Segmenting modulated line textures with S-Gabor filters

This paper describes a novel technique for segmenting frequency modulated line-textures. Textures of this sort abound in nature and are typified by growth patterns in which the deposition rate varies over time. The basic idea underpinning the technique is to use the S-Gabor kernel as a frequency modulated channel response function. According to this channel model, the central frequency changes exponentially with distance from the centre of the kernel. In order to segment the resulting texture response, we use fuzzy clustering to locate peaks in the Fourier power spectrum. In this way we estimate both the centre-frequency and the modulation parameters of the filter bank. We illustrate the effectiveness of our technique on the segmentation of growth patterns on fish scale

Semantic closure demonstrated by the evolution of a universal constructor architecture in an artificial chemistry

We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA being the abstract description, the polymerase being the copier, and the ribosome being the principal machine in expressing what is encoded on the DNA. This architecture is semantically closed as the machine that defines what the abstract description means is itself encoded on that abstract description. We present a series of experiments with the stringmol UCA that show the evolution of the meaning of genomic material, allowing the concept of semantic closure and transitions between semantically closed states to be elucidated in the light of concrete examples. We present results where, for the first time in an in silico system, simultaneous evolution of the genomic material, copier and constructor of a UCA, giving rise to viable offspring

What's the catch? Archaeological application of rapid collagen-based species identification for Pacific Salmon

YesPacific salmon (Oncorhynchus spp.) are ecological and cultural keystone species along the Northwest Coast of North America and are ubiquitous in archaeological sites of the region. The inability to morphologically identify salmonid post-cranial remains to species, however, can limit our understanding of the ecological and cultural role different taxa played in the seasonal subsistence practices of Indigenous groups in the past. Here, we present a rapid, cost-effective ZooMS method to distinguish salmonid species based on collagen peptide mass-fingerprinting. Using modern reference material and an assemblage of 28 DNA-identified salmonid bones from the pre-contact Yup'ik site of Nunalleq, Western Alaska, we apply high-resolution mass spectrometry (LC-MS/MS) to identify a series of potential collagen peptide markers to distinguish Pacific salmon. We then confirm these peptide markers with a blind ZooMS analysis (MALDI-TOF-MS) of the archaeological remains. We successfully distinguish five species of anadromous salmon with this ZooMS approach, including one specimen that could not be identified through ancient DNA analysis. Our biomolecular identification of chum (43%), sockeye (21%), chinook (18%), coho (11%) and pink (7%), confirm the exploitation of all five available species of salmonid at Nunalleq

Defining and simulating open-ended novelty: requirements, guidelines, and challenges

The open-endedness of a system is often defined as a continual production of novelty. Here we pin down this concept more fully by defining several types of novelty that a system may exhibit, classified as variation, innovation, and emergence. We then provide a meta-model for including levels of structure in a system’s model. From there, we define an architecture suitable for building simulations of open-ended novelty-generating systems and discuss how previously proposed systems fit into this framework. We discuss the design principles applicable to those systems and close with some challenges for the community

Designing rockets and growing media

Rational and efficient design of a system typically demands a target endpoint, plus the means to determine progression from one prototype to another in pursuit of that endpoint. If both endpoint and prototypes can be quantified using numerical parameters, then that progression should be amenable to a mathematical description. We will first illustrate this idea using a toy example of rocket design, in which the endpoint is escape velocity and prototype rockets are described numerically using fuel capacity and engine thrust as parameters. Moving to growing media, we motivate numerical parametrisation of media and the development of mathematical relationships linking mixtures. The objective is a predictive model that can be used to rationally design a growing media mix in pursuit of a target crop type and growing system. We propose that this approach offers an alternative to 'look-see' growing trials for assessing growing media performance. Focusing on physical properties, we describe growing media materials and mixtures using three parameters: Air filled porosity, dry bulk density and available water. Materials and mixtures of materials are then represented as points in a three-dimensional parameter space. Plant performance is mapped out over this space via the output of systematic growing trials. A target, for example 'peat-like', can be expressed in terms of its physical parameters. Insight on how to progress a trial mixture toward the target can then be extracted from trends in plant performance, coded as mathematical relations involving media parameters. This mimics the rocket example, in which engine and fuel tank parameters can be used to compare designs and to assess progress toward the goal of escape velocity. This UK Government and industry sponsored project, 'Transition to responsibly sourced growing media use within UK Horticulture' (SP1215/CP138), is a collaborative effort involving growers, industry consultants, growing media producers and academics