Whether, and to what degree, do patents granted on human genes cast a shadow of uncertainty over genomics and its applications? Will owners of patents on individual genes or clusters of genes sue those performing whole-genome analyses on human samples for patent infringement? These are related questions that have haunted molecular diagnostics companies and services, coloring scientific, clinical, and business decisions. Can the profusion of whole-genome analysis methods proceed without fear of patent infringement liability?Whole-genome sequencing is proceeding apace. Academic centers (...) have been performing whole-genome and -exome sequencing in research for at least five years, and academic clinical laboratories with national reach have been doing sequencing for clinical applications for almost as long. Companies have also been offering WGS and WES as a clinical service for a few years now. So far as we know, no one has been sued for infringement of “gene patents” for performing WGS. (shrink)

Noninvasive prenatal screening using cell-free DNA, which analyzes placental DNA circulating in maternal blood to provide information about fetal chromosomal disorders early in pregnancy and without risk to the fetus, has been hailed as a potential “paradigm shift” in prenatal genetic screening. Commercial provision of cell-free DNA screening has contributed to a rapid expansion of the tests included in the screening panels. The tests can include screening for sex chromosome anomalies, rare subchromosomal microdeletions and aneuploidies, and most recently, the entire (...) fetal genome. The benefits of this screening tool are generally framed, by both providers and commercial laboratories, as enhancing reproductive autonomy and choice by providing an earlier, simpler, and more accurate screening while potentially reducing the need for invasive follow-up testing. The majority of the literature has explored these issues empirically or conceptually from a European or North American vantage point, one that assumes normative priorities such as individual reproductive autonomy and the clinical availability of maternal health care or prenatal screening programs within which cell-free DNA screening is offered. While its implementation has raised both challenges and opportunities, very little is known about real-world experiences and the implications of the rapid introduction of cell-free DNA screening outside of North America and Europe, especially in low- and middle-income countries. To begin addressing this gap in knowledge, we organized a four-day international workshop to explore the ethical, legal, social, economic, clinical, and practical implications of the global expansion of cell-free DNA screening. We describe eight key insights that arose from the workshop. (shrink)

Novel computational representations, such as simulation models of complex systems and video games for scientific discovery, are dramatically changing the way discoveries emerge in science and engineering. The cognitive roles played by such computational representations in discovery are not well understood. We present a theoretical analysis of the cognitive roles such representations play, based on an ethnographic study of the building of computational models in a systems biology laboratory. Specifically, we focus on a case of model-building by an engineer that (...) led to a remarkable discovery in basic bioscience. Accounting for such discoveries requires a distributed cognition analysis, as DC focuses on the roles played by external representations in cognitive processes. However, DC analyses by and large have not examined scientific discovery, and they mostly focus on memory offloading, particularly how the use of existing external representations changes the nature of cognitive tasks. In contrast, we study discovery processes and argue that discoveries emerge from the processes of building the computational representation. The building process integrates manipulations in imagination and in the representation, creating a coupled cognitive system of model and modeler, where the model is incorporated into the modeler's imagination. This account extends DC significantly, and we present some of the theoretical and application implications of this extended account. (shrink)

Recent experiments show video games have a range of positive cognitive effects, such as improvement in attention, spatial cognition and mental rotation, and also overcoming of cognitive disabilities such as fear of flying. Further, game environments are now being used to generate scientific discoveries, and bring about novel phenomenological effects, such as out-of-body experiences. These advances provide interesting interaction design possibilities for video games. However, since the cognitive mechanisms underlying these experimental effects are unknown, it is difficult to systematically derive (...) novel systems and interaction designs based on these results. We review the emerging cognitive mechanism known as common coding, and outline how this mechanism could provide an integrated account of the cognitive effects of video games. We then illustrate, using two ongoing projects, how novel video game interaction designs could be derived by extending common coding theory. (shrink)

I present a case study of scientific discovery, where building two functional and behavioral approximations of neurons, one physical and the other computational, led to conceptual and implementation breakthroughs in a neural engineering laboratory. Such building of external systems that mimic target phenomena, and the use of these external systems to generate novel concepts and control structures, is a standard strategy in the new engineering sciences. I develop a model of the cognitive mechanism that connects such built external systems with (...) internal models, and I examine how new discoveries, and consensus on discoveries, could arise from this external‐internal coupling and the building process. The model is based on the emerging framework of common coding, which proposes a shared representation in the brain between the execution, perception, and imagination of movement. (shrink)

