Every cell contains several millions of diffusing and reacting biological molecules. The interactions between these molecules ultimately manifest themselves in all aspects of life, from the smallest bacterium to the largest whale. One of the greatest open scientific challenges is to understand how the microscopic chemistry determines the macroscopic biology. Key to this challenge is the development of mathematical and computational models of biochemistry with molecule-level detail, but which are sufficiently coarse to enable the study of large systems at the cell or organism scale. Two such models are in common usage: the reaction-diffusion master equation, and Brownian dynamics. These models are utterly different in both their history and in their approaches to chemical reactions and diffusion, but they both seek to address the same reaction-diffusion question. Here we make an in-depth study into the physical validity of these models under various biological conditions, determining when they can reliably be used. Taking each model in turn, we propose modifications to the models to better model the realities of the cellular environment, and to enable more efficient computational implementations. We use the models to make predictions about how and why cells behave the way they do, from mechanisms of self-organisation to noise reduction. We conclude that both models are extremely powerful tools for clarifying the details of the mysterious relationship between chemistry and biology.

This study aims at exhibiting the strong correlation between the question of subjectivity and the question of being. If the question of subjectivity is to be formulated in terms of the relation between the inner realm of consciousness and the outer world, then the question will have an epistemological form and becomes the question of the objectivity of our knowledge. In the dissertation, however, it will be claimed with the German philosopher Martin Heidegger that the critical stand taken against the subject-object schema of the Cartesian epistemology must be of an ontological kind, and should criticize the substantial difference between the two realms of being. v In order to fulfill the aforementioned task, Dasein as the entity which is capable of asking the question of being will be claimed to be the ontological condition of possibility for something like subjectivity. By the help of the phenomenological concept of Dasein, we will claim that the most neutral and basic being-in-the-world of human beings is not cognizing or perceiving things, but caring for them. The last objective we hope to fulfill in this study is to show that the only question of philosophy for Heidegger, i.e., the question of being, can first become comprehensible when the philosopher&rsquo / s investigations of the modern philosophy have been well examined. It is our contention that, unless thedead-ends of the modern philosophy of subjectivity is apprehended well enough, the obligation of asking the question of being as such cannot be felt.

The purpose of this thesis is to trace Marx&rsquo / s critique of Hegel from the beginning to the end and to draw attention to his continuous dialogue with Hegel, which results in Marx&rsquo / s appropriation of Hegel&rsquo / s dialectic in all its aspects. To this aim, we will focus on the texts in which Marx criticizes Hegel and try to understand how he develops his position against Hegel&rsquo / s philosophy. Marx has always become in a critical relationship with Hegel&rsquo / s philosophy and considered it as a philosophy which must be transcended since it, for Marx, amounts to justify the present reality which, in Marx&rsquo / s eyes, constitutes a great barrier for human freedom. However, Marx also regards Hegel&rsquo / s philosophy, in which dialectic occupies a central place, as one which includes the most developed conception of science and the true scientific method, and attempts to use Hegel&rsquo / s dialectic in his critique of political economy. In this thesis, by following Marx&rsquo / s critique of Hegel, we will try to show that Marx comes closer to Hegel&rsquo / s dialectic even when he criticizes Hegel&rsquo / s philosophy.

The purpose of this thesis is to trace Marx&rsquo / s critique of Hegel from the beginning to the end and to draw attention to his continuous dialogue with Hegel, which results in Marx&rsquo / s appropriation of Hegel&rsquo / s dialectic in all its aspects. To this aim, we will focus on the texts in which Marx criticizes Hegel and try to understand how he develops his position against Hegel&rsquo / s philosophy. Marx has always become in a critical relationship with Hegel&rsquo / s philosophy and considered it as a philosophy which must be transcended since it, for Marx, amounts to justify the present reality which, in Marx&rsquo / s eyes, constitutes a great barrier for human freedom. However, Marx also regards Hegel&rsquo / s philosophy, in which dialectic occupies a central place, as one which includes the most developed conception of science and the true scientific method, and attempts to use Hegel&rsquo / s dialectic in his critique of political economy. In this thesis, by following Marx&rsquo / s critique of Hegel, we will try to show that Marx comes closer to Hegel&rsquo / s dialectic even when he criticizes Hegel&rsquo / s philosophy.

The methods of denaturing gradient gel electrophoresis (DGGE) and DNA sequencing were used to analyze the ribotypes of microbial communities associated with corals. Both healthy and diseased coral of different species were collected at three locations off the southern coast of Taiwan. Ribotyping results suggested that the microbial communities were diverse. The microbial community profiles, even among the same species of corals from different geographical locations or different times, differ significantly. The coral-associated bacterial communities contain many bacteria common to the habitants of various invertebrates. One ribotype presented on the Black Disease coral tissue is closely related to the Clostridium sp. previously identified from White Plaque-diseased and BBD corals. This Clostridium sp. may be relatived to coral diseased, as this species was also found in many types of diseased coral. The other one ribotype presented on our healthy and diseases coral is closed to denitrifying bacterium Pseudovibrio sp. which had been previously discovered in Kenting National Park Nanwan Bay as a new marine, facultative anaerobic bacterium. However, some bacteria were unexpected. The presence of some unusual species, such as Staphylococcus, Legionella and soil bacteria, associated with corals that were likely the results of human activities. Human activities, such as active fishing and tourism industries in the region might have all contributed to the change in bacterial communities and the death of coral colonies around the region.

