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)

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 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)

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 (...) class='Hi'>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)

Quadruple Helix Collaborations (QHCs) is a cooperation model in which industry, government, academia, and the public interact to innovate. This paper analyses the impact of a training intervention to provide specific knowledge, skills, and attitudes to deal with barriers commonly found in the progress of QHCs. We designed, implemented, and evaluated three training programs in Austrian, Colombian, Danish, and Spanish institutions. We analysed trainees’ (n = 66) and trainers’ (n = 9) perceptions to identify the competencies acquired with the (...) intervention and the approach’s limitations. We used online questionnaires (35 trainees; 9 trainers), semi-structured interviews (10 trainees), and a focus group (6 trainers). Trainees answered positively regarding their self-perception about the impact of the course and highlighted the acquisition of inspiration for their practice (score 4.1 out of 5.0) and knowledge (3.7). In contrast, they perceived that a deeper interaction with other participants (2.7) was challenging. After the courses, 74% of respondents indicated that they know more about how QHCs work in practice, and 86% about collaboration or engagement methods. Moreover, participants plan to be more sensitive towards setting common goals (71%) and power imbalances (63%). Trainers’ perceptions align with those expressed by participants, except that they considered that the interaction amongst participants during the course was higher. Qualitative analysis of interviews with participants and the focus group with trainers provides more detail about the strengths and weaknesses of the intervention. Our study shows that the collaborative design and implementation of training impact the participant’s learning competencies, with potential implications in their medium- to long-term practice. (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://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; 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) 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.

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)

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)

To address societal challenges, research and innovation approaches, involving a wide range of actors, are increasingly promoted by policy communities. This paper explores the practice of Quadruple Helix collaborations for responsible innovation and how these implement the theoretical ambition of including actors from different societal sectors in innovation, including actors from the fields of arts, media and civil society, which is conceptualized as the Fourth Helix in this concept. Referring to cross-sector collaboration literature and based on an empirical (...) investigation, we explore which actors, representing the Fourth Helix, actually engage in innovation collaborations, how this engagement plays out in practice, and the institutional and systemic dynamics involved in output and value creation. We rely on data from three Social Labs in Austria, Germany, and the Netherlands, which constitute qualitative, change-oriented research processes, where we researched and engaged with actors from cases constituting- or aiming for a Quadruple Helix collaboration. This was accompanied by a desktop study including qualitative interviews of 51 further cases. We find that the actual engagement of actors from civil society is fragile and that forces beyond Quadruple Helix cases impact these quite firmly in some cases. (shrink)

R&D collaborations between industry, government, civil society, and research (also known as ‘quadruple helix collaborations’ (QHCs)) have recently gained attention from R&D theorists and practitioners. In aiming to come to grips with their complexity, past models have generally taken a stakeholder-analytical approach based on stakeholder types. Yet stakeholder types are difficult to operationalise. We therefore argue that a processual model is more suited for studying the interaction in QHCs because it eschews matters of titles and identities. We develop such (...) a model in which the QHC is represented as a process of generating four types of value: research value, market value, political value, and societal value. We then apply this processual model in analysing reallife cases of friction in QHCs. Friction is seen, not as an interpersonal clash, but as a discrepancy between two or more value-creation processes that compete for limited resources (some overperforming while others under-performing). (shrink)

R&D collaborations between industry, government, civil society, and research ) have recently gained attention from R&D theorists and practitioners. In aiming to come to grips with their complexity, past models have generally taken a stakeholder-analytical approach based on stakeholder types. Yet stakeholder types are difficult to operationalise. We therefore argue that a processual model is more suited for studying the interaction in QHCs because it eschews matters of titles and identities. We develop such a model in which the QHC is (...) represented as a process of generating four types of value: research value, market value, political value, and societal value. We then apply this processual model in analysing real-life cases of friction in QHCs. Friction is seen, not as an interpersonal clash, but as a discrepancy between two or more value-creation processes that compete for limited resources. (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)

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)

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)

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. -/- .

