New References of Interest

A disclaimer: finding scientific articles dealing with the subjects covered in "Emergent Computation: Emphasizing Bioinformatics" requires a great deal of work and time. The major reason for this is that the subjects of Bioinformatics from the point of view of Mathematical Linguistics as well as applications of Mathematical Linguistics in areas such as Biology, Meteorology, Oceanography, Geology, Chemistry, etc. are not yet recognized as a discipline of study. As a consequence, it is not claimed that the scientific articles or books cited here constitute all the relevant articles that may have been published, just those that have come to light. To ease organization and thus help in locating papers, the papers have been organized into three categories:

Recently Published Papers by Category

Much of the information contained at this web site is either entirely new material (such as the use of DNA, RNA or Proteins in Nanotechnology), or is new material that extends what has been discussed in "Emergent Computation: Emphasizing Bioinformatics" or else is background information that helps in understanding subject matter. Specific examples of thirty-six languages (or aspects of Automata Theory) that make use of some of the new reference material are pointed out here.

• Syrian Golden Hamster Food-hoarding, One Chomsky Finite-State Language
• Bengalese finches, Two Finite-State automata
• Equal Matrix Grammars may be used in Bioinformatics, One Equal Matrix Grammar
• Nanotechnology DNA Self-Assembly, Three Shape Languages
• Nanotechnology DDX DNA Self-Assembly, One 3-D Shape Language
• Nanotechnology DNA Quadruplex-Self-Assembly, One Shape Languages
• Nanotechnology RNA Self-Assembly, One Chomsky Type 2 Language
• Nanotechnology Tiled DNA, One Shape Language
• Nanotechnology DNA Holliday structures, One Shape Language
• Rolling Circle Replication, One Chomsky Language
• kDNA unimolecular minicircle DNA with Quadruplexes, One Shape Language
• PNA/DNA hybrids, One Shape Language
• Artificial Zinc-finger triplex endonucleases, One Shape Language
• RuvC Holliday Structure Cleavage, One Shape Language
• DNA Holliday Structures, One Matrix or Array Grammar
• Tetrad formation/cleavage, One Shape Language
• Plasmid Partitioning Foci, One Lindenmeyer systyem
• Viroid movement of infection, One shape grammar
• Prion Propagation, One Shape Language
• 3D Pentaplex, One Shape Language
• 3D Quadruplex, One Shape Language
• 3D Quadruplex, One Shape Language
• i-motif (intercalated) DNA, One Shape Language
• DNA/RNA Hybrid Triplexes, One Shape Language
• DNA Triple Helix, One Matrix or Array Grammar
• Synthetic urocanamide DNA Triple Helix, One Shape Language
• New Triple-Helix Cleavage Based Upon Plasmids, One Shape Language
• Pseudoknot Chaining, One modified Context-Free "rearranging" Language
• Stochastic TAG/CYK, One Context-Sensitive Stochastic Language
• Alluvial River Channel Morphology, One Shape Language
• Geology of Lithology, One (partial) Chomsky Language
• Meteorology of Vorteces, One Shape Language
• Evolution of Languages, A class of Chomsky languages

That the study of linguistics when not focused upon human languages requires a different semantics has escaped most researchers in linguistics. N. Chomsky limits semantics only to human languages. Thus it should be no surprise that N. Chomsky rejects applying linguistics except to human beings. Almost all the examples of languages discussed in "Emergent Computation: Emphasizing Bioinformatics" do not consciously and explicitly explore questions of semantics (although the author has explicitly discussed this viewpoint). However, in this web site, a few authors should be noted when considering questions of semantics.

1. Languages and Genetics (an explicit discussion of semantics)
2. The linguistic morphology found in nucleotide sequences (an explicit discussion of semantics)
3. Linguistic study of aspects of geology (but no explicit discussion of semantics)
4. Syrian Golden Hamster Food-hoarding, One Chomsky Finite-State Language (but no explicit discussion of semantics)
5. Bengalese finches, two Chomsky Finite-State automata (with an explicit discussion of semantics)
6. Pseudoknot Chaining, One modified Context-Free "rearranging" Language (but no explicit discussion of semantics)
7. Stochastic TAG/CYK, One Context-Sensitive Stochastic Language (but no explicit discussion of semantics)

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