The biological sciences study (bio)complex living systems. Research directed at the mechanistic explanation of the "live" state truly requires a pluralist research program, i.e. BioComplexity research. The program should apply multiple intra-level and inter-level theories and methodologies. We substantiate this thesis with analysis of BioComplexity: metabolic and modular control analysis of metabolic pathways, emergence of oscillations, and the analysis of the functioning of glycolysis.

The Big Thicket is an ill-defined region of southeast Texas on the coastal plain of the Gulf of Mexico between the Trinity and Sabine rivers, not far from Houston. Because the biological-diversity...

The Big Thicket is an ill-defined region of southeast Texas on the coastal plain of the Gulf of Mexico between the Trinity and Sabine rivers, not far from Houston. Because the biological-diversity...

Codes of ethics were drafted by participants in the European and North American Congresses of DIYbio, a single global organization of informal biotechnology practitioners, in 2011. In general, the existence of a code of ethics amongst a community is itself significant. Codes of professional ethics are common in scientific and engineering fields, as well as in DIY communities. It is also significant, and highly unusual, that DIYbio has maintained two separate codes of ethics years after their drafting. While agreement was (...) reached within the congress for each geographic region, with considerable commonality between the two codes drafted, they are far from identical. There are differences in the ordering of items, the wording of common items, and the presence/absence of items. I will argue that these differences are meaningful, and consider them with respect to cultural variation, ethics, and societal implications. Finally, I recommend that the entire DIYbio organization unite under a single code of ethics, and that one of the existing drafts is superior to the other for this purpose. (shrink)

How does the complex nature of ecological systems affect ecologists' ability to study them? This Element argues that ecological systems are complex in a rather special way: they are causally heterogeneous. The author presents an updated philosophical account with an optimistic outlook of the methods and status of ecological research.

The book you hold in your hands is the outcome of the "ISCS 2013: Interdisciplinary Symposium on Complex Systems" held at the historical capital of Bohemia as a continuation of our series of symposia in the science of complex systems. Prague, one of the most beautiful European cities, has its own beautiful genius loci. Here, a great number of important discoveries were made and many important scientists spent fruitful and creative years to leave unforgettable traces. The perhaps most significant period (...) was the time of Rudolf II who was a great supporter of the art and the science and attracted a great number of prominent minds to Prague. This trend would continue. Tycho Brahe, Niels Henrik Abel, Johannes Kepler, Bernard Bolzano, August Cauchy Christian Doppler, Ernst Mach, Albert Einstein and many others followed developing fundamental mathematical and physical theories or expanding them. Thus in the beginning of the 17th century, Kepler formulated here the first two of his three laws of planetary motion on the basis of Tycho Brahe’s observations. In the 19th century, nowhere differentiable continuous functions (of a fractal character) were constructed here by Bolzano along with a treatise on infinite sets, titled “Paradoxes of Infinity” (1851). Weierstrass would later publish a similar function in 1872. In 1842, Doppler as a professor of mathematics at the Technical University of Prague here first lectured about a physical effect to bear his name later. And the epoch-making physicist Albert Einstein – while being a chaired professor of theoretical physics at the German University of Prague – arrived at the decisive steps of his later finished theory of general relativity during the years 1911–1912. In Prague, also many famous philosophers and writers accomplished their works; for instance, playwright arel ape coined the word "robot" in Prague (“robot” comes from the Czech word “robota” which means “forced labor”). (shrink)

"Both superb and essential... Succi, with clarity and wit, takes us from quarks and Boltzmann to soft matter - precisely the frontier of physics and life." Stuart Kauffman, MacArthur Fellow, Fellow of the Royal Society of Canada, Gold Medal Accademia Lincea We live in a world of utmost complexity, outside and within us. There are thousand of billions of billions of stars out there in the Universe, a hundred times more molecules in a glass of water, and another hundred times (...) more in our body, all working in sync to keep us alive and well. At face value, such numbers spell certain doom for our ability to make any sense at all of the world around and within us. And yet, they don't. Why, and how - this book endeavours to provide an answer to these questions with specific reference to a selected window of the physics-biology interface. The story unfolds over four main Parts. Part I provides an introduction to the main organizational principles which govern the functioning of complex systems in general, such as nonlinearity, nonlocality and ultra-dimensions. Part II deals with thermodynamics, the science of change, starting with its historical foundations laid down in the 19th century, and then moving on to its modern and still open developments in connection with biology and cosmology. Part III deals with the main character of this book, free energy, and the wondrous scenarios opened up by its merger with the modern tools of statistical physics. It also describes the basic facts about soft matter, the state of matter most relevant to biological organisms. Finally, Part IV discusses the connection between time and complexity, and its profound implications on the human condition, i.e. the one-sided nature of time and the awareness of human mortality. It concludes with a few personal considerations about the special place of emotions and humility in science. (shrink)