We outline three challenges involved in designing external representations that promote sustainable use of natural resources. First, the task environment of sustainable resource-use is highly unstructured, and involves many uncoordinated and asynchronous actions. Following from this complex nature of the task environment, more task constraints and task interactions are involved in designing representations promoting sustainability, compared to representations that seek to make tasks easier in structured task environments, such as aircraft cockpits and control rooms. Second, external representations promoting sustainable resource-use (...) need to motivate people to make decisions that sustain resources, and persist with this behavior, even though alternate behaviors are easier and commonplace. Third, external representations promoting sustainability also need to lower the cognitive load involved in sustainability decisions. This three-tiered function (meeting complex task constraints, providing motivation, lowering cognitive load) makes such representations challenging to design. However, some early prototype designs promoting sustainable resource-use have appeared recently, primarily addressing electricity use. Analyzing these digital prototypes, we outline three design principles they share, and show how these seek to address the complexities of the sustainability problem-space (complexity of task environments, goals, and representations). We then argue that at least two further cognitive scaffolds are required for effectively promoting sustainable resource use (action scripts, deconstruction). We close with some of the limitations of this approach to promoting sustainability, and outline future work. (shrink)

We outline three challenges involved in designing external representations that promote sustainable use of natural resources. First, the task environment of sustainable resource-use is highly unstructured, and involves many uncoordinated and asynchronous actions. Following from this complex nature of the task environment, more task constraints and task interactions are involved in designing representations promoting sustainability, compared to representations that seek to make tasks easier in structured task environments, such as aircraft cockpits and control rooms. Second, external representations promoting sustainable resource-use (...) need to motivate people to make decisions that sustain resources, and persist with this behavior, even though alternate behaviors are easier and commonplace. Third, external representations promoting sustainability also need to lower the cognitive load involved in sustainability decisions. This three-tiered function makes such representations challenging to design. However, some early prototype designs promoting sustainable resource-use have appeared recently, primarily addressing electricity use. Analyzing these digital prototypes, we outline three design principles they share, and show how these seek to address the complexities of the sustainability problem-space. We then argue that at least two further cognitive scaffolds are required for effectively promoting sustainable resource use. We close with some of the limitations of this approach to promoting sustainability, and outline future work. (shrink)

The emergence of new computational media is radically changing the practices of science, particularly in the way computational models are built and used to understand and engineer complex biological systems. These new practices present a novel variation of model-based reasoning, based on dynamic and opaque models. A new cognitive account of MBR is needed to understand the nature of this practice and its implications. To develop such an account, I first outline two cases where the building and use of computational (...) models led to discoveries. A theoretical model of the possible cognitive and neural mechanisms underlying such discoveries is then presented, based on the way the body schema is extended during tool use. This account suggests that the process of building the computational model gradually ‘incorporates’ the external model as a part of the internal imagination system, similar to the way tools are incorporated into the body schema through their active use. A central feature of this incorporation account is the critical role played by tacit and implicit reasoning. Based on this account, I examine how computational modeling would change model-based reasoning in science and science education. (shrink)

The notion of mutation is applicable to the generation of novel designs and solutions in engineering and science. This suggests that engineers and scientists have to work against the biases identified in counterfactual thinking. Therefore, imagination appears a lot less rational than claimed in the target article.

Recent experiments show video games have a range of positive cognitive effects, such as improvement in attention, spatial cognition and mental rotation, and also overcoming of cognitive disabilities such as fear of flying. Further, game environments are now being used to generate scientific discoveries, and bring about novel phenomenological effects, such as out-of-body experiences. These advances provide interesting interaction design possibilities for video games. However, since the cognitive mechanisms underlying these experimental effects are unknown, it is difficult to systematically derive (...) novel systems and interaction designs based on these results. We review the emerging cognitive mechanism known as common coding, and outline how this mechanism could provide an integrated account of the cognitive effects of video games. We then illustrate, using two ongoing projects, how novel video game interaction designs could be derived by extending common coding theory. (shrink)

A testable model of the origin of money is outlined. Based on the notion of epistemic structures, the account integrates the tool and drug views using a common underlying model, and addresses the two puzzles presented by Lea & Webley (L&W) – money's biological roots and the adaptive significance of our tendency to acquire money. (Published Online April 5 2006).

