Ever since the advent of molecular biology in the 1970s, mechanical models have become the dogma in the field, where a "true" understanding of any subject is equated to a mechanistic description. This has been to the detriment of the biomedical sciences, where, barring some exceptions, notable new feats of understanding have arguably not been achieved in normal and disease biology, including neurodegenerative disease and cancer pathobiology. I argue for a "mechanism-plus-X" paradigm, where mainstay elements of mechanistic models such as (...) hierarchy and correlation are combined with nomological principles such as general operative rules and generative principles. Depending on the question at hand and the nature of the inquiry, X could range from proven physical laws to speculative biological generalizations, such as the notional principle of cellular synchrony. I argue that the "mechanism-plus-X" approach should ultimately aim to move biological inquiries out of the deadlock of oft-encountered mechanistic pitfalls and reposition biology to its former capacity of illuminating fundamental truths about the world. (shrink)

Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...) This could in part be explained by a relatively recent tendency in which a "data first", rather than a "theory first", approach is preferred. Moreover, generating hypotheses has at times become procedural rather than theoretical, therefore perhaps inadvertently leading some hypotheses to become perfunctory in nature. This situation leaves our understanding enmeshed in data, which should be disentangled from much noise. Given the many unresolved questions in biology and medicine, big and small, ranging from the problem of protein folding to unifying causative frameworks of complex non-Mendelian human diseases, it seems apt to revive the role of pure theory in the biological sciences. This paper, using the current biomedical literature and historical precedents, makes the case for a "philosophical biology" (philbiology), distinct from but quite complementary to philosophy of biology (philobiology), which would entail biological investigation through philosophical approaches. Philbiology would thus be a reincarnation of theoretical biology, adopting the true sense of the word "theory" and making use of a rich tradition of serious philosophical approaches in the natural sciences. A philbiological investigation, after clearly defining a given biological problem, would aim to propose a set of empirical questions, along with a class of possible solutions, about that problem. Importantly, whether or not the questions can be tested using current experimental paradigms would be secondary to whether the questions are inherently empirical or not. These issues will be illustrated using a range of specific examples. The final goal of a philbiological investigation would be to develop a theoretical framework that can lead observational and/or interventional experimental studies of the defined problem, a framework that is structured, generative and expandable, and, crucially, one that simplifies some aspect(s) of the said problem. (shrink)

The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in (...) this chapter is that philosophy is essential in this process. By reviewing select examples from the history of science and philosophy, disciplines which were indistinguishable until the mid-nineteenth century, I argue that progress toward the many impasses in biomedicine can be achieved by emphasizing theoretical work (in the true sense of the word 'theory') as a vital foundation for experimental biology. Furthermore, a philosophical biology program that could provide a framework for theoretical investigations is outlined. (shrink)

This paper is about interpreting the aim of Plato's Sophist in a linguistic framework and arguing that in its attempt at resolving the conundrum of what the true meaning and essence of the word "sophist" could be, it resembles a number of themes encountered in contemporary linguistics. I think it is important to put our findings from the Sophist in a broader Platonic context: in other words, I assume—I think not too unreasonably—that Plato pursued (or at least had in mind) (...) a number of overall projects ('OP' for short) throughout some or most of the dialogues, while each one of the dialogues would in addition have more specific projects ('SP') as part of its individual blueprint. To be sure, the OPs, if they actually existed, might have evolved from the earlier-written to later dialogues, but their foundational premises should have remained intact. In Section A, I provide evidence for reading the Sophist on a linguistic basis. In Section B, I focus on two OPs that I think are relevant to our discussion, one having to do with language and meaning acquisition, and the second concerning the "mind" or a "thought faculty". Ultimately, in Section C, I will use the OPs to contextualise two (related) SPs in the Sophist: (i) identifying cases of intentional referrals for names versus (ii) identifying internal references when searching for word meanings without particular referable instances. At the end of this section, I will draw close parallels between this interpretation of the dialogue and a congruous project of modern 'generative' linguistics. (shrink)

