The twentieth century unveiled the world of molecular biology, including DNA, the genetic code, proteins, and the molecular basis for modern genetics. Such findings, according to Neo Darwinists, nicely supported evolution. Evolutionary change was fueled by variation arising from genetic mutations. How the genes, and their supporting cast, arose in the first place was a more difficult question. But given their existence the evolutionary narrative was held with great confidence. This straightforward narrative is now understood, however, to be too simplistic. For instance, we now understand that biological variation often arises not from changes in the genes but rather from changes in the expression levels of the genes. Even those celebrated beaks of Darwin's finches appear to be changing via variation in gene expression levels. And more significant variation, such as body plan differences in related insects, also correlate with varying gene expression levels. These new findings do not bode well for traditional evolutionary theory.
From yeast to humans, studies reveal that biological variation can correlate with gene expression levels. Interestingly, as one recent paper explains, these varying levels of gene expression repeatedly show up in some genes but not others. The mechanisms that control the gene expression levels, though varied, focus on these genes.
For instance, recent studies have found that the similar genes in similar species may have substantial differences in expression levels, while other types of genes share conserved expression levels.
In fact, varying expression levels correlate with changes even within a species. New research published this week reveals that gene expression levels can vary significantly between people who otherwise, of course, share extremely similar genomes. As one researcher explained:
the bulk of the differences among individuals are not found in the genes themselves, but in regions we know relatively little about. Now we see that these differences profoundly impact protein binding and gene expression.
In fact, not only do gene expression levels vary between related species and individuals within the same species, they also vary within the same individual, for instance in response to different environmental changes. As one evolutionist explains, when the expression of a gene is strongly regulated between different conditions, it also evolves rapidly between related strains or species. It seems the line between physiology and evolution is blurred:
Thus, it is possible that genes differ in their capacity for expression flexibility, which is manifested at various timescales: during evolution in response to mutations; during physiological responses to environmental changes; and within a population of cells as a result of stochastic fluctuations.
He concludes:
As noted above, expression divergence (the extent to which expression of a gene evolves) correlates with expression responsiveness (the extent to which expression of a gene is changed in response to the environment). We believe that the promoter elements discussed above underlie expression flexibility of these genes on short timescales (responsiveness and noise), which are instrumental in the immediate response of a cell to the environment, as well as on longer timescales (expression divergence), which may allow evolutionary adaptation to novel conditions. In other words, the correlation between responsiveness and expression divergence may be due to their dependence on the same promoter properties.
But the mechanisms that influence the gene expression levels are not simple. They involve proteins and DNA sequences. With the traditional theory of evolution we must believe that mutations created such mechanisms, one step at a time while they had little or no ability to influence expression levels. We therefore must contrive imaginary functions that would conveniently lead to their powerful expression level control capabilities.
Furthermore these expression level mechanisms needed to be applied only to certain genes. Not only are the mechanisms complex, but they must arise in the right place.
But the problems do not stop there. For such mechanisms, even when fully operational, would have limited usefulness. They must await environmental challenges to reveal their true worth. When such challenges arise the expression levels of those certain genes must change in the right way. The mechanism, if it works correctly, becomes invaluable. But until then it waits.
So now evolutionists speak of the evolvability of gene expression. The right genes, they say, have an inherent capacity to evolve its expression. In other words, evolution created the mechanisms which caused more evolution to occur—evolution creates evolution.
