This article presents an update on known and unknown biological codes. While the genetic code has been recognized as a code for decades, most other codes were hidden in the shadow of this hallmark discovery. It was the dawn of the new millennium when the histone language and code were proclaimed in the years 2000 and 2001, respectively, marking the start of an explosion in the number of published codes across all biological disciplines since then. Actually, there are hundreds to (...) thousands of biological codes, but only a fraction—although still a substantial number—have been explicitly described as such. A first assessment of those codes allows for a simple categorization into structural and regulatory codes, at the same time maintaining Marcello Barbieri´s initial differentiation of organic versus neural codes. The article reviews prominent codes and showcases restriction-modification and toxin-antitoxin systems as code systems that have gone unrecognized until today. This article should read as a motivation for all those who want to discover ever more new codes—from literature or in the field. (shrink)

The visible human body is composed of flesh and bones for the most part, yet an invisible orchestra of sensations and perceptions creates a virtual or phantom body that behaves like a shadow following every movement and gesture of its anatomical complement. This shadow becomes only “visible” to the individual when bodily integrity is affected, anatomically or cognitively. Phantom limbs have been known for a long time. They refer to the felt presence of a missing hand, leg, or other body (...) part as if it was still in place. Reciprocally and of a supposedly cognitive origin, phantom extremities are reported by some patients that feel the virtual presence of a supernumerary limb – signifying anatomical “overcompleteness.” However, other patients feel as one of their limbs does not belong to their body – signifying “foreignness”. Various shades of the so-called body integrity identity disorder exemplify the assumed complex signification processes within the human body. The Peircean theory of signs and the Uexküllian concept of endosemiosis are combined to approach the still poorly understood phantom phenomena in light of representation and embodiment. (shrink)

The article reconciles contentious issues between code biology and biosemiotics. The framework of semantic biology and molecular meaning woven around organic codes by Marcello Barbieri defied classical informational conceptualizations of meaning in the biological realm while the discourse on meaning and agency and their respective (in)dependency on interpretation continues. Whereas the role of codes in agency is often secondary to other aspects, I present here a more consistent picture– integrating codes and artifacts to smoothly transcend from the world of mechanistic (...) molecular meaning to organismic agency. Interpretation is presented as a call-to-action based on intraindividual states, and sense-making as call-to-change based on interindividual communication. (shrink)