DNA Computing by Self-Assembly

Information and algorithms appear to be central to biological organization and processes, from the storage and reproduction of genetic information to the control of developmental processes to the sophisticated computations performed by the nervous system. Much as human technology uses electronic microprocessors to control electromechanical devices, biological organisms use biochemical circuits to control molecular and chemical events. The engineering and programming of biochemical circuits, in vivo and in vitro, would transform industries that use chemical and nanostructured materials. Although the construction of biochemical circuits has been explored theoretically since the birth of molecular biology, our practical experience with the capabilities and possible programming of biochemical algorithms is still very young

How crystals that sense and respond to their environments could evolve

An enduring mystery in biology is how a physical entity simple enough to have arisen spontaneously could have evolved into the complex life seen on Earth today. Cairns-Smith has proposed that life might have originated in clays which stored genomes consisting of an arrangement of crystal monomers that was replicated during growth. While a clay genome is simple enough to have conceivably arisen spontaneously, it is not obvious how it might have produced more complex forms as a result of evolution. Here, we examine this possibility in the tile assembly model, a generalized model of crystal growth that has been used to study the self-assembly of DNA tiles. We describe hypothetical crystals for which evolution of complex crystal sequences is driven by the scarceness of resources required for growth. We show how, under certain circumstances, crystal growth that performs computation can predict which resources are abundant. In such cases, crystals executing programs that make these predictions most accurately will grow fastest. Since crystals can perform universal computation, the complexity of computation that can be used to optimize growth is unbounded. To the extent that lessons derived from the tile assembly model might be applicable to mineral crystals, our results suggest that resource scarcity could conceivably have provided the evolutionary pressures necessary to produce complex clay genomes that sense and respond to changes in their environment

Why do spatial abilities predict mathematical performance?

Spatial ability predicts performance in mathematics and eventual expertise in science, technology and engineering. Spatial skills have also been shown to rely on neuronal networks partially shared with mathematics. Understanding the nature of this association can inform educational practices and intervention for mathematical underperformance. Using data on two aspects of spatial ability and three domains of mathematical ability from 4174 pairs of 12-year-old twins, we examined the relative genetic and environmental contributions to variation in spatial ability and to its relationship with different aspects of mathematics. Environmental effects explained most of the variation in spatial ability (~70%) and in mathematical ability (~60%) at this age, and the effects were the same for boys and girls. Genetic factors explained about 60% of the observed relationship between spatial ability and mathematics, with a substantial portion of the relationship explained by common environmental influences (26% and 14% by shared and non-shared environments respectively). These findings call for further research aimed at identifying specific environmental mediators of the spatial–mathematics relationship

Quantum fluctuations and life

There have been many claims that quantum mechanics plays a key role in the origin and/or operation of biological organisms, beyond merely providing the basis for the shapes and sizes of biological molecules and their chemical affinities. These range from the suggestion by Schrodinger that quantum fluctuations produce mutations, to the conjecture by Hameroff and Penrose that quantum coherence in microtubules is linked to consciousness. I review some of these claims in this paper, and discuss the serious problem of decoherence. I advance some further conjectures about quantum information processing in bio-systems. Some possible experiments are suggested.Comment: 10 pages, no figures, conference pape

Self-Assembly of 4-sided Fractals in the Two-handed Tile Assembly Model

We consider the self-assembly of fractals in one of the most well-studied models of tile based self-assembling systems known as the Two-handed Tile Assembly Model (2HAM). In particular, we focus our attention on a class of fractals called discrete self-similar fractals (a class of fractals that includes the discrete Sierpi\'nski carpet). We present a 2HAM system that finitely self-assembles the discrete Sierpi\'nski carpet with scale factor 1. Moreover, the 2HAM system that we give lends itself to being generalized and we describe how this system can be modified to obtain a 2HAM system that finitely self-assembles one of any fractal from an infinite set of fractals which we call 4-sided fractals. The 2HAM systems we give in this paper are the first examples of systems that finitely self-assemble discrete self-similar fractals at scale factor 1 in a purely growth model of self-assembly. Finally, we show that there exists a 3-sided fractal (which is not a tree fractal) that cannot be finitely self-assembled by any 2HAM system