Why the 'Gene' Concept Holds Back Evolutionary Thinking
Posted: 11/30/2012 2:12 pm
James A. ShapiroAuthor, 'Evolution: A View from the 21st Century'; Professor of Microbiology, University of Chicago
Wendell Read just sent me notice of a new paper inGenome Biology linking transposable elements, long intergenic non-coding RNAs, and cell type. This paper highlights difficulties in understanding genome evolution using the conventional idea of "genes."
In the early days of genetics, following the rediscovery of Mendel's principles in 1900, there was a furious effort to define the nature of Mendel's regularly segregating "factors" (a properly neutral term). In 1909, the Danish botanist Wilhelm Johannsen coined the term "gene" ("gen" in German) to denote a fundamental unit of heredity.
Over the following decades, genes took on a theoretical life all their own, as described in Evelyn Fox Keller's 2002 book, The Century of the Gene. In a 1948 Scientific Americanarticle, soon-to-be Nobel Laureate George Beadle wrote: "genes are the basic units of all living things."
When Barbara McClintock and Curt Stern demonstrated simultaneously in 1931 that genetic markers of plants (maize) and animals (Drosophila) locate on visible chromosomes, the idea began to crystallize that that the genotype consisted of linear arrays of genes strung along chromosomes like "beads on a string."
This notion of the genome as a collection of discrete gene units prevailed when the neo-Darwinian "Modern Synthesis" emerged in the pre-DNA 1940s. Some prominent theorists even proposed that evolution could be defined simply as a change over time in the frequencies of different gene forms in a population.
The identification of DNA as the key molecule of heredity and Crick's Central Dogma of Molecule Biology initially seemed to confirm Beadle and Tatum's "one gene -- one enzyme" hypothesis. However, molecular genetics quickly introduced difficulties with the theory of atomistic genes aligned like beads on a string.
A major challenge was Britten and Kohne's1968 discovery of massive amounts of repetitive DNA in certain genomes. Today, we know our DNA contains over 30 times as many base-pairs in repeats as it does in protein coding sequences. By the conventional view, if genes are the only important actors, then these surprisingly abundant "intergenic" repeats must constitute "junk DNA" and be "ultimate parasites" in the genome.
As readers of this and other science blogs know well, the junk DNA idea has been challenged by the large-scale ENCODE project, designed to produce the "Encyclopedia Of DNA Elements" independently of theoretical prejudices. In its first few years, ENCODE has documented cell type-specific biochemical activity in over 80 percent of this repetitive DNA and known functions in 20 percent.
The basic issue is that molecular genetics has made it impossible to provide a consistent, or even useful, definition of the term "gene." In March 2009, I attended a workshop at the Santa Fe Institute entitled "Complexity of the Gene Concept." Although we had a lot of smart people around the table, we failed as a group to agree on a clear meaning for the term.
The modern concept of the genome has no basic units. It has literally become "systems all the way down." There are piecemeal coding sequences, expression signals, splicing signals, regulatory signals, epigenetic formatting signals, and many other "DNA elements" (to use the neutral ENCODE terminology) that participate in the multiple functions involved in genome expression, replication, transmission, repair and evolution.
Por que sou ‘pós-darwinista’? Porque já fui evolucionista de carteirinha. Hoje, sou cético da teoria macroevolutiva como verdade científica. Contudo, meu ceticismo ao ‘dogma central’ darwinista não é baseado em relatos da criação de textos sagrados. Foi a séria e conflituosa consideração do debate que ocorre intramuros e nas publicações científicas há muitos anos sobre a insuficiência epistêmica da teoria geral da evolução. Eu fui ateu marxista-leninista. Hoje, não tenho mais fé cega no ateísmo. Não creio mais na interpretação literal dos dogmas de Darwin aceitos ‘a priori’ e defendidos ideologicamente com unhas e dentes pela Nomenklatura científica. A Ciência me deu esta convicção. Aprendi na universidade: quando uma teoria científica não é apoiada pelas evidências, ela deve ser revista ou simplesmente descartada. Sou pós-darwinista me antecipando à iminente e eminente ruptura paradigmática em biologia evolutiva. Chegou a hora de dizer adeus a Darwin. Mestre em História da Ciência – PUC-SP. CV Plataforma Lattes: http://lattes.cnpq.br/6602620537249723