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)

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)

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)

The presented study introduces a new theoretical model of collapse for social, cultural, or political systems. Based on the current form of quantum anthropology conceptualized by Heidi Ann Russell, further development of this field is provided. The new theoretical model is called the spiral model of collapses, and is suggested to provide an analytical framework for collapses in social, cultural, and political systems. The main conclusions of this study are: 1) The individual crises in the period before a collapse of (...) social, cultural, and political systems form the trajectory of a conical helix similar to a vortex. 2) The occurrences of crises in the period before a collapse have the shape of the trajectory on the surface of the circular cone with a convex wall narrowing up to its peak. The shape of this cone is based on the Fibonacci sequence coiled into the three-dimensional space. 3) The constant circular movement along the trajectory of crises can occur in exceptional situations in the development of social, cultural, and political systems; however, such a state is always temporary. In such cases, the trajectory of the crisis does not follow the Fibonacci sequence, but the shape of a regular helix. Remaining on the trajectory of a regular helix in the long-term is highly improbable for social, cultural, and political systems. 4) The creation of new potentialities after the final collapse of a system is explained by the conception of topological inversion, when the heretofore embodied part of the energy-information field returns to the global, wave-particle energy-information potential. 5) The global, wave-particle energy-information potential is a source of energy-information for future embodiments in the sense of the future collapses of wave functions. (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)

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)

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.

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.

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

Abstract: Fish are important for both nutritional and economic reasons. They are a good source of protein, vitamins, and minerals and play a significant role in human diets, especially in coastal and island communities. In addition, fishing and fish farming are major industries that provide employment and income for millions of people worldwide. Moreover, fish play a critical role in marine ecosystems, serving as prey for larger predators and helping to maintain the balance of aquatic food chains. Overall, fish (...) play a vital role in supporting human well-being and the health of our planet. . Fishes have a lots of types such that: Red Mullet, Sea Bass, Striped Red Mullet and Shrimp. Each of them has its own shape and characteristics that differ from other types. We proposed a system that recognize nine types of fishes using deep learning. We trained the model with a dataset that contain 9000 images that were slit into 6300 images for training, 1350 for validation and 1350 for testing. The proposed model achieved accuracy (99.68%), precision (99.69%), recall (99.68%), and f1-score (99.68%). This indicates that our proposed model can effectively predicate and classify different types of fish with very high accuracy. (shrink)

This paper explores the evolution of consciousness and subjectivity through a biological framework for understanding the universe. It posits that functional patterns in biological systems mirror cosmic mathematical principles, defining our objective reality. Similar to wave and Fibonacci patterns in different physical phenomena, biological patterns are intrinsic to all things and can be quantified using Dedre Gentner’s approach to analogy. For example, Earth’s ocean currents and the melting and freezing of Antarctica resemble the circulatory system and heart, while the production (...) of music from instruments is analogous to ribosomal protein synthesis. Shelves, tables, and chairs function like cytosol by holding objects in space, and a coffee cup mirrors red blood cell distribution. These analogies reveal a universal order rooted in biology’s functional patterns, essential for shaping the emergence and evolution of life. The paper traces the development of consciousness from its rudimentary cellular states to complex human cognition, highlighting the role of biologically-patterned environments in driving evolutionary changes. Organisms that recognized and organized according to these patterns evolved as “pattern recognition engines” crucial for survival—thus, Life (survival) being the primary measure of consciousness. Humans advanced this capacity, gaining cognitive freedom by insulating themselves from environmental constraints, but faced increased subjectivity complexity. Consciousness, while inherently subjective and necessary for cognitive development, evolves in humans to understand objective reality and its biological nature, so to understand and navigate complexities of subjectivity. Ultimately, the paper asserts consciousness is the ability to recognize and adhere to life-sustaining patterns and principles. Successful adherence deems them worthy of continued existence, while failure leads to demise. Parallels with historical concepts like Atman and Brahman in Hinduism suggest ancient recognition of the correspondence between human and universal patterns. This ancient understanding, coupled with modern scientific evidence, reveals the interconnectedness and intrinsic biological nature of reality. (shrink)

