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It is believed that the so-called master control genes that produce proteins that act
as TFs to control expression of other genes and induce development of widely differ-
ent structures. This also does not support the modern synthesis paradigm. Even if this
were the case, it is not easy to understand how these highly conserved and least evolv-
ing genes could promote evolution. Moreover, sometimes the evolutionary progress is
characterized by the loss of Hox genes. For example, the sea anemone, Nematostella
vectensis , an anthozoan of the phylum Cnidaria , has more Hox genes than Drosophila ,
which is a far more complex organism with five times as many cell types ( Ryan et al.,
2006 ) or the worm Caenorhabditis elegans , which has lost half of its ancestral Hox
genes ( Aboobaker and Blaxter, 2010 ). If it is argued that evolution depends on changes
in expression patterns of genes rather than gene evolution, increasing evidence shows
that expression of Hox genes and cell differentiation are epigenetic processes.
Evo-devo studies created new difficulties for the neoDarwinian explanations of
evolution. These studies led to the new biological concept that the nature and devel-
opment of species depends not on the number or kinds of genes in its genome but
instead primarily on the expression patterns of the control genes.
These failures are the reason why more and more biologists are becoming
inclined to favor alternative hypotheses on the driving forces and mechanisms of
organic evolution. These failures have stimulated the development of numerous
alternative explanations of organic evolution. By the same token, the abundance of
hypotheses on evolution is an eloquent indication of the serious challenges the the-
ory of evolution is confronting.
Other Hypotheses on Evolution
Updating the Explanations of the neoDarwinian Paradigm
Numerous attempts are made to reconcile the modern synthesis with the new devel-
opments in biology, especially in evo-devo, primarily by incorporating into it the
idea of a genetic control of gene expression.
The “Regulatory” Hypothesis of Morphological Evolution
As pointed out by Sean B. Carroll, this is a special hypothesis on the evolution of
animal morphology rather than a general hypothesis on the evolution of the liv-
ing world ( Carroll, 2008 ). In a nutshell, the hypothesis posits that the evolution
of animal morphology does not depend on gene mutations and evolution of genes
(including toolkit genes and Hox genes) and proteins, which generally are function-
ally conserved. Evolution of the morphological diversity in the animal kingdom is
determined by changes in the spatiotemporal expression of the same generally con-
served gene proteins. Such changes may result from accidental changes in the base
sequences of the cis-regulatory elements (CREs) of genes. In turn, changes in the
CREs may lead to changes in the elements and wiring of gene regulatory networks
(GRNs), which are the primary sources of morphological novelties.
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