This book is based on the outcome of the ""2012 Interdisciplinary Symposium on Complex Systems"" held at the island of Kos. The book consists of 12 selected papers of the symposium starting with a comprehensive overview and classification of complexity problems, continuing by chapters about complexity, its observation, modeling and its applications to solving various problems including real-life applications. More exactly, readers will have an encounter with the structural complexity of vortex flows, the use of chaotic dynamics within evolutionary algorithms, (...) complexity in synthetic biology. (shrink)

Introduction to complexity and complex systems -- Introduction to large linear systems -- Introduction to biochemical oscillators and nonlinear biochemical systems -- Modularity, redundancy, degeneracy, pleiotropy and robustness in complex biological systems -- The evolution of biological complexity; invertebrate immune systems -- Irreducible and specified complexity in living systems -- The complex adaptive and innate human immune systems -- Complexity in quasispecies : microRNAs -- Introduction to complexity in economic systems -- Complexity in quasispecies : micrornas -- Dealing with complexity.

The Nanosilver Linings role play case offers participants first-person experience with interpersonal interaction in the context of the wicked problems of emerging technology macroethics. In the fictional scenario, diverse societal stakeholders convene at a town hall meeting to consider whether a nanotechnology-enabled food packaging industry should be offered incentives to establish an operation in their economically struggling Midwestern city. This original creative work was built with a combination of elements, selected for their established pedagogical efficacy and as topical dimensions of (...) the realistic scenario. The product life cycle is used as a framework for integrated consideration of scientific, societal, and ethical issues. The Nanosilver Linings hypothetical case was delivered through the format of the 3-hour workshop Ethics when Biocomplexity meets Human Complexity, providing an immersive, holistic ethics learning experience for STEM graduate students. Through their participation in the Nanosilver Linings case and Ethics when Biocomplexity meets Human Complexity workshop, four cohorts of science and engineering doctoral students reported the achievement of specific learning objectives pertaining to a range of macroethics concepts and professional practices, including stakeholder perspectives, communication, human values, and ethical frameworks. Automated text analysis of workshop transcripts revealed differences in sentiment and in ethical framework preference between societal stakeholder roles. These resources have been recognized as ethics education exemplars by the U.S. National Academy of Engineering. (shrink)

Perceptual diversity allows human beings to access knowledge through a variety of perceptual processes, rather than merely through everyday waking reality. Many of these perceptual processes are transrational altered states of consciousness (meditation, trance, dreams, imagination) and are not considered valid processes for accessing knowledge by science (which is based primarily upon quantification, reductionism, and the experimental method). According to Erika Bourguignon's (1973) research in the 1970s, approximately 90 percent of cultures have institutionalized forms of altered states of consciousness, meaning (...) that such types of consciousness are to be found in most human societies and are "normal." Now, however, transrational consciousness is being devalued in many societies as it is simultaneously being replaced by the monophasic consciousness of "developed" nations. Not only are we are losing (1) biodiversity (biocomplexity) in environments and (2) cultural diversity in societies, we also are losing (3) perceptual diversity in human cognitive processes. All three losses of diversity (bio, cultural, and cognitive) are interrelated.Cultures that value perceptual diversity are more adaptable than cultures that do not. Perceptually diverse cultures are better able to understand whole systems (because they use a variety of perceptual processes to understand systems) than are cultures that rely only on the scientific method, which dissects systems. They also are better stewards of their environments, because they grasp the value of the whole of biodiversity (biocomplexity) through transrational as well as scientific processes. Understanding through perceptual diversity leads to a higher degree of adaptability and evolutionary competence.From the perspective of an anthropologist who has worked with development organizations, development will continue to destroy perceptual diversity because it exports the dominant cognitive process of "developed" nations, i.e., monophasic consciousness. Destroying perceptual diversity, in turn, leads to the destruction of cultural diversity and biocomplexity. Drawing from research I conducted among traditional healers in Namibia, I conclude that development organizations need to listen to those who use transrational perceptual processes and also need to find a way to incorporate and validate perceptual diversity in their theoretical and applied frameworks. (shrink)