The human species' adaptive advantage is driven by its ability to build new material structures and artefacts. Engineering is the modern manifestation of this building instinct, and its advent has made the construction and use of technologies the central pattern of human life. In parallel, efficiency, the overarching narrative driving technology and related life practices, has pervaded most occupations as a value, forming a cultural backdrop that implicitly guides decisions and behaviour. We examine the process through which this backdrop has (...) developed, and argue that it emerged through the constant presence and use of built artefacts and structures, which function as manifestations of the engineering value of efficiency. The constant presence and use of built structures leads to the slow percolation of their building values into society, forming a cultural narrative that emphasises efficiency. This narrative then feeds back, to further reinforce efficiency-driven engineering processes. This loop creates a runaway building system that is highly resistant to change, even when faced with the prospect of the species going extinct. Any effort towards sustainability can be successful only when this all-pervading - and hence invisible - building loop is made explicit, and compensated for, through a counter-loop where building manifests sustainable engineering values. As a first step in revealing this structure, we characterise the emergence of the efficiency value as a cultural narrative, and analyse its wide-ranging environmental effects. We then present the design principle of 'Solving for Pattern' (SfP) as an illustrative contrast case. SfP, first articulated by Wendell Berry, focuses on interconnectedness and flourishing of all species as central design principles. We argue that these ecological principles can be extended to engineering, and can thus support the development of a robust operational-level building movement that manifests value systems oriented towards sustainability. To ground this proposal in actual practice, we outline two case studies of technology design that illustrates SfP. We also discuss three cases that illustrate SfP at a larger scale, and examine how these extend existing design approaches such as systems engineering. We conclude with a proposal to include SfP in engineering education curricula, to facilitate a faster cultural shift towards flourishing, which is required given the limited time window available to move to sustainable building practices. (shrink)

Building computational models of engineered exemplars, or prototypes, is a common practice in the bioengineering sciences. Computational models in this domain are often built in a patchwork fashion, drawing on data and bits of theory from many different domains, and in tandem with actual physical models, as the key objective is to engineer these prototypes of natural phenomena. Interestingly, such patchy model building, often combined with visualizations, whose format is open to a wide range of choice, leads to the discovery (...) of new concepts and control structures. Two key questions are raised by this practice: how could discoveries arise from building external representations for which there is wide latitude in choice of the components from which they are built, and thus can be considered significantly arbitrary, and how could such discoveries allow engineering a real-world prototype system. To examine these questions, we present two case studies of discoveries that emerged from the building of such computational models in the bioengineering sciences. We then develop a process model that accounts for the discovery and transfer problems raised by both these cases, focusing on the process of building the model. Specifically, to account for the discovery problem, we propose that the process of building such models gradually leads to a close coupling between the modeler’s internal processes and the external dynamic model. To account for the transfer problem, we propose that the process of building the model leads to the creation of an enactive model that is generic, which closely enacts, and thus reveals, the way the system-level behavior of the engineered prototype emerges in time through the interaction of its parts. This enactive replication process leads to the model and the prototype forming a new class, which allows concepts and control structures developed for the computational model to be transfered to the real-world prototype. We argue that this account requires rethinking correspondence in engineering sciences as a plastic and enactive relation. A closer focus on the process of building models is required to develop a general account of this emerging approach to discovery. (shrink)

Manipulation of physical models such as tangrams and tiles is a popular approach to teaching early mathematics concepts. This pedagogical approach is extended by new computational media, where mathematical entities such as equations and vectors can be virtually manipulated. The cognitive and neural mechanisms supporting such manipulation-based learning—particularly how actions generate new internal structures that support problem-solving—are not understood. We develop a model of the way manipulations generate internal traces embedding actions, and how these action-traces recombine during problem-solving. This model (...) is based on a study of two groups of sixth-grade students solving area problems. Before problem-solving, one group manipulated a tangram, the other group answered a descriptive test. Eye-movement trajectories during problem-solving were different between the groups. A second study showed that this difference required the tangram's geometrical structure, just manipulation was not enough. We propose a theoretical model accounting for these results, and discuss its implications. (shrink)

Computer simulation and thought experiments seem to produce knowledge about the world without intervening in the world. This has called for a comparison between the two methods. However, Chandrasekharan et al. argue that the nature of contemporary science is too complex for using TEs. They suggest CS as the tool for contemporary sciences and conclude that it will replace TEs. In this paper, by discussing a few TEs from the history of science, I show that the replacement thesis about (...) TE is a failure. The paper is divided into three sections. The first section discusses the arguments of Chandrasekharan et al. and demonstrates the three distinct aspects of the replacement thesis. The second section examines the argument against TE and shows that they are inadequate to prove the withering of TE from science. The third section discusses Albert Einstein’s Magnet and Conductor TE and demonstrates that replacing such TE with CS yield no advantage. (shrink)