Biomolecules and particularly proteins and DNA exhibit some mysterious features that cannot find satisfactory explanation by quantum mechanical modes of atoms. One of them, known as a Levinthal’s paradox, is the ability to preserve their complex three-dimensional structure in appropriate environments. Another one is that they possess some unknown energy mechanism. The Basic Structures of Matter Supergravitation Unified Theory (BSM-SG) allows uncovering the real physical structures of the elementary particles and their spatial arrangement in atomic nuclei. The resulting physical models (...) of the atoms are characterized by the same interaction energies as the quantum mechanical models, while the structure of the elementary particles influence their spatial arrangement in the nuclei. The resulting atomic models with fully identifiable parameters and angular positions of the quantum orbits permit studying the physical conditions behind the structural and bonding restrictions of the atoms connected in molecules. A new method for a theoretical analysis of biomolecules is proposed. The analysis of a DNA molecule leads to formulation of hypotheses about the energy storage mechanism in DNA and its role in the cell cycle synchronization. This permits shedding a light on the DNA feature known as a C-value paradox. The analysis of a tRNA molecule leads to formulation of a hypothesis about a binary decoding mechanism behind the 20 flavors of the complex aminoacyle-tRNA synthetases - tRNA, known as a paradox. (shrink)

I consider some hitherto unexplored examples of teleological language in the sciences. In explicating these examples, I aim to show (a) that such language is not the sole preserve of the biological sciences, and (b) that not all such talk is reducible to the ascription of functions. In chemistry and biochemistry, scientists explaining molecular rearrangements and protein folding talk informally of molecules rearranging “in order to” maximize stability. Evolutionary biologists, meanwhile, often speak of traits evolving “in order to” optimize (...) some fitness-relevant variable. I argue that in all three contexts such locutions are best interpreted as shorthands for more detailed explanations which, were we to spell them out in full, would show that the relevant process would robustly converge towards the same end-point despite variation in initial conditions. This suggests that, in biology, such talk presupposes a substantial form of adaptationism. The upshot is that such shorthands may be more applicable in the physical sciences than the biological. (shrink)

The concept of Generative Artificial Intelligence (GenAI) is ubiquitous in the public and semi-technical domain, yet rarely defined precisely. We clarify main concepts that are usually discussed in connection to GenAI and argue that one ought to distinguish between the technical and the public discourse. In order to show its complex development and associated conceptual ambiguities, we offer a historical-systematic reconstruction of GenAI and explicitly discuss two exemplary cases: the generative status of the Large Language Model BERT and the differences (...) between protein structure predictions from AlphaFold 2 and 3. Our analysis shows that there is no unique and unambiguous definition of GenAI based on a purely technical account of the term. Following this conclusion, we argue that the public discourse is not simply a less complex way of speaking, but instead transcends its technical basis. As a means to structure this newly emerging discussion landscape we introduce a non-exhaustive list of four central aspects of GenAI: (multi-)modality, interaction, flexibility, and productivity. These dimensions constitute a first step towards defining GenAI beyond its technical basis. (shrink)

In the quest for a new social turn in philosophy of science, exploring the prospects of a Vygotskian perspective could be of significant interest, especially due to his emphasis on the role of culture and socialisation in the development of cognitive functions. However, a philosophical reassessment of Vygotsky's ideas in general has yet to be done. As a step towards this direction, I attempt to elaborate an approach on scientific representations by drawing inspirations from Vygotsky. Specifically, I work upon Vygotsky’s (...) understanding on the nature and function of concepts, mediation and zone of proximal development. -/- I maintain that scientific representations mediate scientific cognition in a tool-like fashion (like Vygotsky’s signs). Scientific representations are consciously acquired through deliberate inquiry in a specific context, where it turns to be part of a whole system, reflecting the social practices related to scientific inquiry, just scientific concepts do in Vygotsky’s understanding. They surrogate the real processes or effects under study, by conveying some of the features of the represented systems. Vygotsky’s solution to the problem of the ontological status of concepts points to an analogous understanding for abstract models, which should be regarded neither as fictions nor as abstract objects. -/- I elucidate these views by using the examples of the double-helix model of DNA structure and the development of our understanding of the photoelectric effect. (shrink)

