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The phenogenetic logic of life

Key Points

  • There are parallels between Darwinian evolution — a history of individuals — and development — a history of cells within individuals.

  • Darwin's theory explained how traits occur but not which traits will occur or their phenogenetics; that is, how genes produce biological traits.

  • A key to these principles is their logic: they are relational principles that depend on the interaction of components, rather than the specific physical attributes of the components themselves.

  • Phenogenetic logic comprises a small number of basic and simple characteristics of genomes, which can help to account for the diversity of biological traits through a few basic developmental processes.

  • Fundamental to phenogenetics are duplication, modularity, the hierarchical organization and partial sequestration of components, inductive patterning — including dynamic repetitive patterning — the use of diverse types of arbitrary codes, and various kinds of budding and branching phenomena.

  • These principles are fundamental to the nature of life, and have operational value for understanding life and for experimental as well as evolutionary biology.

  • This review is an attempt to identify the elements of phenogenetic logic and to synthesize their role in the generating biological traits.

  • Together, the symmetries of evolutionary processes and phenogenetic logic provide an elegant, simple and comprehensive view of the organization of life.

Abstract

For nearly a century we have understood that life works through genes, and so have had an elegant theory for general evolution. But this did not explain the kinds of traits that characterize organisms, nor how genes produce them. Advances in recent decades have opened the way for an understanding of the phenogenetic logic or relational principles of life, by which a few basic characteristics of genomes produce biological phenotypes through some basic developmental processes. This logic provides a general explanation of the nature and source of organismal design, and a powerful programme for research.

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Figure 1: A phenogenetic metaphor.
Figure 2: Basic principles of phenogenetic logic.
Figure 3: Ubiquity of branching structures in living organisms.
Figure 4: Dynamic patterning: complexity made simply.

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Acknowledgements

This paper is an attempt to synthesize an expansive literature, rather than a literature review or report of new results. My citations have concentrated on reviews or overviews where detailed primary references can be found. Details on the covered topics can also easily be found by searching the internet. I thank Anne Buchanan and Sam Sholtis, and the reviewers for help in the development of these ideas and this manuscript.

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FURTHER INFORMATION

Chladni figures for violin plates

Gene Ontology Consortium

Kenneth Weiss' laboratory

Glossary

SERIAL ANALYSIS OF GENE EXPRESSION

A method for quantitative and simultaneous analysis of a large number of transcripts; short sequence tags from the mRNAs that are produced in a cell are isolated, concentrated and cloned; their sequencing reveals a gene-expression pattern that is characteristic of the tissue or cell type from which the tags were isolated.

DIFFERENTIAL DISPLAY

A technique for detecting those genes that are expressed only under specific conditions; it involves isolation and comparison of mRNA from two or more populations of cells.

GEL-SHIFT ASSAY

An electrophoretic gel-based assay in which proteins that bind to a DNA fragment are detected by virtue of the reduced migration of the DNA. The assay is often used to detect transcription-factor binding.

YEAST ONE-HYBRID ASSAY

An assay that identifies DNA-binding proteins from cDNA libraries or known gene sequences.

BIOFILMS

Microbial biofilms are populations of microorganisms that are concentrated at an interface (usually solid–liquid) and are typically surrounded by an extracellular polymeric substance (EPS) matrix. Aggregates of cells that are not attached to a surface are sometimes termed 'flocs' and have many of the same characteristics as biofilms.

R-GENES

Genes that are used by plants for immunological response to pathogens.

GAP JUNCTION

A junction between two adjacent cells that consists of pores that allow the passage of molecules (up to 1 kD).

MERISTEM

In plants, this is a zone (for example, the apex of the shoot) that contains undifferentiated cells that continue to divide, providing cells for further growth and differentiation.

TRACHEOLES

Fine terminal branches of respiratory tubes.

OMMATIDIA

The elements of the compound eye of insects (in Drosophila melanogaster, the eye is formed from 800 ommatidia), each of which is an independent visual unit that contains eight photoreceptor cells, surrounded by four cone cells that secrete the lens, and seven pigment cells.

PROGRESS ZONE

The progress-zone model proposes that positional information in a growing system can be specified by the time that the cells spend in a zone where growth and differential signalling occur; in a vertebrate limb, the progress zone is specified by the apical ectodermal ridge.

LIPOPROTEINS

Complexes of cholesterol, triglycerides and proteins that transport lipids in the aqueous blood stream environment.

ADIPOCYTES

Fat cells that are found in the adipose tissue.

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Weiss, K. The phenogenetic logic of life. Nat Rev Genet 6, 36–45 (2005). https://doi.org/10.1038/nrg1502

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