How Research on Microbiomes is Changing Biology: A Discussion on the Concept of the Organism

Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems (digestive, immune, nervous, etc.) of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is a problem with this suggestion, since there is no such thing as a universal concept of the organism which could constitute a basis for all biological sciences. Rather, the opposite is true: numerous alternative definitions exist. Therefore, comprehending how microbiomics is changing our understanding of organisms may be a very complex matter. In this paper we will demonstrate that this pluralism proves that claims about a change in our understanding of organisms can be treated as both true and untrue. Mainly, we assert that the existing concepts differ substantially, and that only some of them have to be reconsidered in order to incorporate the discoveries of microbiomics, while others are already flexible enough to do so. Taking into account the plurality of conceptualisations within different branches of modern biology, we will conduct our discussion using the developmental and the cooperation–conflict concepts of the organism. Then we will explain our results by referring to the recent philosophical debate on the nature of the concept of the organism within biology.     

Initializing K-means Batch Clustering: A Critical Evaluation of Several Techniques

K-means clustering is arguably the most popular technique for partitioning data. Unfortunately, K-means suffers from the well-known problem of locally optimal solutions. Furthermore, the final partition is dependent upon the initial configuration, making the choice of starting partitions all the more important. This paper evaluates 12 procedures proposed in the literature and provides recommendations for best practices.     

Seeking Allies: Modelling How Listeners Choose Their Musical Friends

In this paper we describe in some detail a formal computer model of inferential discourse based on a belief system. The key issue is that a logical model in a computer, based on rational sets, can usefully model a human situation based on irrational sets. The background of this work is explained elsewhere, as is the issue of rational and irrational sets (Billinge and Addis, in: Magnani and Dossena (eds.), Computing, philosophy and cognition, 2004; Stepney et al., Journey: Non-classical philosophy—socially sensitive computing in journeys non-classical computation: A grand challenge for computing research, 2004). The model is based on the Belief System (Addis and Gooding, Proceedings of the AISB’99 Symposium on Scientific Creativity, 1999) and it provides a mechanism for choosing queries based on a range of belief. We explain how it provides a way to update the belief based on query results, thus modelling others’ experience by inference. We also demonstrate that for the same internal experience, different models can be built for different actors.

On the Foundations of Constructive Mathematics – Especially in Relation to the Theory of Continuous Functions

We discuss the foundations of constructive mathematics, including recursive mathematics and intuitionism, in relation to classical mathematics. There are connections with the foundations of physics, due to the way in which the different branches of mathematics reflect reality. Many different axioms and their interrelationship are discussed. We show that there is a fundamental problem in BISH (Bishop’s school of constructive mathematics) with regard to its current definition of ‘continuous function’. This problem is closely related to the definition in BISH of ‘locally compact’. Possible approaches to this problem are discussed. Topology seems to be a key to understanding many issues. We offer several new simplifying axioms, which can form bridges between the various branches of constructive mathematics and classical mathematics (‘reuniting the antipodes’). We give a simplification of basic intuitionistic theory, especially with regard to so-called ‘bar induction’. We then plead for a limited number of axiomatic systems, which differentiate between the various branches of mathematics. Finally, in the appendix we offer BISH an elegant topological definition of ‘locally compact’, which unlike the current definition is equivalent to the usual classical and/or intuitionistic definition in classical and intuitionistic mathematics, respectively.     

Quantum Theory and the Nature of Consciousness

Our interest focusses on the idea, that consciousness is a powerful acting entity. Up to now there does not exist a scientific concept for this idea. This is not due to problems within the field of psychology or brain research, but rather in resisting theories of modern physics. That is, why we have to search for a solution in the field of physics. A solution can be found in a new understanding of the basics of physical theory. That could be given by abstract and absolute quantum bits of information (AQI bits). To avoid the popular misunderstanding of “information” as “meaningful” it was necessary to find a new word for the free-of-meaning AQI bits: the AQI bits establish a quantum pre-structure termed “Protyposis” (Greek: “pre-formation”), out of which real objects can be formed, starting from energetical and material elementary particles. The Protyposis AQI bits provide a pre-structure for all entities in natural sciences. They are the basic entities, whereof the physical nature of the brain, on the one hand, and the mental nature of consciousness, on the other hand, were formed during the cosmological and the following biological evolution. A deeper understanding of quantum structures may help to overcome the resistance against quantum theory in the field of brain research and consciousness. The key for an understanding is the concept of Protyposis, which means an abstract quantum information free of any definite meaning. With the AQI bits of the Protyposis, both, massless and massive quantum particles can be constructed. Even quantum information with special meanings, in example grammatically formulated thoughts, eventually could be explained. As long as the fundamental basis of quantum theory is misunderstood as being formed by a manifold of some small objects like atoms, quarks, or strings, the problem of understanding consciousness has no solution. If instead we understand quantum theory as based on truly simple quantum structures, there would be no longer fundamental problems for an understanding of consciousness.     

The Applicability of Mathematics as a Philosophical Problem: Mathematization as Exploration

This paper discerns two types of mathematization, a foundational and an explorative one. The foundational perspective is well-established, but we argue that the explorative type is essential when approaching the problem of applicability and how it influences our conception of mathematics. The first part of the paper argues that a philosophical transformation made explorative mathematization possible. This transformation took place in early modernity when sense acquired partial independence from reference. The second part of the paper discusses a series of examples from the history of mathematics that highlight the complementary nature of the foundational and exploratory types of mathematization.     

Sufficient Reason and Reason Enough

I offer an analysis of the Principle of Sufficient Reason and its relevancy for the scientific endeavour. I submit that the world is not, and cannot be, rational—only some brained beings are. The Principle of Sufficient Reason is not a necessary truth nor a physical law. It is just a guiding metanomological hypothesis justified a posteriori by its success in helping us to unveil the mechanisms that operate in Nature.