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)

The study area was a small lowland river valley within a range of 4750 m length and approx. 150 m width (about 62 ha), situated in the south-east of Poland, in the middle of Sandomierz Basin (Fig. 1). Flora and the chosen most valuable plant communities of the river bed with adjacent ecotone zone were investigated in 2007. During the study 291 species of vascular plants were found. Among them 10 are protected: Batrachium peltatum, Convallaria majalis, Dactylorhiza majalis, Daphne mezereum, (...) Frangula alnus, Hedera helix, Lycopodium annotium, Nuphar lutea, Utricularia vulgaris, and Viburnum opulus. Other species were considered to be value-raising, e.g. Achillea ptarmica, Batrachium circinatum, Calla palustris, Crepis paludosa, Hottonia palustris, Hypochoeris glabra, Senecio ovatus or Valeriana dioica. The number of antropophytes with the amount of 10% is relatively low. Most valuable plant communities represent 3 types of Nature 2000 habitats: natural eutrophic lakes with Magnopotamion or Hydrocharition – code 3150, transition and quaking bogs – code 7140-1, and alluvial forests with Alnus glutinosa and Fraxinus excelsior – code 91E0-3. Human activities brought about the emergence of 3 different areas within the valley: channeled river site (K), natural river bed site (N) and agricultural field site (P). Those areas differ significantly in terms of the composition of flora, vegetation and biological diversity. Most valuable is (P) and the least is (K). The greatest potential source of danger for biodiversity is the wrong forester’s management, especially interference in the natural processes (the planned building of the extra pond) and preventing wooden biomass accumulation. (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)

Despite the Nazi horrors, in 1953 the new eugenics was founded, when Watson and Crick postulated the double helix of DNA as the basis of chemical heredity. In 1961, scientists have deciphered the genetic code of DNA, laying the groundwork for code manipulation and the potential building of new life forms. After thirty years from the discovery of the DNA structure, the experimenters began to carry out the first clinical studies of human somatic cell therapy. The practice of prenatal (...) genetic tests identifies genes or unwanted genetic markers. Parents can choose to continue pregnancy or give up the fetus. Once the preimplantation genetic diagnosis occurs, potential parents can choose to use in vitro fertilization and then test early embryonic cells to identify embryos with genes they prefer or avoid. Because of concerns about eugenics, genetic counseling is based on a "non-directive" policy to ensure respect for reproductive autonomy. The argument for this counseling service is that we should balance parental autonomy with child's autonomy in the future. Specialists have not yet given a clear answer to the question of whether these practices should be considered eugenic practices, or if they are moral practices. DOI: 10.13140/RG.2.2.28777.95849. (shrink)

If non-human animals have high moral status, then we commit a grave moral error by eating them. Eating animals is thus morally risky, while many agree that it is morally permissible to not eat animals. According to some philosophers, then, non-animal ethicists should err on the side of caution and refrain from eating animals. I argue that this precautionary argument assumes a false dichotomy of dietary options: a diet that includes farm-raised animals or a diet that does not include animals (...) of any kind. There is a third dietary option, namely, a diet of plants and non-traditional animal protein, and there is evidence that such a diet results in the least amount of harm to animals. It follows therefore that moral uncertainty does not support the adoption of a vegetarian diet. (shrink)

