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One popular assumption regarding biological systems is that traits have evolved to be optimized with respect to function. This is a standard goal in evolutionary computation, and while not always embraced in the biological sciences, is an underlying assumption of what happens when fitness is maximized. The implication of this is that a signaling pathway or phylogeny should show evidence of minimizing the number of steps required to produce a biochemical product or phenotypic adaptation. In this paper, it will be shown that a principle of maximum intermediate steps may also characterize complex biological systems, especially those in which extreme historical contingency or a combination of mutation and recombination are key features. The contribution to existing literature is two-fold: demonstrating both the potential for non-optimality in engineered systems with lifelike attributes, and the underpinnings of non-optimality in naturalistic contexts. This will be demonstrated by using the Rube Goldberg Machine (RGM) analogy. Mechanical RGMs will be introduced, and their relationship to conceptual biological RGMs. Exemplars of these biological RGMs and their evolution (e.g. introduction of mutations and recombination-like
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been extensive stand
Standard techniques for studying biological systems largely focus on their dynamical, or, more recently, their informational properties, usually taking either a reductionist or holistic perspective. Yet, studying only individual system elements or th
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannons concept of informa
In this paper, we describe a Graphical User Interface (GUI) designed to manage large quantities of image data of a biological system. After setting the design requirements for the system, we developed an ecology quantification GUI that assists biolog
In cellular reprogramming, almost all epigenetic memories of differentiated cells are erased by the overexpression of few genes, regaining pluripotency, potentiality for differentiation. Considering the interplay between oscillatory gene expression a