Year: 2022

MISSING AGENTS. "To further complicate matters, some complex systems appear to require initial conditions or agents that have long disappeared from the system but were necessary for the system to evolve to its present state -- such situations are common for ecosystems." https://lnkd.in/dEpJBda View in LinkedIn

MISSING PATHWAYS. "Cells first appeared on earth over 3.5 billion years ago and remained in the unicellular state for some 2.5 billion years. Much of the cellular machinery of today's prokaryotes is believed to have been in place very early, although we have no direct knowledge of this." https://lnkd.in/dEpJBda View in LinkedIn

SMALL NUMBERS GIVE RISE TO BIG NUMBERS. "Although the panorama of interactions of natural products with cellular targets is vast, the number of fundamental mechanisms for these interactions is limited." https://lnkd.in/dEpJBda View in LinkedIn

MODULAR MOLECULAR MACHINE. "Here is the beauty of the transcription-translation machine; it is a modular arrangement of proteins whose core functioning units are repeated over and over again in various transcriptional factors, each of which has specific receptor sites that recognize one another and recognize the steroid-bound protein that initiates the transcription at the specific gene on the DNA." https://lnkd.in/dEpJBda View in LinkedIn

COMMON MOTIFS. "Another characteristic of some natural products: the recurrence of certain structure types. Although we marvel at the seeming endless array of natural product structure types, note should be taken that many structure types, e.g. steroids, are used commonly across life." https://lnkd.in/dEpJBda View in LinkedIn

SO ENDS this first of two weekends contemplating the evolution of metabolism. Bewildering in its complexity, it has a small number of simple motifs. And many of these complexities have been repurposed over time, contributing to the complexity. In some cases by wholesale acquisition of pathways by horizontal gene transfers; in others, by huge macro events such as the Great Oxygenation which required a complete retooling. No wonder the wiring systems are not logical or simple. View in LinkedIn

"LANGTON LOOPS are a particular "species" of artificial life in a cellular automaton created in 1984 by Christopher Langton. They consist of a loop of cells containing genetic information, which flows continuously around the loop and out along an "arm" (or pseudopod), which will become the daughter loop. The "genes" instruct it to make three left turns, completing the loop, which then disconnects from its parent." https://lnkd.in/dX4P4qb View in LinkedIn

CELLULAR AUTOMATA. "Langton’s self-reproducing loop is one of the most famous models of self-reproduction using cellular automata." https://lnkd.in/dSdcD2A View in LinkedIn

INSUFFICIENT. "Langton observed that although the capacity for universal construction, as studied by von Neumann and Codd, is a sufficient condition for self-replication, it is not a necessary one. Furthermore, natural systems are probably not capable of universal construction." https://lnkd.in/dvjjarA View in LinkedIn

REPLICONS ALONE. "Langton and his successors Byl, Reggia et al., developed self-replicating automata which are much simpler than the universal constructor. These machines, however, lack any computing and constructing capabilities, their sole functionality being that of self-replication." https://lnkd.in/dvjjarA View in LinkedIn