Sheep production is the most representative livestock activities in Brazil and in the world. However, the reproductive performance of these animals is determined by factors genetic, physical environment, management and, especially, nutritional. Thirty half-breed lambs from Dorper × Santa Inês were used, with initial weight and age of 31.87 ± 0.5 kg and 157 days, respectively. These animals were prepared on a diet with three food levels (ad libitum, 30% and 70%). Morphometric measurements were measured at intervals of 16 to (...) 20 days in 56 experimental days. The measurements performed were scrotal circumference (CE), chest circumference (CT), body condition score (ECC), withers height (AC) and scrotal bag thickness (EBE), body weight (CP) and semen collection. Interaction occurrence for biometric measurements between food levels and age (p <0.05). The TC and ECC values were higher in animals fed ad libitum (p <0.001). EBE had higher values in animals ad libitum and at 211 days of age (p <0.001). The CP was increasing for the animals ad libitum and (p <0.05) throughout the experiment, while the T30 was only in the initial period. T70 animals did not grow during the whole experiment. CE was influenced by diet (p <0.001) and age (p <0.001) independently. So that animals under food restriction had less development and was higher in older animals. The AC values were influenced only by age (p <0.001), demonstrating the effect of age growth. We conclude that it is not advantageous to submit lambs, it corrects food reproduction. Although it was not possible to assess whether initial malnutrition would bring future problems for the animal's seminal quality, it proved to be immensely negative for the onset of puberty and the development of reproductive structures. -/- REFERÊNCIAS BIBLIOGRÁFICAS AKUMBUGU, F. E., et al. 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Morphometric and endocrine analyses of the effects of nutrition on the testis of mature Merino rams. Reproduction, v. 113, n. 2, p. 217-230, 1998. Instituto Brasileiro de Geografia e Estatística (IBGE). Produção Pecuária municipal. Rio de Janeiro, v. 46, p.1-8, 2018. KENYON, P. R.; MALONEY, S. K.; BLACHE, D. Review of sheep body condition score in relation to production characteristics. New Zealand Journal of Agricultural Research, v. 57, n. 1, p. 38-64, 2014. KHERADMAND, A.; BABAEI, H.; ALI BATAVANI, R. Effect of improved diet on semen quality and scrotal circumference in the ram. Veterinarski arhiv, v. 76, n. 4, p. 333-341, 2006. KORKMAZ, M. K.; EMSEN, E. Growth and reproductive traits of purebred and crossbred Romanov lambs in Eastern Anatolia. Anim. Reprod., v. 13, n. 1, p. 3-6, 2016. KRIDLI, R. T. et al. Age at puberty and some biological parameters of Awassi and its first crosses with Charollais and Romanov rams. Italian journal of animal science, v. 5, n. 2, p. 193-202, 2006. LOUW, D. F. J.; JOUBERT, D. M. Puberty in the male Dorper sheep and Boer goat. S. Afr. J. Agric. Sci, v. 7, p. 509-520, 1964. MAIA, A. S. C.; SILVA, R. G.; ANDRADE, P. C. Efeitos da temperatura e da movimentação do ar sobre o isolamento térmico do velo de ovinos em câmara