Contemporary materialism, which tries to explain the working principles of the mind and the universe, become less meaningful after the developments in the modern physics. The modern physics showed that the definition of matter, as it is used in defining materialism, is no longer valid. Chomsky states his position as &ldquo / Chomsky&#039 / s challenge to materialism&rdquo / by claiming that with the abolishment of the definition of the matter, there is no reason to defend materialism, which depends on that definition. Therefore, materialism becomes an empty doctrine thus cannot be used in explaining the mind. The developments in the modern physics creates the need for a new doctrine, which can explain the mind and at the same time be compatible with the modern physics and possible any future physics. This new doctrine, the methodological physicalism, aims to explain the mind by using the modern physics. Creating such a doctrine requires understanding of materialism and its form as well as understanding the problems of materialism and its forms. By identifying the defects in materialism and by using the modern physics as a standing point methodological physicalism can achieve a more successful understanding of the working of the mind. By using the modern physics, the methodological physicalism can explain why the currents models of the mind fail. Moreover, it can explain how certain models of the mind constructed, which employs the quantum mechanics while explaining the mind. The methodological physicalism will help understanding the mind where materialism fails to do so.

This thesis analyzes the reasons for Socrates&#039 / being presented as a paradoxical figure in the early dialogues of Plato. Irony as a fundamental philosophical attitude in Socratic philosophy is discussed with reference to some of the major philosophers of the history of philosophy. The thesis also suggests the possibility of seeing philosophy as an ironic activity and it traces the etymology of the concept of irony in terms of its philosophical importance.

The self-knowledge has been a central problem throughout the history of philosophy, but it has remained, as Kant also declares, as the

Many philosophers tend to defend the view that there is a significant relation between the problem of determinism / indeterminism and the problem of free will. The belief that there exists such a significant relation is supported by our intuitions / however, in this thesis, I defend just the opposite view: free will has no significant dependence on the deterministic or indeterministic character of causal relations. In the same way, I propose that the question, whether or not determinism is true, cannot be answered based on observations about the problem of free will. I believe that the genuine question whose answer would illuminate the darkness surrounding free will is whether or not will supervenes on anything other than itself. Therefore, in order to decide whether or not we are free, the question we should ask is &ldquo / Does will supervene upon something other than itself?&rdquo / Moreover, I defend the position that no matter whether the world is deterministic or indeterministic, if physicalism is true, i.e. if properties of free will supervene upon physical properties, then we cannot enjoy genuine freedom. The position of the thesis has some important ethical implications: If we cannot be genuinely free, we cannot be genuinely responsible for our actions either. This implies that retributive and admirative desires towards other persons are rationally untenable. I defend the view that only practical attitudes like reinforcement and punishment or isolation and inclusion are rationally tenable.

This thesis argues that Western feminist theoretical models of identity can be productively complicated by the insights of postcolonial feminisms. In particular, it explores ways that Western feminist theory might more adequately sustain a focus on 'women' while keeping open a space for differences such as race and nation. Part One identifies a number of themes that emerge from recent Indian feminist scholarship on the intersections of sex, gender, race, nation and community identities. Part Two uses these insights to look critically at the work of four Western theorists, Rosi Braidotti, Judith Butler, Donna Haraway and Luce Irigaray. I argue that strategies which privilege sexual difference as primary cannot deal adequately with differences such as race and nation. But I also argue that strategies which privilege destabilizing identity can be equally constrained by the logic of dualisms which has made it so difficult for feminists to sustain a focus on women and their differences. Part Three discusses how the insights to be drawn from Indian ferninisms might be taken on board by Western ferninisms in order to develop more complex models of power, identity and the self. Throughout the thesis I draw on a Foucauldian understanding of power as productive, and on Foucault's insight that subjects and identities emerge, not through the imperatives of a single symbolic system, but through the intersection of multiple networks of discourses, material practices and institutions. I argue that, by attending to women's complex location within intersecting landscapes of gender, nation, race and other community identities, feminist models of identity can dispense with a logic of dualisms in order to redefine, and not only destabilize 'women' as the subject of/for feminism. This requires working against purity on three levels. First, it requires a model of power that gives up on the search for pure, power-free zones and works instead with the instabilities power produces as it both enables and constrains women. Second, it requires seeing 'women' as a complex, impure category that bleeds across the apparently coherent borders of identity categories such as gender, race and nation, and contesting discursive constructs of 'Woman' as the pure space of origin upon which these apparently discrete categories stand. Third, it requires the development of alternative models of the self that take these complex, impure spaces as a valid and valorised position from which to act and to speak.