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:
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 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 Language
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
Tetrad formation/cleavage, one Shape Language
Plasmid Partitioning Foci, one Lindenmeyer system
Viroid movement of infection, one shape grammar
Prion Propagation, one Shape Language
3D Pentaplex, one Shape Language
3D Quadruplex, one Shape Language
i-motif (intercalated) DNA, one Shape Language
DNA/RNA Hybrid Triplexes, 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
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.
Languages and Genetics (an explicit discussion of semantics)
The linguistic morphology found in nucleotide sequences (an explicit discussion of semantics)
Linguistic study of aspects of geology (but no explicit discussion of semantics)
Syrian Golden Hamster Food-hoarding, one Chomsky Finite-State Language (but no explicit discussion of semantics)
Bengalese finches, two Chomsky Finite-State automata (with an explicit discussion of semantics)
Pseudoknot Chaining, one modified Context-Free "rearranging" Language (but no explicit discussion of semantics)
Stochastic TAG/CYK, one Context-Sensitive Stochastic Language (but no explicit discussion of semantics)