Following an analysis of the state of investigations and clinical outcomes in the Alzheimer's research field, I argue that the widely-accepted 'amyloid cascade' mechanistic explanation of Alzheimer's disease appears to be fundamentally incomplete. In this context, I propose that a framework termed 'principled mechanism' (PM) can help with remedying this problem. First, using a series of five 'tests', PM systematically compares different components of a given mechanistic explanation against a paradigmatic set of criteria, and hints at various ways of making (...) the mechanistic explanation more 'complete'. These steps will be demonstrated using the amyloid explanation, and its missing or problematic mechanistic elements will be highlighted. Second, PM makes an appeal for the discovery and application of 'biological principles' (BPs), which approximate ceteris paribus laws and are operative at the level of a biological cell. As such, although thermodynamic, evolutionary, ecological and other laws or principles from chemistry and the broader life sciences could inform them, BPs should be considered ontologically unique. BPs could augment different facets of the mechanistic explanation but also allow further independent nomological explanation of the phenomenon. Whilst this overall strategy can be complementary to certain 'New Mechanist' approaches, an important distinction of the PM framework is its equal attention to the explanatory utility of biological principles. Lastly, I detail two hypothetical BPs, and show how they could each inform and improve the potentially incomplete mechanistic aspects of the amyloid explanation and also how they could provide independent explanations of the cellular features associated with Alzheimer's disease. (shrink)

How do philosophers and psychologists receive paradigmatic cases from pathology? More specifically, how are some essential features of ‘normal’ cognitive, affective or perceptual functions derived from these pathological cases? In this paper, I argue that Maurice Merleau-Ponty offers a fecund answer to this question by putting forth a logic of supplementation in pathology that distinguishes the coping behavior of the organic world in contrast to an inorganic one. Supplementation, instead of substitution, marks the world of the living, particularly in its (...) higher forms, as it denotes a persistence through impairment governed by an organic norm. A prominent example of this appears in his reading of the patient Schneider case, a classic example from Goldstein and Gelb’s Gestalt psychology. While earlier commentators were interested in underlying whether or not Merleau-Ponty used this example to denote the persistence of a key function or the disruption of another, what has been missed, on my view, is a far more consequential point about pathologies and how they structure our relation to our world. -/- . (shrink)

Historic preservation, which is a vital act for conveying people’s understanding of the past, such as events, ideas, and places to the future, allows people to preserve history for future generations. Additionally, since the historic properties are currently concentrated in urban areas, an urban-oriented approach will contribute to the issue. Hence, public awareness is a key factor that paves the way for this conservation. Public history, a history with a public audience and special methods of representation, can serve society in (...) this regard. Historical video games, which get their game objectives from the past, can be considered a form of public history, raising people’s awareness and letting them gain historical experience. While plenty of studies focused on this content with various approaches, this study takes the topic under consideration with a player-oriented focus. The research uses the Steam video game digital distribution service database to explore the existing historical games based on their genre, player scale, dimension, VR compatibility attributes, and player rating. The database includes 1,148 games published between 2002 and 2022, filtered as historical by Steam tags and sorted by player review. For the data collection, the study uses the Octoparse web scraping tool for data extraction, and for the data analysis, it uses RapidMiner Studio data mining software. The study aims to provide a framework applicable to the development of commercially playable historical video games contributing to heritage preservation by raising public awareness in the context of public history. (shrink)

The pandemic brought new norms and techniques of pedagogical strategies in formal education. The synchronous/ asynchronous video streaming brought an emphasis on virtual and augmented realities, which are rapidly replacing textbooks as the main medium for learning and teaching. This transformation requires more extensive online and interactive content with simpler user interfaces. The aim of this study is to report on the design, implementation, and testing of a game based on low-cost and user-friendly content for digital cultural heritage. In this (...) project, a game aimed at inclusive and equitable education was developed using 360° images of the targeted architectural heritage geographically distributed in a pilot site. We promote lifelong learning opportunities for all, following the SDG4, aiming for quality education with the easy-to-use online platform and easy access to immersive education through mobile platforms. Towards a post-carbon future without the need for travel, computational design methods such as using 360° videos and images in combination with virtual reality (VR) headsets allow a low-cost approach to remotely experiencing cultural heritage. We propose developing and testing a GIS-based educational game using a low-cost 360° virtual tour of architectural heritage, more specifically, caravanserais of Anatolia. (shrink)

Designing a virtual environment within a digital game occupies a large part of the design procedure, requiring holistic attention and a broad arrangement of the game constituents. Considering other design disciplines, they occupy a unified design methodology; however, a comprehensive literature review reveals the lack of the intended design methodology in the digital game domain's virtual environment development, despite a currently proposed theoretical methodology trying to dissolve the issue. Hence, this research aims to determine the industry's requirements and provide a (...) set of assets included in current digital games as an initial step of providing such a design methodology for the domain. In this regard, the researchers reverse-engineered ten selected digital games, understanding the current condition of digital games via adopting the mentioned currently available design methodology. This dataset reveals a lack in the assets of the story layer in the recent digital games, despite their focus on being story-based. This dilemma leads to long text or speech conversations between game characters, disrupting the players while following the game. The current design focuses on environmental resources only, however, as a virtual landscape, the story needs to be reinforced to be a balanced and well-designed game. Hence, increasing the ratio of the assets in this layer will advance the games' interactivity. Also, as future work, this data set could pave the way for a digital game industry design tool regarding the virtual environment. (shrink)