climática. Revista Brasileira de Zootecnia, v. 38, n. 1, p. 104-108, 2009. MARTINS, R. D. et al. Avaliação da sazonalidade reprodutiva de carneiros Santa Inês criados no Distrito Federal. R. Bras. Zootec., Viçosa, v. 32, n. 6, supl. 1, p. 1594-1603, Dec. 2003. MENDES, A. M. P. et al. Zoneamento bioclimático para a raça ovina Dorper no Estado de Pernambuco. Pesquisa Agropecuária Brasileira, v. 49, n. 12, p. 986-993, 2014. MOULLA, F. et al. Characterization of the onset of puberty in Tazegzawt lambs, an endangered Algerian sheep: Body weight, thoracic perimeter, testicular growth, and seminal parameters. Veterinary world, v. 11, n. 7, p. 889, 2018. NATIONAL RESEARCH COUNCIL (NRC). Nutrient Requirements of Small Ruminants: Sheep, Goats, Cervids, and New World Camelids. Washington, D.C.: National Academy Press, 2007. NOTTER, D. R.; LUCAS, J. R.; MCCLAUGHERTY, F. S. Accuracy of estimation of testis weight from in situ testis measures in ram lambs. Theriogenology, v. 15, n. 2, p. 227-234, 1981. SEJIAN, V. et al. Effect of body condition score on the allometric measurements and reproductive performance of Garole X Malpura ewes under hot semi-arid environment. Journal of Dairy, Veterinary & Animal Research, v. 2, n. 6, p. 1-4, 2015. PACHECO, A.; MADELLA-OLIVEIRA, A. F.; QUIRINO, C. R. Biometria e formas dos testículos em cordeiros da raça Santa Inês explorados em regime de manejo intensivo. Revista Brasileira de Ciências Agrárias, v. 5, n. 1, p. 123-128, 2010. REGO NETO, A. A. et al. Population genetic structure of Santa Inês sheep in Brazil. Tropical animal health and production, v. 50, n. 3, p. 503-508, 2018. RHIND, S. M. Effects of maternal nutrition on fetal and neonatal reproductive development and function. Animal Reproduction Science, v. 82, p. 169-181, 2004. RIBEIRO, E. L. A.; GONZÁLEZ-GARCÍA, E. Indigenous sheep breeds in Brazil: potential role for contributing to the sustainability of production systems. Tropical animal health and production, v. 48, n. 7, p. 1305-1313, 2016. RIBEIRO, M. S. et al. Repeatability and effect of age on reproductive characteristics in Santa Ines rams. Archivos de zootecnia, v. 67, n. 257, p. 143-147, 2018. RUSSEL, A. J. F.; DONEY, J. M.; GUNN, R. G. Subjective assessment of body fat in live sheep. The Journal of Agricultural Science, v. 72, n. 3, p. 451-454, 1969. SILVA, N. V. et al. Medidas in vivo e da carcaça e constituintes não carcaça de ovinos alimentados com diferentes níveis do subproduto agroindustrial da goiaba. Revista Brasileira de Saúde e Produção Animal, v. 17, n. 1, p. 101-115, 2016. SILVA, P. et al. Influence of placentally mediated fetal growth restriction on the onset of puberty in male and female lambs. Reproduction, v. 122, n. 3, p. 375-383, 2001. SIQUEIRA FILHO, E. R. Influência dos níveis protéicos fornecidos na dieta sobre o sistema reprodutivo de carneiros. 2007. 75 f. Dissertação (mestrado) - Universidade Estadual Paulista, Faculdade de Medicina Veterinária e Zootecnia de Botucatu, 2007. SOUZA, J. S da et al. Biometric measurements of Santa Inês meat sheep reared on Brachiaria brizantha pastures in Northeast Brazil. Plos one, v. 14, n. 7, p. e0219343, 2019. (shrink)

