DNA supercoiling as a pattern for understanding psycho-social twistedness

Engaging with Questions of Higher Order: cognitive vigilance required for higher degrees of twistedness (Part #5)

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The insights above regarding "twistedness" reflect an intuitive "global" comprehension of complexity which calls for deeper and more detailed understanding how twistedness works and why it may be vitally important in some psycho-social processes -- as well as being highly problematic in others. Part of the difficulty in approaching this matter is that "twistedness" is in most cases used unthinkingly as a pejorative term to characterize a pattern which is felt to inhibit right-thinking and clarity. The argument here is that, given its importance at every scale in nature, from the organization of nebula to the organization of the human cell, there is a case for distinguishing various forms of twistedness and understanding their function. This could be especially valuable to reconciling apparently irreconcilable understandings in society.

A review of twistedness in DNA is provided in an annex to this paper (see DNA Supercoiling as a Pattern for Understanding Psycho-social Twistedness, 2004). This is used as a basis for the discussion below. The annex has the following components:

Introduction
Structure of DNA
Forms of DNA
-- Supercoiled (or "knotted")
-- Relaxed
Descriptive properties associated with supercoiling
-- Writhing
-- Twisting
-- Linking number
-- Density
-- Replication
-- Denaturation, melting, breathing and unzipping
-- DNA-knots
Energy associated with different structures
-- Minimum energy (stable)
-- Higher energy (unstable)
References

Understanding of how DNA works has been much enriched by concepts from topology -- as a branch of mathematics that deals with structural properties that are unchanged by deformations such as stretching and bending. This use of mathematics is especially important because there is no experimental way to observe the dynamics of enzymatic action directly, notably with respect to knotting and coiling of DNA (see De Witt Sumners. Lifting the Curtain: Using Topology to Probe the Hidden Action of Enzymes, 1995; Xiaoyan R. Bao, et al. Behavior of Complex Knots in Single DNA Molecules, 2003).

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