lördag 15 oktober 2011

Biology needs a mathematical theory. The INBIOSA project.

The INBIOSA Project (www.inbiosa.eu) was launched in January 2011 with the support of the EU FP7 . The project will continue until the end of December 2011. The project investigators are Dr.Plamen L. Simeonov (JSRC, Germany) and Professor Leslie S.Smith (University of Stirling, UK) INBIOSA PP Presentation, Summary (long).

The long-term aim of the INBIOSA Project is to deliver answers to such questions as:

- what is computation? – in biological context;

- how useful is a computation? – for living systems, where “usefulness” is studied from the viewpoint of the entity performing the computation;

- to what extent can a computation be carried out? – in an organism or an ecosystem, with the available resources (power, time, number of computing elements, etc.).

Driving principles of the INBIOSA initiative:

• focusing on non-mainstream scientific research in mathematics and computation engineering targeting a synergetic integration and exchange with natural and life science disciplines;

• enforcing multidisciplinary approaches to investigation;

• identifying research areas which are crucial for accelerated, yet balanced, transformation of the future information society towards eco-awareness.

This project aims to investigate the imperatives of mathematics and computation in a cardinal new way by comprehending the fundamental principles of emergence, development and evolution in biology. The goal will be a set of novel mathematical formalisms capable of addressing the multiple facets of an integral model and a general theory of biocomputation within an adequate frame of relevance. Its base will be the realization of a long-term fundamental research programme in mathematics, biology and computation that we call Integral Biomathics (arxive-paper). A Post-Newtonian View into the Logos of Bios (On the New Meaning, Relations and Principles of Life in Science)...focused on the phenomena of emergence, adaptive dynamics and evolution of self-assembling, self-organizing, self-maintaining and self-replicating biosynthetic systems viewed from a newly-arranged perspective and understanding of computation and communication in the living nature.

Integral Biomathics is envisioned to discover and establish new relationships and deliver new insights into the interaction and interdependence between natural and artificial (human-created) phenomena for a number of scientific fields. It is expected to invent and develop new mathematical formalisms and provide a generalized framework and ecology for research in life, physical, social and engineering sciences.


Accelerating the Discovery of the Biological Imperatives of a Computational Model of Life

The focus of the transformative research is biology-centric. The key leverageable idea is that careful extension of the science of living systems can be more effectively applied to modern problems than the prevailing paradigm. That paradigm is extended from abstractions in physics. While they have some universal application, and computational advantages, their use need not be the default.A new set of abstractions from biology can now be similarly extended. This is made possible by new formal tools to understand abstraction and enable computability.

We are in need of a theory which describes the biological processes in living organisms.

The commonly acknowledged opinion is that the problem of modern-day biological science is the absence of a unified theory. Dr. Plamen L. Simeonov (JSRC, Germany), coordinator of the project, commented: “Until now an enormous amount of data has been collected in the science of life, but that data alone doesn’t make a theory. The time is ripe for the establishment of a research program in the area which will support and eventually lead to the creation of a new biological theory.”

The laws and methods of physics cannot be unconditionally applied to the biological sciences due to the inconsistency of the systems in biology, and more generally to the differences in nature of the subjects studied by these two scientific disciplines. A new type of super-mathematics, unifying and extending diverse fields of mathematics to tackle biological problems is necessary, according to the attending the conference scientists. “We need a mathematics that can describe such an ever-changing, indeterminate, yet persistent “thing” , including how it maintains its “identity” within certain boundary conditions, yet ceases to function outside of those boundaries. Such an emergent, developmental and evolutionary mathematics does not exist“, is the opinion of the scientists.

“Equations of motion for biological system may not be appropriate. We should seek rules of organisation for living systems, and also rules of organisation for neural systems“, commentedProf. Leslie S. Smith, University of Stirling, UK, co-investigator on the project and organizer of the Stirling conference. “There may be generalizations of logic which include stochasticity. Further, we should also consider generalizations of information and information theory which might be more appropriate for living systems”, he added.

In contrast to the classical science, which is based on the externalist approach (or third person descriptions) in most of its areas, we also need to adopt the internalist approach (first person descriptions) when dealing with biological problems.

“We should consider time, and also versions of central pattern generators that apply to cognitive (rather than motor) systems”, is one of the conclusions the scientists reached.

Research roadmaps in computational systems biology, autonomic computing and communications target the enrichment of knowledge and technology transfer between (analytic) life sciences and (synthetic) engineering sciences. We claim that it is impossible to make significant progress in this transdisciplinary field without a breakthrough paradigm change towards biologically driven mathematics and computation. A profoundly new understanding of the role of biology in natural and engineering sciences needs to be set out.

“We are unable at present to identify in rigorous fashion what it is about cellular processes that set them apart from synthetic devices made of silicon and steel,” stated Prof. Dennis Bray (University of Cambridge, UK), the author of “Wetware: A Computer in Every Living Cell”.

3 kommentarer:

  1. http://arxiv.org/ftp/cs/papers/0703/0703002.pdf

    Represents a departure from tradition. associated with abstract information structures and processes about systems and emergence, self-organization and -assembly. Reshapes the virtual science. A paradigm change is necessary. New science is integral, based on principles of dynamic interdependence of dishiplines and evolving relationships.

    Explores the potential and virtue to reshape contemporary science in line with Poppers critical rationalism from 1934, together with autopoietic and non-Darwinian way.

    Thesis: The wandering logic intelligence, http://www.simeio.org/pages/details/papers/dis/wli_dis_v12_last.pdf

    the four principles of the Wandering Network – Dualistic Congruence, Multidimensional Feedback, Self-Reference, and Pulsating Metamorphosis,
    • Knowledge quantum
    • Genetic transcoding
    • Network resonance.

    Generic architectures for netbots (active mobile nodes) and shuttles (active packets) which can transport executable genetic code about a node/network state/process

    Extending adaptability to four dimensions of network reconfiguration and programming:
    1. Applications
    2. Operating system resources
    3. Node hardware components
    4. Clusters of nodes
    • A two-level profiling scheme for functional components in a reconfigurable network architecture
    horizontal inter-node functional wandering (self-organization) of the active nodes (netbots), called 1st Level Profiling, and
    virtual vertical intra-node overlay functional wandering (self-organization), called 2d Level Profiling, etc. Creation and pilots

  2. The arxive paper - A Biological Relativity theory? After Raschevsky, Rosen, Martinez - multilevel biosystems with no priviledged level of causation. Nottale, Auffray and Noble. Analyzed from a double view of traditional systems anal. and engineering anal.
    horizontal inter-node functional wandering (self-organization) of the active nodes (netbots), called 1st Level Profiling, and
    o virtual vertical intra-node overlay functional wandering (self-organization), called 2d Level Profiling.

  3. http://rsfs.royalsocietypublishing.org/content/2/1/55.full
    A theory of biological relativity: no privileged level of causation, by Denis Noble 2012.

    Must higher level biological processes always be derivable from lower level data and mechanisms, as assumed by the idea that an organism is completely defined by its genome? Or are higher level properties necessarily also causes of lower level behaviour, involving actions and interactions both ways? This article uses modelling of the heart, and its experimental basis, to show that downward causation is necessary and that this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes. These insights are then generalized. A priori, there is no privileged level of causation. The relations between this form of ‘biological relativity’ and forms of relativity in physics are discussed. Biological relativity can be seen as an extension of the relativity principle by avoiding the assumption that there is a privileged scale at which biological functions are determined.

    Have we reached the limits of applicability of the relativity principle? And could it have relevance to biology?