Computer Science - Computational Molecular Biology
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Computer Science: Computational Molecular Biology
David Husband, via DHRF, believes that they are pioneering a new branch of Computer Science which DH/DHRF calls Computational Molecular Biology
Or to put it formally: Computer Science: Computational Molecular Biology, which DH/DHRF defines as:
“The application of the known and established principles and practices of Computer Science and in particular of Software Engineering, to the functionality of DNA as a Data Stream which is a series or sequence of symbols and/or Tokens in the chemical/biological/molecular domains…“
Important Note: There is already a well-established branch of Biology known as “Computational Molecular Biology” and/or “Computational Biology”
The Use of Symbols
Numeral Systems use Symbols
“A numeral system (or system of numeration) is a writing system for expressing numbers; that is, a mathematical notation for representing numbers of a given set, using digits or other symbols in a consistent manner”
Source: Wikipedia (my emphasis)
Important Note: DH/DHRF at the present time has no evidence to suggest that any of the DNA Symbols represent numbers…
Binary Symbols
The Binary Symbols “0” (zero) and “1” (one) are used to represent Binary Numbers
Binary Numbers
“A binary number is a number expressed in the base-2 numeral system or binary numeral system, a method of mathematical expression which uses only two symbols”
Source: Wikipedia (my emphasis)
Binary as Hexadecimal
“In mathematics and computing, the hexadecimal (also base 16 or simply hex) numeral system is a positional numeral system that represents numbers using a radix (base) of 16. Unlike the decimal system representing numbers using 10 symbols, hexadecimal uses 16 distinct symbols, most often the symbols “0”–”9” to represent values 0 to 9, and “A”–”F” (or alternatively “a”–”f”) to represent values from 10 to 15”
Source: Wikipedia (my emphasis)
“Software developers and system designers widely use hexadecimal numbers because they provide a human-friendly representation of binary-coded values. Each hexadecimal digit represents four bits (binary digits), also known as a nibble (or nybble). For example, an 8-bit byte can have values ranging from 00000000 to 11111111 in binary form, which can be conveniently represented as 00 to FF in hexadecimal” Source: Wikipedia
Quaternary Numbers
There is already a numeral system called Quaternary that uses the four numerical symbols 0,1,2 & 3
“A quaternary numeral system is base-4. It uses the digits 0, 1, 2 and 3 to represent any real number”
Source: Wikipedia
There are other numeral systems (listed)
“There are many different numeral systems, that is, writing systems for expressing numbers…“ Wikipedia
DNA Symbols
However, and within the context of the “Important Note” above, we have already established that DNA uses 4 symbols to code with: A, C, G & T, so DH/DHRF has devised and proposes a DNA symbol system that it calls DNA-Quad
RNA Symbols
Based upon what is said above, DH/DHRF has also devised and proposes an RNA symbol system that it calls RNA-Quad
To Avoid any Misunderstandings…
… given that there seem to be a number of different “knowledge domains” being used and it seems they are very similar and have some overlap…
WE REPEAT - We believe DHRF is pioneering a new branch of Computer Science, we call “Computational Molecular Biology”
“Biology” Defined
“Biology Is the Science of Life… In its broadest sense, biology is the study of living things”
Understanding Biology 2nd Ed. Mason et al McGraw-Hill Education, 2018 ISBN 978-1-259-59241-6
“Molecular Biology” Defined
“… molecular biology is the study of all types of biological systems at the molecular level”
“The term molecular biology was first coined in 1938 by Warren Weaver at the Rockefeller Institute (now Rockefeller University) [Stanford University 2005]” (Robert B. Northrop 2008)
“Computational Molecular Biology” Defined
“Computational molecular biology brings together computational, statistical, experimental, and technological methods in order to further scientific discovery and develop new analytical tools for molecular biology…“
MIT Press
“Computational Biology” Defined
“Computational biology is the science that answers the question ‘How can we learn and use models of biological systems constructed from experimental measurements?’“ Carnegie Mellon University
“… computational biology is the application of computer science, statistics, and mathematics to problems in biology. Computational biology spans a wide range of fields within biology, including genomics/genetics, biophysics, cell biology, biochemistry, and evolution” Cornell University
“gene expression and regulation • DNA, RNA, and protein sequence, structure, and interactions • molecular evolution • protein design • network and systems biology • cell and tissue form and function • disease gene mapping • machine learning • quantitative and analytical modeling” MIT Biology
“Biochemistry” Defined
From: “Studies of Life at the Molecular Level:”
“… it uses the principles and language of one science, chemistry, to explain the other science, biology at the molecular level…“ (Tsai 2002)
“Computational Biochemistry” Defined
“The application of computer technology to Biochemistry…“ (Tsai 2002)
“Bioinformatics” Defined
“… we can define bioinformatics as the computational branch of molecular biology” (Jean-Michel Claverie 2006)
There is some superficial 2 overlap with DH/DHRF’s work and the field of Bioinformatics but not a surprise as Bioinformatics is an “interdisciplinary field of science”…
References:
Robert B. Northrop, A. N. C., 2008. Introduction to Molecular Biology, Genomics and Proteomics for Biomedical Engineers. Taylor & Francis Ltd.
Tsai, C. S., 2002. An Introduction to Computational Biochemistry. John Wiley & Sons, Inc.
Jean-Michel Claverie, C. N., 2006. Bioinformatics For Dummies. Wiley John + Sons.
In view of DHRF’s commitment to support learning, there is a much higher “learning content” in the Research Work Streams & elsewhere than would otherwise be the case… Please be aware of that ↩
“not complete and involving only the most obvious things” & “only on the surface of something” Cambridge Dictionary ↩