When considering the question of possible transformation and disappearance of scientific objects, it is useful to distinguish between epistemic and technical objects. This paper presents preliminary observations and offers a typology of obsolescence. It is based on several case studies drawn from the history of life sciences. The paper proceeds as follows: first, the dynamics of epistemic objects is considered through the examples of Carl Correns’ study of “xenia”, Alfred Kühn’s work on physiological developmental genetics, and Paul Zamecnik’s research on (...) the protein biosynthesis. Second, the phasing out of technical objects is then separately discussed and illustrated by the example of radioactive tracing in biology – until recently, an established technique of visualization. (shrink)

In a now classic paper published in 1991, Alberch introduced the concept of genotype–phenotype (G!P) mapping to provide a framework for a more sophisticated discussion of the integration between genetics and developmental biology that was then available. The advent of evo-devo first and of the genomic era later would seem to have superseded talk of transitions in phenotypic space and the like, central to Alberch’s approach. On the contrary, this paper shows that recent empirical and theoretical advances have only sharpened (...) the need for a different conceptual treat- ment of how phenotypes are produced. Old-fashioned metaphors like genetic blueprint and genetic programme are not only woefully inadequate but positively misleading about the nature of G!P, and are being replaced by an algorithmic approach emerging from the study of a variety of actual G!P maps. These include RNA folding, protein function and the study of evolvable soft- ware. Some generalities are emerging from these disparate fields of analysis, and I suggest that the concept of ‘developmental encoding’ (as opposed to the classical one of genetic encoding) provides a promising computational–theoretical underpinning to coherently integrate ideas on evolvability, modularity and robustness and foster a fruitful framing of the G!P mapping problem. (shrink)

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction (...) of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes. (shrink)

This paper examines the adequacy of causal graph theory as a tool for modeling biological phenomena and formalizing biological explanations. I point out that the causal graph approach reaches it limits when it comes to modeling biological phenomena that involve complex spatial and structural relations. Using a case study from molecular biology, DNA-binding and -recognition of proteins, I argue that causal graph models fail to adequately represent and explain causal phenomena in this field. The inadequacy of these models is due (...) to their failure to include relevant spatial and structural information in a way that does not render the model non-explanatory, unmanageable, or inconsistent with basic assumptions of causal graph theory. (shrink)

Background: A bean is the seed of one of several genera of the flowering plant family Fabaceae, which are used as vegetables for human or animal food. They can be cooked in many different ways, including boiling, frying, and baking, and are used in many traditional dishes throughout the world. Beans are one of the longest-cultivated plants. Broad beans, also called fava beans, in their wild state the size of a small fingernail, were gathered in Afghanistan and the Himalayan foothills. (...) In a form improved from naturally occurring types, Beans were an important source of protein throughout old and new world history, and still are today. Objectives: The main goal of this expert system is to get the appropriate diagnosis of disease and the correct treatment. Methods: In this paper, the design of the proposed Expert System was produced to help farmers and those interested in agriculture in diagnosing many of the Bean diseases such as Fusarium wilt, Charcoal rot or ashy stem blight, Bacterial leaf spot and blight, Mung bean yellow mosaic virus, Cercospora leaf spot. The proposed expert system presents an overview of Bean diseases are given, the cause of diseases outlined and the treatment of disease whenever possible is given out. CLIPS Expert System language was used for designing and implementing the proposed expert system. Results: The proposed Bean diseases diagnosis expert system was evaluated by Agricultural experts and some friends interested in agriculture and they were satisfied with its performance. Conclusions: The proposed expert system is very useful for Farmers and those interested in agriculture. (shrink)

Digitalization processes are global and performed in all spheres of economic activities. The development of the digital economy correlates with the dynamics of educational, scientific and technical, and innovative activities in the country. Higher education particularly affects the development of the digital economy because it is a system training highly qualified personnel, conducting quality research, and generating innovations. The purpose of the article is the identification of promising vectors of higher education system development under the conditions of digitalization of national (...) economy. Section 1 of the article presents the authors’ methodological approach to assessment the impact of educational, research, and innovation components on digital economy development. The implementation of the authors’ approach covers the phased use of methods of statistical, index, cluster and system analysis. The influence of higher education on the structural components of the digital economy (educational, research, innovative ones) is grounded. The result of the study was the identification of main trends in the development of higher education under the conditions of digital economy. The problems of the development of higher education are systematized in the groups: contextual, legal, organizational and economic, financial, logistical problems, and problems of internationalization. Based on the results of the analysis, the authors conclude the necessity of development of a conceptual base for increasing the digital adaptability of the higher education system to new socio-economic conditions. Section 2 of the article describes the concept of the digital adaptability strategy of the higher education system. The concept was developed on the base of structural and functional, systemic and synergetic, and institutional approaches. The proposed concept is based on the idea of deepening the long-term partnership of universities with stakeholders within the Quadruple Helix model. In the conclusion section, the authors highlight the key priorities of the digital adaptability strategy of the higher education system. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)