This paper presents the design, development, and potential impact of Echoes of Union Depot, a virtual reality (VR) game aimed at promoting historic preservation and raising public awareness about El Paso's Union Depot, a building listed on the National Register of Historic Places Inventory. The game leverages the immersive capabilities of VR technology and 360° images to engage players in exploring the site's rich history and architectural evolution. Players assume the role of a time-traveling detective, guiding lost spirits to resolve (...) their past and move on. The paper outlines the development process, highlighting the use of 360° panoramic images and 3D Vista Virtual Tour Pro software to create an accessible and user-friendly experience that fosters historic preservation awareness and cultural appreciation. The study also discusses limitations and areas for future research, including expanding the scope to include other heritage sites, working with historians and cultural consultants for accurate representations, and evaluating the game's effectiveness in promoting awareness and fostering a sense of community pride. (shrink)

Life is getting digital more than ever as technology improves. While the Internet is responsible for two percent of global greenhouse gas emissions, it is underestimated as a pollutant. Since public awareness is one of the most important preservation methods, it can contribute to protecting the environment from carbon emissions by raising people's understanding. In this regard, serious games, as a type of gamification transmitting educational content besides entertainment, immerse the player in enjoyment while teaching them a specific topic or (...) enhancing their skills in a field. This study proposes a serious game, taking the digital unseen carbon footprint and its effects on the landscape into the topic. The game considers SDG goals provided by the United Nations Department of Economic and Social Affairs. In this regard, the research uses SDGs 4 and 7 by providing quality education for all and access to sustainable energy by changing people's everyday habits. (shrink)

With the increasing population growth of human beings, the world is being threatened by the water scarcity problem, causing insecurity in water accessibility. Therefore, a deliberated water management gains fatal importance. In addition, the awareness of the issue through education, specifically in the early ages, plays a crucial role in this path. This research considers the water issue of Istanbul in its content. However, regarding the target audience, which is the kids, it uses a novel approach to tackle the problem. (...) The paper proposes a visually enriched and nonlinear, serious game for the children to teach them about the importance of water and its impact on the planet, specific to Istanbul. The game is inspired by National Geographic Turkey's documentary named 25 Liters: In Pursuit of Water, asking the players to survive in a drought situation in the future. It aims to change the kid's lifestyle to revive the country's in-danger future. (shrink)

The emergence of the need for orientation since the past times led the universities to invent innovative ways to prepare their students for the activities and courses they will face. Hence, various types of orientation have been provided during history. However, today with the outbreak of the Covid-19 and the closure of the schools, most of the students are continuing their studies as distance learning. While this situation is very disappointing for all freshmen students who do not know the university's (...) atmosphere, it is extremely disruptive, specifically for the design ones, which are passing tactile courses, demanding being held face to face. This ascertains the research's problem as a need for an interactive solution for the issue to lessen the consequent problems. Game-based orientation (GBO) is a tool, engaging the freshmen students as players with the provided data in it, which are the essentials for a novel student to know before entering the university. It allows the student to be dealt with the school services, Istanbul Technical University in this case, and use them in terms of the game's tasks. The scoring system, the ultimate certificate, the leaderboard leading them to prizes, and the game's non-linearity will attract the students to use GBO frequently to finish it and experience all the possible scenarios. (shrink)

Water is the source of life for our planet, guided the ancient civilizations, and formed its current footprint on the earth. Water has always been a crucial element of our biological survival; consequently, humankind has permanently settled around it while carrying the responsibility of protecting it. To understand the water pattern in various cities throughout history and analyze how the emerging problems were overcome, Istanbul Technical University Landscape Architecture Department Graduate Level Design Studio was held under the theme of "Around (...) Water". Despite the adverse effects of the Covid-19 pandemic on education, international researchers contribute to the studio in a beneficial and diversified manner with the effective use of online tools. As a result of the literature review and the online, multidisciplinary education, and research-based design requirements, a new studio method was developed. Water-based case studies worldwide produced enriched outputs. While creating new discussion environments, the diversified outcomes of the studio "Around Water" contributed to the creation of cumulative studio knowledge. (shrink)