Emerging semantics to link phenotype and environment

abstract: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.The final version of this article, as published in PeerJ, can be viewed online at: https://peerj.com/articles/1470

Autopoietic-extended architecture: can buildings think?

To incorporate bioremedial functions into the performance of buildings and to balance generative architecture's dominant focus on computational programming and digital fabrication, this thesis first hybridizes theories of autopoiesis into extended cognition in order to research biological domains that include synthetic biology and biocomputation. Under the rubric of living technology I survey multidisciplinary fields to gather perspective for student design of bioremedial and/or metabolic components in generative architecture where generative not only denotes the use of computation but also includes biochemical, biomechanical, and metabolic functions. I trace computation and digital simulations back to Alan Turing's early 1950s Morphogenetic drawings, reaction-diffusion algorithms, and pioneering artificial intelligence (AI) in order to establish generative architecture's point of origin. I ask provocatively: Can buildings think? as a question echoing Turing's own "Can machines think?" Thereafter, I anticipate not only future bioperformative materials but also theories capable of underpinning strains of metabolic intelligences made possible via AI, synthetic biology, and living technology. I do not imply that metabolic architectural intelligence will be like human cognition. I suggest, rather, that new research and pedagogies involving the intelligence of bacteria, plants, synthetic biology, and algorithms define approaches that generative architecture should take in order to source new forms of autonomous life that will be deployable as corrective environmental interfaces. I call the research protocol autopoietic-extended design, theorizing it as an operating system (OS), a research methodology, and an app schematic for design studios and distance learning that makes use of in-field, e-, and m-learning technologies. A quest of this complexity requires scaffolding for coordinating theory-driven teaching with practice-oriented learning. Accordingly, I fuse Maturana and Varela's biological autopoiesis and its definitions of minimal biological life with Andy Clark's hypothesis of extended cognition and its cognition-to-environment linkages. I articulate a generative design strategy and student research method explained via architectural history interpreted from Louis Sullivan's 1924 pedagogical drawing system, Le Corbusier's Modernist pronouncements, and Greg Lynn's Animate Form. Thus, autopoietic-extended design organizes thinking about the generation of ideas for design prior to computational production and fabrication, necessitating a fresh relationship between nature/science/technology and design cognition. To systematize such a program requires the avoidance of simple binaries (mind/body, mind/nature) as well as the stationing of tool making, technology, and architecture within the ream of nature. Hence, I argue, in relation to extended phenotypes, plant-neurobiology, and recent genetic research: Consequently, autopoietic-extended design advances design protocols grounded in morphology, anatomy, cognition, biology, and technology in order to appropriate metabolic and intelligent properties for sensory/response duty in buildings. At m-learning levels smartphones, social media, and design apps source data from nature for students to mediate on-site research by extending 3D pedagogical reach into new university design programs. I intend the creation of a dialectical investigation of animal/human architecture and computational history augmented by theory relevant to current algorithmic design and fablab production. The autopoietic-extended design dialectic sets out ways to articulate opposition/differences outside the Cartesian either/or philosophy in order to prototype metabolic architecture, while dialectically maintaining: Buildings can think

Contemporary Natural Philosophy and Philosophies - Part 2

Modern technology has eliminated barriers posed by geographic distances between people around the globe, making the world more interdependent. However, in spite of global collaboration within research domains, fragmentation among research fields persists and even escalates. Disintegrated knowledge has become subservient to the competition in the technological and economic race, leading in the direction chosen not by reason and intellect but rather by the preferences of politics and markets. To restore the authority of knowledge in guiding humanity, we have to reconnect its scattered isolated parts and offer an evolving and diverse but shared vision of objective reality connecting the sciences and other knowledge domains and informed by and in communication with ethical and esthetic thinking and being. This collection of articles responds to the second call from the journal Philosophies to build a new, networked world of knowledge with domain specialists from different disciplines interacting and connecting with the rest of the knowledge-producing and knowledge-consuming communities in an inclusive, extended natural-philosophic, human-centric manner. In this process of reconnection, scientific and philosophical investigations enrich each other, with sciences informing philosophies about the best current knowledge of the world, both natural and human-made, while philosophies scrutinize the ontological, epistemological, and methodological foundations of sciences

