Complexity, BioComplexity, the Connectionist Conjecture and Ontology of Complexity\ud

This paper develops and integrates major ideas and concepts on complexity and biocomplexity - the connectionist conjecture, universal ontology of complexity, irreducible complexity of totality & inherent randomness, perpetual evolution of information, emergence of criticality and equivalence of symmetry & complexity. This paper introduces the Connectionist Conjecture which states that the one and only representation of Totality is the connectionist one i.e. in terms of nodes and edges. This paper also introduces an idea of Universal Ontology of Complexity and develops concepts in that direction. The paper also develops ideas and concepts on the perpetual evolution of information, irreducibility and computability of totality, all in the context of the Connectionist Conjecture. The paper indicates that the control and communication are the prime functionals that are responsible for the symmetry and complexity of complex phenomenon. The paper takes the stand that the phenomenon of life (including its evolution) is probably the nearest to what we can describe with the term “complexity”. The paper also assumes that signaling and communication within the living world and of the living world with the environment creates the connectionist structure of the biocomplexity. With life and its evolution as the substrate, the paper develops ideas towards the ontology of complexity. The paper introduces new complexity theoretic interpretations of fundamental biomolecular parameters. The paper also develops ideas on the methodology to determine the complexity of “true” complex phenomena.\u

Quantum Hall Effect in Graphene with Interface-Induced Spin-Orbit Coupling

We consider an effective model for graphene with interface-induced spin-orbit coupling and calculate the quantum Hall effect in the low-energy limit. We perform a systematic analysis of the contribution of the different terms of the effective Hamiltonian to the quantum Hall effect (QHE). By analysing the spin-splitting of the quantum Hall states as a function of magnetic field and gate-voltage, we obtain different scaling laws that can be used to characterise the spin-orbit coupling in experiments. Furthermore, we employ a real-space quantum transport approach to calculate the quantum Hall conductivity and investigate the robustness of the QHE to disorder introduced by hydrogen impurities. For that purpose, we combine first-principles calculations and a genetic algorithm strategy to obtain a graphene-only Hamiltonian that models the impurity

Human-chimpanzee alignment: Ortholog Exponentials and Paralog Power Laws

Genomic subsequences conserved between closely related species such as human and chimpanzee exhibit an exponential length distribution, in contrast to the algebraic length distribution observed for sequences shared between distantly related genomes. We find that the former exponential can be further decomposed into an exponential component primarily composed of orthologous sequences, and a truncated algebraic component primarily composed of paralogous sequences.Comment: Main text: 31 pages, 13 figures, 1 table; Supplementary materials: 9 pages, 9 figures, 1 tabl

Sequential and asynchronous processes driven by stochastic or quantum grammars and their application to genomics: a survey

We present the formalism of sequential and asynchronous processes defined in terms of random or quantum grammars and argue that these processes have relevance in genomics. To make the article accessible to the non-mathematicians, we keep the mathematical exposition as elementary as possible, focusing on some general ideas behind the formalism and stating the implications of the known mathematical results. We close with a set of open challenging problems.Comment: Presented at the European Congress on Mathematical and Theoretical Biology, Dresden 18--22 July 200

Genes in the postgenomic era

We outline three very different concepts of the gene - 'instrumental', 'nominal', and 'postgenomic'. The instrumental gene has a critical role in the construction and interpretation of experiments in which the relationship between genotype and phenotype is explored via hybridization between organisms or directly between nucleic acid molecules. It also plays an important theoretical role in the foundations of disciplines such as quantitative genetics and population genetics. The nominal gene is a critical practical tool, allowing stable communication between bioscientists in a wide range of fields grounded in well-defined sequences of nucleotides, but this concept does not embody major theoretical insights into genome structure or function. The post-genomic gene embodies the continuing project of understanding how genome structure supports genome function, but with a deflationary picture of the gene as a structural unit. This final concept of the gene poses a significant challenge to conventional assumptions about the relationship between genome structure and function, and between genotype and phenotype

Towards data grids for microarray expression profiles

The UK DTI funded Biomedical Research Informatics Delivered by Grid Enabled Services (BRIDGES) project developed a Grid infrastructure through which research into the genetic causes of hypertension could be supported by scientists within the large Wellcome Trust funded Cardiovascular Functional Genomics project. The BRIDGES project had a focus on developing a compute Grid and a data Grid infrastructure with security at its heart. Building on the work within BRIDGES, the BBSRC funded Grid enabled Microarray Expression Profile Search (GEMEPS) project plans to provide an enhanced data Grid infrastructure to support richer queries needed for the discovery and analysis of microarray data sets, also based upon a fine-grained security infrastructure. This paper outlines the experiences gained within BRIDGES and outlines the status of the GEMEPS project, the open challenges that remain and plans for the future

Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages

Non-toxigenic Vibrio cholerae isolates have been found associated with diarrheal disease globally, however, the global picture of non-toxigenic infections is largely unknown. Among non-toxigenic V. cholerae, ctxAB negative, tcpA positive (CNTP) isolates have the highest risk of disease. From 2001 to 2012, 71 infectious diarrhea cases were reported in Hangzhou, China, caused by CNTP serogroup O1 isolates. We sequenced 119 V. cholerae genomes isolated from patients, carriers and the environment in Hangzhou between 2001 and 2012, and compared them with 850 publicly available global isolates. We found that CNTP isolates from Hangzhou belonged to two distinctive lineages, named L3b and L9. Both lineages caused disease over a long time period with usually mild or moderate clinical symptoms. Within Hangzhou, the spread route of the L3b lineage was apparently from rural to urban areas, with aquatic food products being the most likely medium. Both lineages had been previously reported as causing local endemic disease in Latin America, but here we show that global spread of them has occurred, with the most likely origin of L3b lineage being in Central Asia. The L3b lineage has spread to China on at least three occasions. Other spread events, including from China to Thailand and to Latin America were also observed. We fill the missing links in the global spread of the two non-toxigenic serogroup O1 V. cholerae lineages that can cause human infection. The results are important for the design of future disease control strategies: surveillance of V. cholerae should not be limited to ctxAB positive strains

Sociobiology, universal Darwinism and their transcendence: An investigation of the history, philosophy and critique of Darwinian paradigms, especially gene-Darwinism, process-Darwinism, and their types of reductionism towards a theory of the evolution of evolutionary processes, evolutionary freedom and ecological idealism

Based on a review of different Darwinian paradigms, particularly sociobiology, this work, both, historically and philosophically, develops a metaphysic of gene-Darwinism and process-Darwinism, and then criticises and transcends these Darwinian paradigms in order to achieve a truly evolutionary theory of evolution. Part I introduces essential aspects of current sociobiology as the original challenge to this investigation. The claim of some sociobiologists that ethics should become biologized in a gene-egoistic way, is shown to be tied to certain biological views, which ethically lead to problematic results. In part II a historical investigation into sociobiology and Darwinism in general provides us, as historical epistemology', with a deeper understanding of the structure and background of these approaches. Gene-Darwinism, which presently dominates sociobiology and is linked to Dawkins' selfish gene view of evolution, is compared to Darwin's Darwinism and the evolutionary' synthesis and becomes defined more strictly. An account of the external history of Darwinism and its subparadigms shows how cultural intellectual presuppositions, like Malthusianism or the Newtonian concept of the unchangeable laws of nature, also influenced biological theory' construction. In part III universal 'process-Darwinism' is elaborated based on the historical interaction of Darwinism with non-biological subject areas. Building blocks for this are found in psychology, the theory of science and economics. Additionally, a metaphysical argument for the universality of process- Darwinism, linked to Hume's and Popper's problem of induction, is proposed. In part IV gene-Darwinism and process-Darwinism are criticised. Gene-Darwinism—despite its merits—is challenged as being one-sided in advocating 'gene-atomism', 'germ-line reductionism' and 'process-monism'. My alternative proposals develop and try to unify different criticisms often found. In respect of gene-atomism I advocate a many-level approach, opposing the necessary radical selfishness of single genes. I develop the concept of higher-level genes, propose a concept of systemic selection, which may stabilise group properties, without relying on permanent group selection and extend the applicability of a certain group selectionist model generally to small open groups. Proposals of mine linked to the critique of germ-line reductionism are: 'exformation', phenotypes as evolutionary factors and a field theoretic understanding of causa formalis (resembling Aristotelian hylemorphism). Finally the process-monism of gene-Darwinism, process-Darwinism and, if defined strictly, Darwinism in general is criticised. 1 argue that our ontology and ethics would be improved by replacing the Newtoman-Paleyian deist metaphor of an eternal and unchangeable law of nature, which lies at tire very heart of Darwinism, by a truly evolutionary understanding of evolution where new processes may gain a certain autonomy. All this results in a view that I call 'ecological idealism', which, although still very much based on Darwinism, clearly transcends a Darwinian world view