The Biological Plausibility of the Blob Model

Abstract

A biomolecular computer is a computer constructed using materials and concepts borrowed from the disciplines biochemistry and molecular biology. So far, biomolecular computers have been more akin to specialized Boolean circuits than to a “computer” in the normal understanding of the word, in the sense that each computer is constructed for one specific purpose, thus not being programmable. The Blob Model is an abstract computational model that models a “biologically plausible,” naturally programmable computer. This thesis concerns the actual realizability in biomolecular substrates of the Blob Model. We present the following results: a) a survey of existing work on biomolecular computation; b) a classification of computers into either of the two groups mechanically universal and linguistically universal, establishing a distinction between Turing-universality in the sense that any computable function can be built and Turing-universality in the sense that any computable function can be programmed; c) an evaluation of the realizability of the Blob Model in the context of DNA self-assembly, four different versions of biomolecular Boolean gates, and FokI restriction; d) a theoretical implementation scheme, disregarding the use of actual tested laboratory methods. We find that the Blob Model cannot be realized in any one of the studied biomolecular substrates. This indicates that the Blob Model should be revised in order to maintain its biological plausibility.

@mastersthesis{grathwohl2011a,
  abstract = {A biomolecular computer is a computer constructed using materials and
            concepts borrowed from the disciplines biochemistry and molecular biology.
            So far, biomolecular computers have been more akin to specialized Boolean
            circuits than to a ``computer'' in the normal understanding of the word,
            in the sense that each computer is constructed for one specific purpose,
            thus not being programmable.
            The Blob Model is an abstract computational model that models a
            ``biologically plausible,'' naturally programmable computer. This thesis
            concerns the actual realizability in biomolecular substrates of the Blob
            Model. We present the following results: a) a survey of existing work
            on biomolecular computation; b) a classification of computers into either
            of the two groups mechanically universal and linguistically universal,
            establishing a distinction between Turing-universality in the sense that
            any computable function can be built and Turing-universality in the sense
            that any computable function can be programmed; c) an evaluation of
            the realizability of the Blob Model in the context of DNA self-assembly,
            four different versions of biomolecular Boolean gates, and FokI restriction;
            d) a theoretical implementation scheme, disregarding the use of actual
            tested laboratory methods.
            We find that the Blob Model cannot be realized in any one of the
            studied biomolecular substrates. This indicates that the Blob Model
            should be revised in order to maintain its biological plausibility.},
  author = {Niels Bj{\o}rn Bugge Grathwohl},
  month = {October},
  note = {Master's Thesis},
  school = {University of Copenhagen},
  title = {The Biological Plausibility of the Blob Model},
  year = {2011},
}