Transition Fingerprints: A Needle‑Eye Principle for Detecting Minimal Life and Trojan Entities Across Scales

Abstract

Minimal biological entities—from single proteins to ultra‑reduced archaea and viral RNA elements—occupy a "twilight zone" between living and non‑living systems. Traditional characterization focuses on static composition (genome size, morphology, marker genes), which often fails to capture their functional role in larger ecological and evolutionary networks. Here we propose the Transition Fingerprint Principle: minimal and trojan entities are most reliably detected not by their static properties, but by the topology of their passage through bottlenecks—physical, energetic, informational or field‑based. We term this generic structure a needle‑eye topology. We build on recent advances in nanopore sensing of single proteins, where stick–slip dynamics of individual molecules traversing a nanometer‑scale pore yield near‑instantaneous identification via machine‑learning on current traces. We extend this idea across scales to five seemingly disparate systems: (1) nanopore protein sensing, (2) RNA Obelisks in the human microbiome, (3) Candidatus Sukunaarchaeum—an ultra‑reduced archaeal symbiont, (4) trojan nblA genes carried by cyanophages that rewire oceanic photosynthesis, and (5) magnetofossils as fossilized traces of ancient magnetic navigation. For each case, we identify a bottleneck , an entity , the resulting transition trace and a candidate topological signature . We formulate a conjecture: in multi‑scale systems, minimal and trojan entities are stably identifiable by the topology of their transition traces through bottlenecks, not by static state alone. We outline three falsifiable predictions using nanopore design, topological data analysis (TDA) and minimal‑genome network topology, and we connect this framework to prior work on Temporal‑Betti Loops (TBL), microbiome clocks and topological sensing architectures. We suggest that needle‑eye topologies provide a unifying language for the detection, interpretation and eventual design of boundary‑layer life—entities that operate at the edge of what we call "living".