From Assessing to Conserving biodiversity. Conceptual and Practical Challenges

This open access book features essays written by philosophers, biologists, ecologists and conservation scientists facing the current biodiversity crisis. Despite increasing communication, accelerating policy and management responses, and notwithstanding improving ecosystem assessment and endangered species knowledge, conserving biodiversity continues to be more a concern than an accomplished task. Why is it so? The overexploitation of natural resources by our species is a frequently recognised factor, while the short-term economic interests of governments and stakeholders typically clash with the burdens that implementing conservation actions imply. But this is not the whole story. This book develops a different perspective on the problem by exploring the conceptual challenges and practical defiance posed by conserving biodiversity, namely: on the one hand, the difficulties in defining what biodiversity is and characterizing that “thing” to which the word ‘biodiversity’ refers to; on the other hand, the reasons why assessing biodiversity and putting in place effective conservation actions is arduous. ; Features essays that are explicitly critical of the species approach to biodiversity Presents bio-philosophical perspectives on the interaction between biodiversity’s units, levels, and scales Serves as an interdisciplinary contribution to the emergent field of biodiversity studie

Everything Flows

This collection of essays explores the metaphysical thesis that the living world is not ontologically made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organized as an interdependent hierarchy of processes, which are stabilized and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which have tended to use Alfred North Whitehead’s panpsychist metaphysics as a foundation, this book takes a naturalistic approach to metaphysics. It submits that the main motivations for replacing an ontology of substances with one of processes are to be looked for in the empirical findings of science. Biology provides compelling reasons for thinking that the living realm is fundamentally dynamic and that the existence of things is always conditional on the existence of processes. The phenomenon of life cries out for theories that prioritize processes over things, and it suggests that the central explanandum of biology is not change but rather stability—or, more precisely, stability attained through constant change. This multicontributor volume brings together philosophers of science and metaphysicians interested in exploring the consequences of a processual philosophy of biology. The contributors draw on an extremely wide range of biological case studies and employ a process perspective to cast new light on a number of traditional philosophical problems such as identity, persistence, and individuality

Loading World: (re)Creating Life, Nature and Cosmos in Evolutionary Computer Games

As a generalised field of study, artificial life has produced specific meanings and narratives about what it means to be alive: structured around the concepts of code, information, evolution, connectionism, emergence and cybernetics that connect silicon and carbon life together. Evolutionary computer games and popular programs have introduced the general player and user to advanced artificial life creations, with games based on the nurturing and breeding of silicon creatures placed within new digital natures conceived as computational regimes. Considered is the question of how it has become possible to talk of silicon entities as being alive, and to explore their relationship with carbon life as presented within evolutionary computer games. Similarities between digital and material proposed within computational regimes are also investigated. Playing computer games is developed as a productive practice that constructs meanings, stories and narratives within play. Tracing spiritual and scientific myths and narratives of construction, creation and change, reveals how common stories about life, nature and cosmos are employed in the building of bonds between silicon and carbon. Evolutionary computer games are presented as actively promoting themselves as artificial life products creating links with the life and biological sciences. Meaning produced within play is shown to naturalise and normalise specific definitions of life steeped in neo·Darwinian evolutionism and cybernetics, and how our digital creations have become perfected examples of the essence of this life. Whether this conceptualisation of life, nature and cosmos works within computational regimes is questioned and discussed. Reflecting similar arguments contesting the neo·Darwinian evolutionary perspective within biology, the assumptions employed within this framework are investigated and challenged. Utilising Bruno Latour's program of political ecology and his concepts of proposition and habit. An alternative framework is suggested to examine artificial life, utilising Bruno Latour's program of political ecology, his concepts of proposition and habit, and our relation with these entities

Homo deceptus: How language creates its own reality

Homo deceptus is a book that brings together new ideas on language, consciousness and physics into a comprehensive theory that unifies science and philosophy in a different kind of Theory of Everything. The subject of how we are to make sense of the world is addressed in a structured and ordered manner, which starts with a recognition that scientific truths are constructed within a linguistic framework. The author argues that an epistemic foundation of natural language must be understood before laying claim to any notion of reality. This foundation begins with Ludwig Wittgenstein’s Tractatus Logico-Philosophicus and the relationship of language to formal logic. Ultimately, we arrive at an answer to the question of why people believe the things they do. This is effectively a modification of Alfred Tarski’s semantic theory of truth. The second major issue addressed is the ‘dreaded’ Hard Problem of Consciousness as first stated by David Chalmers in 1995. The solution is found in the unification of consciousness, information theory and notions of physicalism. The physical world is shown to be an isomorphic representation of the phenomenological conscious experience. New concepts in understanding how language operates help to explain why this relationship has been so difficult to appreciate. The inclusion of concepts from information theory shows how a digital mechanics resolves heretofore conflicting theories in physics, cognitive science and linguistics. Scientific orthodoxy is supported, but viewed in a different light. Mainstream science is not challenged, but findings are interpreted in a manner that unifies consciousness without contradiction. Digital mechanics and formal systems of logic play central roles in combining language, consciousness and the physical world into a unified theory where all can be understood within a single consistent framework

The Gene Ontology Handbook

bioinformatics; biotechnolog