Developments in the tools and methodologies of synthetic biology.

Synthetic biology is principally concerned with the rational design and engineering of biologically based parts, devices, or systems. However, biological systems are generally complex and unpredictable, and are therefore, intrinsically difficult to engineer. In order to address these fundamental challenges, synthetic biology is aiming to unify a body of knowledge from several foundational scientific fields, within the context of a set of engineering principles. This shift in perspective is enabling synthetic biologists to address complexity, such that robust biological systems can be designed, assembled, and tested as part of a biological design cycle. The design cycle takes a forward-design approach in which a biological system is specified, modeled, analyzed, assembled, and its functionality tested. At each stage of the design cycle, an expanding repertoire of tools is being developed. In this review, we highlight several of these tools in terms of their applications and benefits to the synthetic biology community

Synovial joint lubrication – does nature teach more effective engineering lubrication strategies?

Nature shows numerous examples of systems which show energy efficiency, elegance in their design and optimum use of materials. Biomimetics is an emerging field of research in engineering and successes have been documented in the diverse fields of robotics, mechanics, materials engineering and many more. To date little biomimetics research has been directed towards tribology in terms of transferring technologies from biological systems into engineering applications. The potential for biomimicry has been recognised in terms of replicating natural lubricants but this system reviews the potential for mimicking the synovial joint as an efficient and durable tribological system for potential engineering systems. The use of materials and the integration of materials technology and fluid/surface interactions are central to the discussion

Synthetic biology—putting engineering into biology

Synthetic biology is interpreted as the engineering-driven building of increasingly complex biological entities for novel applications. Encouraged by progress in the design of artificial gene networks, de novo DNA synthesis and protein engineering, we review the case for this emerging discipline. Key aspects of an engineering approach are purpose-orientation, deep insight into the underlying scientific principles, a hierarchy of abstraction including suitable interfaces between and within the levels of the hierarchy, standardization and the separation of design and fabrication. Synthetic biology investigates possibilities to implement these requirements into the process of engineering biological systems. This is illustrated on the DNA level by the implementation of engineering-inspired artificial operations such as toggle switching, oscillating or production of spatial patterns. On the protein level, the functionally self-contained domain structure of a number of proteins suggests possibilities for essentially Lego-like recombination which can be exploited for reprogramming DNA binding domain specificities or signaling pathways. Alternatively, computational design emerges to rationally reprogram enzyme function. Finally, the increasing facility of de novo DNA synthesis—synthetic biology’s system fabrication process—supplies the possibility to implement novel designs for ever more complex systems. Some of these elements have merged to realize the first tangible synthetic biology applications in the area of manufacturing of pharmaceutical compounds.

Methodological Flaws in Cognitive Animat Research

In the field of convergence between research in autonomous machine construction and biological systems understanding it is usually argued that building robots for research on auton- omy by replicating extant animals is a valuable strategy for engineering autonomous intelligent systems. In this paper we will address the very issue of animat construction, the ratio- nale behind this, their current implementations and the value they are producing. It will be shown that current activity, as it is done today, is deeply flawed and useless as research in the science and engineering of autonomy

Stochastic Resonance Can Drive Adaptive Physiological Processes

Stochastic resonance (SR) is a concept from the physics and engineering communities that has applicability to both systems physiology and other living systems. In this paper, it will be argued that stochastic resonance plays a role in driving behavior in neuromechanical systems. The theory of stochastic resonance will be discussed, followed by a series of expected outcomes, and two tests of stochastic resonance in an experimental setting. These tests are exploratory in nature, and provide a means to parameterize systems that couple biological and mechanical components. Finally, the potential role of stochastic resonance in adaptive physiological systems will be discussed

Engineering the Interface Between Cellular Chassis and Integrated Biological Systems

The engineering of biological systems with predictable behavior is a challenging problem. One reason for this difficulty is that engineered biological systems are embedded within complex and variable host cells. To help enable the future engineering of biological systems, I will study and optimize the interface between an engineered biological system and its host cell or “chassis”. Other engineering disciplines use modularity to make interacting systems interchangeable and to insulate one system from another. Engineered biological systems are more likely to work as predicted if system function is decoupled from the state of the host cell. Also, specifying and standardizing the interfaces between a system and the chassis will allow systems to be engineered independent of chassis and allow systems to be interchanged between different chassis. To this end, I will build dedicated transcription and translation systems, independent from the equivalent host cell systems. In parallel, I will develop test systems and metrics to measure the interactions between an engineered system and its chassis. Lastly, I will explore methods to “port” a simple engineered system from a prokaryotic to a eukaryotic organism so that the system can function in both organisms