximation in multi-component systems in which activation and inhibition are systems parameters subsuming the action of several agents. Gradients, symmetric and periodic patterns, in one or two dimensions, stable or pulsing in time, can be generated on this basis. Our basic concept of autocatalysis in conjunction with lateral inhibition accounts for self-regulatory biological features, including the reproducible formation of structures from near-uniform initial conditions as required by the logic of the generation cycle. Real tissue form, for instance that of budding Hydra, may often be traced back to local curvature arising within an initially relatively flat cell sheet, the position of evagination being determined by morphogenetic fields. Shell theory developed for architecture may also be applied to such biological processes. (shrink)