"Natural Genetic Engineering" and an "Internal Evolutionary Mechanism" ©2002 John Latter ([email protected])

 Contents:

1) Introduction

2) A Note on the 'Internal Evolutionary Mechanism'

3) Abstract from 'A 21st Century View of Evolution'

4) Salient features of 'Natural Genetic Engineering'

5) Comments

1) Introduction [back to top]

James Shapiro[1] is a molecular biologist at the University of Chicago who has developed the concept of "Natural Genetic Engineering". The following briefly examines salient features of this idea, as described in "A 21st Century View of evolution"[2], in order to ascertain its 'degree of compatability' with the seperate proposal of an Internal Evolutionary Mechanism[3].

2) A Note on the 'Internal Evolutionary Mechanism' [back to top]

The mechanism is based on the initial premise, that if organisms are naturally integrated, then there is a center to that integration. Specifically a localized area of equilibrium at the 'apex' of the homeostatic hierarchy. A fuller description can be found at the appended reference.

3) Abstract from 'A 21st Century View of Evolution' [back to top]

"Physicists question whether there are "universals" in biology. One reason is that the prevailing theory of biological evolution postulates a random walk to each new adaptation. In the last 50 years, molecular genetics has revealed features of DNA sequence organization, protein structure and cellular processes of genetic change that suggest evolution by natural genetic engineering. Genomes are hierarchically organized as systems assembled from DNA modules, which themselves generally constitute systems at lower levels. Each genome is formatted and integrated by sequence elements that do not code for proteins. These formatting elements constitute codons in multiple genetic codes for distinct functions such as transcription, replication, DNA compaction and genome distribution to daughter cells. Consequently, the genome has a computational system architecture. Proteins are systems composed of functionally distinct domains connected in polypeptide chains. Whole-genome sequencing indicates that rearrangement of genetic modules plus duplication and reuse of existing genomic systems are fundamental events in evolution. Studies of genetic change show that cells possess mobile genetic elements and other natural genetic engineering activities to carry out the necessary DNA reorganizations. Natural genetic engineering functions are sensitive to biological inputs, and their non-random operations help explain how novel system architectures can arise in evolution."

4) Salient features of 'Natural Genetic Engineering' [back to top]

a)  "Genomes are hierarchically organized" being "built (Lego-like) of hierarchically organized modular systems"

b) New functions can arise via the "cut-and-splice rearrangement of genetic modules" effected by "mobile genetic elements and other natural genetic engineering activities".

c) Using the analogy of a computer genomes are described as "information storage organelles (cf. disk drive)" that are integrated into "cellular information processing".

d) Shapiro stresses that "genomes only function through interaction with other dynamic information systems in the cell. By itself, DNA is inert."

e) Genomic re-organization can occur "locally, regionally or globally" and the 'non-randomness' of such events is "evident at three levels: mechanism, timing, and sites of action".

5) Comments [back to top]

When the possibility of an internal evolutionary mechanism was first considered a search was made for phenomena showing any signs of the anticipated 'homeostatic signature'. "Stationary-Phase Mutations", as an example, gave every appearance of meeting the requirements but lack of expertise in this area made the subsequent description necessarily tentative. James Shapiro, on the other hand, is both knowledgable and experienced in this field thus enabling him to provide an appropriate degree of detail with which to support the proposal of "Natural Genetic Engineering". The question is "Are the two proposals compatable?".

The 'bottom line' answer is that the concept of "Natural Genetic Engineering" is entirely consistent with the proposed "Internal Evolutionary Mechanism". Certainly there is a difference in perspective (partially reflecting the respective origin of each proposal) which is illustrated by Shapiro's statement:

"natural genetic engineering occurs episodically and non-randomly in response to stress events"

From the perspective of the internal mechanism it is the effect of 'stress' upon internal equilibrium that is important.

The focus of this non-exhaustive 'first response', however, is on that area where the two proposals do not quite meet:

While recognizing hierarchical organization "Natural Genetic Engineering' doesn't appear to consider, that by definition, every hierarchy has an 'apex' - be it point, plateau, or any irregularity inbetween. It is at this apex (or 'center', from a three dimensional perspective) that the proposed internal mechanism places a 'localized area of equilibrium' thereby providing, from a conventional viewpoint, the necessary 'co-ordinating function' that "Natural Genetic Engineering" currently lacks.

Shapiro states, for example, that:

"Molecular genetics has amply confirmed McClintock’s discovery that living organisms actively reorganize their genomes. It has also supported her view that the genome can "sense danger" and respond accordingly."

The problem, of course, lies in how something that only exists at the molecular level can ever "respond accordingly" to the level at which the organism itself exists. The concept of the Internal Mechanism places the 'localized area of equilibrium' in both organism and genome and this 'connectivity' reflects the continuity of being actually found in nature.

[1] James Shapiro's Homepage at the University of Chicago [return to text]
      http://shapiro.bsd.uchicago.edu/

[2] A 21st Century View of evolution [return to text]
      http://shapiro.bsd.uchicago.edu/21st_Cent_View_Evol.html

[3] Model of an Internal Evolutionary Mechanism [return to text]
      http://members.aol.com/jorolat/TEM.html

"Words frozen in time should be differentiated from those carved in stone" - John Latter

["Natural Genetic Engineering" and an "Internal Evolutionary Mechanism" will also be posted in the "Where Darwin meets Lamarck?" discussion forum]

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