Boyle, L. | Search bioRxiv

bioRxiv2026

Compatible Comma-Free Codes and the Origin of the Genetic Code

The genetic code is the rule that (apart from minor modifications) is used by all contemporary life on Earth to translate genes into proteins. It is summarized by a 4x4x4 table which maps the 64 possible triplet RNA codons to the 20 canonical amino acids ("AAs"). Understanding the origin of this code is a fundamental open problem in biology. We review the idea of a comma-free code, and put forward a general reason to suspect the primordial code was comma-free (even though the modern code is not). We explain why this primordial code should then persist as a comma-free subcode within the modern code, and identify the five optimal candidates for such a subcode. We then introduce the idea of "compatible comma-free codes" and explain how they allow multiple codes to evolve in parallel, circumventing a standard argument suggesting that code evolution should effectively freeze when the associated genome becomes sufficiently complex. In particular, we highlight the possibility that the original code was a comma-free doublet code, which was then overtaken by a compatible comma-free triplet code, which finally evolved (after the evolution of the start codon and ribosome) to the modern saturated triplet code. To assess this idea, we classify all inequivalent compatible comma-free doublet-triplet codes and, among these, identify the three most promising predecessors of the modern code. Consistency between these three best codes and the "wobble rules" in gene translation provide non-trivial evidence for this possibility.

evolutionary biology↗

bioRxiv2026

Mechanical, rheological, and sensory characterization of lion's mane mushroom steak

Mushrooms are increasingly recognized as delicious, nutritious, and sustainable foods, with an intrinsic umami flavor and fibrous microstructure that can approximate meat-like texture. Among them, lions mane mushroom has emerged as a promising candidate for whole-cut meat alternatives. Yet, its mechanical, rheological, and sensory properties remain largely unquantified. Here we show that a minimally processed lions mane mushroom steak exhibits distinctive mechanical, rheological, and sensory characteristics that position it favorably among existing meat alternatives. Despite its pronounced fibrous morphology, lions mane steak behaves predominantly as an isotropic material under both mechanical loading and rheological testing, with elastic stiffnesses of E = 33.2 kPa and E = 34.8 kPa in-plane and cross-plane. A fundamental challenge in alternative protein development is to understand how these measurable physical properties relate to human texture perception. In a complementary sensory survey, n = 21 participants ranked lions mane steak as more fatty, fibrous, moist, and meaty than eight animal- and plant-based comparison meats. Strikingly, our perceived sensory softness correlates inversely with our experimentally measured mechanical stiffness ({tau}=-0.60, p = 0.02) and rheological loss modulus ({tau}=-0.56, p = 0.03). Taken together, our results demonstrate that lions mane steak combines favorable mechanical performance with desirable sensory attributes and provide a mechanistic link between physics and taste. Our findings highlight lions mane mushroom as a compelling whole-cut alternative protein and underscore the value of integrated mechanical-sensory characterization for rational food design.

bioengineering↗