Near infrared (NIR) spectral patterns from seeds carry surprisingly consistent information on functional food quality that seems almost unreasonable. In the developing cereal seed, all genes interact with all other active genes. This is proven by manipulating the immense complexity of physiological expression by single seed mutants in a barley seed model at a constant gene background/environment. Miraculously, it is possible to get a causal relation between the mutated gene and its NIR spectral pattern. When combining under controlled conditions, Nature’s and the near infrared spectroscopy (NIRS) instrument’s combined ability to reproduce the physiochemical composition of a seed population of a DNA-specific genotype, we obtain at stunning absorption log 1/R 10–4–10–5 mean distance between two similar single seed spectra. The deterministic gene/genotype-specific NIRS patterns from single seeds/populations and the corresponding deterministic metabolite patterns are interpreted, in the light of the present achievements in molecular and quantum biology, as a discovery of a global decision mechanism by “set probability”. It involves a global cell/seed/plant communication resulting in individual specific NIRS and chemical metabolic patterns that prevail on all levels of the phenotype. This ensnaring phenomenon is here labelled as “biological entanglement” with a possible explanation in the quantum world of physics. The observed gene interaction leading to conserved physiochemical fingerprints has consequences with regard to the assessment and breeding for cereal food quality. Only by targeting the food functional complex by a spectral pattern from a certified quality cereal line, that includes an overview of gene interaction, is it possible to get the selection target right from the beginning. Selection by functional NIR spectral fingerprinting first is more effective than by quantitative trait locus (QTL) markers for single quantitative traits, because these DNA markers do not include information on the global gene interaction. The cost of using integrated NIRS breeding is less than one per cent of the costs for molecular QTL breeding. For a new NIRS fingerprinting culture to take on in industry, plant breeding and basic science—an inverse engineering strategy is needed with a library for functional fingerprint evaluation that builds a confidence into each user based on own experience, on how to read the meaning out of every single NIR spectrum.