The multifarious nature of biodiversity is considered in relation to difficulties of definite determination and managerial mandates for monitoring. At a micro scale there is some convergence with the concept of community, but the linkage is largely lost in the spectra of temporal scope, spatial scales, successional seres, and taxonomic trajectories. Practicality points to selecting suitable suites of indicators as surrogates for particular purposes. Domains of partial ordering on multiple indicators constitute comparable collectives, whereas different domains require recognition of special (...) situations. Theoretical treatise and practical process can proceed in parallel, with dialogue and cross-fertilization serving to invigorate and inspire; whereas compulsive concern for completeness and consistency can be counter-productive as well as unduly expensive. Inability to completely capture all aspects of biodiversity in one full formulation is interesting and integral to issues of biocomplexity. (shrink)

We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; this information processing has one overall function—to perpetuate itself; and the processing method is filtration of, and synthesis of, information at lower levels to appear at higher levels in complex (...) systems . We show how information patterns, are united by the creation of mutual context, generating persistent consequences, to result in ‘functional information’. This constructive process forms arbitrarily large complexes of information, the combined effects of which include the functions of life. Molecules and simple organisms have already been measured in terms of functional information content; we show how quantification may be extended to each level of organisation up to the ecological. In terms of a computer analogy, life is both the data and the program and its biochemical structure is the way the information is embodied. This idea supports the seamless integration of life at all scales with the physical universe. The innovation reported here is essentially to integrate these ideas, basing information on the ‘general definition’ of information, rather than simply the statistics of information, thereby explaining how functional information operates throughout life. (shrink)

Qu'y a-t-il de commun entre l'Univers, l'animal, la machine et la ville? A priori pas grand-chose si l'on prend en considération les différences d'échelle ou encore le fait que l'on cherche à rapprocher deux concepts "naturels", l'Univers et l'animal, à deux types de "constructions" humaines, la machine et la ville. Le propos de cet ouvrage est précisément de démontrer le contraire : des constatations identiques ou analogues peuvent s'appliquer à chacun d'eux. Notre appréhension de ces différentes entités a progressé de (...) façon considérable au cours du temps et notoirement au cours des dernières années. Les quatre termes deviennent de plus en plus complexes en même temps que nos analyses deviennent plus performantes. Chacun d'eux est constitué de structures emboîtées : ils sont en mosaïques, ensembles faits d'éléments distincts qui se juxtaposent, mais qui sont toujours plus que la simple somme de leurs éléments. Ils évoluent au cours du temps, et cette évolution est darwinienne : ils s'adaptent, cherchent l'équilibre, et seules subsistent les structures les plus robustes. Et ce qui est le plus réussi, le plus adapté, est aussi bien souvent ce que nous trouvons le plus beau... Mettre en parallèle les regards d'un astrophysicien, d'un biologiste, d'un architecte et d'un roboticien permet à chacune de ses disciplines d'apporter un éclairage nouveau sur les trois autres : un bel exercice de dialogue. (shrink)

This book provides a short, hands-on introduction to the science of complexity using simple computational models of natural complex systems--with models and exercises drawn from physics, chemistry, geology, and biology. By working through the models and engaging in additional computational explorations suggested at the end of each chapter, readers very quickly develop an understanding of how complex structures and behaviors can emerge in natural phenomena as diverse as avalanches, forest fires, earthquakes, chemical reactions, animal flocks, and epidemic diseases. Natural Complexity (...) provides the necessary topical background, complete source codes in Python, and detailed explanations for all computational models. (shrink)