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POLYKETIDE SYNTHESASES. "Single giant proteins with multiple catalytic domains, repeated in modules, oligomerize and transform small units to build up complex natural products. These varied enzymatic properties ensure overall catalytic plasticity in the world of natural products." https://lnkd.in/dEpJBda View in LinkedIn

BUT NOT QUITE RASA. "As with all genetic algorithms, there was work involved with designing the fitness function. The fitness function is equivalent to describing to the AI what you’re looking for. In this way, creating the fitness function itself, is a bit like programming (on behalf of the human). If it were possible for the AI to develop its own fitness function, this would be a step forward." https://lnkd.in/ddNuyJD View in LinkedIn

LACK OF EUKARYOTIC LOGIC. "One of the striking differences between this arrangement in prokaryotes and that found in eukaryotes is that typically, not only are the genes of metabolic pathways in eukaryotes not organized in clusters, but they are often located on different chromosomes. Thus, unlike the metabolic genes of prokaryotes, those of eukaryotes are not organized spatially." https://lnkd.in/dEpJBda View in LinkedIn

PROKARYOTE LOGIC. "Not only are the genes aligned sequentially...but they are also usually aligned along the same direction in the DNA strand." https://lnkd.in/dEpJBda View in LinkedIn

LOGICALAL PROKARYOTIC STRUCTURES. "In prokaryotes, the genes for metabolic pathways are typically organized into operons and, upon transcription, give polycistronic m-RNA. Such unidirectional, clustered, and organized genes would appear to make good engineering sense." https://lnkd.in/dEpJBda View in LinkedIn

OPTIMIZED PATHWAYS. "Some computational studies have proposed that the topology of specific metabolic pathways may have evolved towards maximal efficiency, minimal number of steps, or that network properties may reflect optimal organization." https://lnkd.in/dUHqnYU View in LinkedIn

ADAPTED PATHWAYS. "Baldwin and Krebs suggested that biochemical network topologies may reflect the adaptation toward optimally efficient metabolic strategies, and that manifold use of certain molecules may be a crucial element of this adaptation, as “it is indeed a general principle of evolution that multiple use is made of given resources." https://lnkd.in/dUHqnYU View in LinkedIn

DEEPLY ORGANIZED. "Despite the simplicity of the model employed, we find that the ensuing pathways display a surprisingly rich set of properties, including the existence of autocatalytic cycles and hierarchical modules, the appearance of universally preferable metabolites and reactions, and a logarithmic trend of pathway length as a function of input/output molecule size." https://lnkd.in/dUHqnYU View in LinkedIn

RECURRING TOPOLOGIES. "We find that optimal pathways in our idealized chemistry display a logarithmic dependence of pathway length on input/output molecule size. They also display recurring topologies, including autocatalytic cycles reminiscent of ancient and highly conserved cores of real biochemistry. Finally, across all optimal pathways, we identify universally important metabolites and reactions, as well as a characteristic distribution of reaction utilization." https://lnkd.in/dUHqnYU View in LinkedIn

SELECTION AND METABOLIC WIRING. "Especially during major transitions, such as the early stages of life's appearance or the rise of oxygen in the Earth's atmosphere, selective forces must have shaped the metabolic wiring itself. Comparative genomics can provide top-down insight into some long-term evolution of metabolic pathways." https://lnkd.in/dUHqnYU View in LinkedIn