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Explore Evolution is part of a longstanding effort by creationists, many of them authors of Explore Evolution, to mischaracterize and obscure scientific critiques of a gene-centric view of biology. In 1994, an argument was put forth by Jonathan Wells, a Senior Fellow at the Discovery Institute whose discredited arguments are repeated throughout Explore Evolution, in a publication of the Unification Church, often called "Moonies", that genes do not determine the "floor plan" - morphological development - of organisms.

So DNA does not program the development of the embryo… In a developing organism, the DNA contains templates for producing proteins-the building materials.To a very limited extent, it also contains information about the order in which those proteins should be produced-assembly instructions. But it does not contain the basic floor plan. The floor plan and many of the assembly instructions reside elsewhere (nobody yet knows where).
Jonathan Wells (1994) Why I Went for a Second Ph.D

The next year, the Nobel Prizes in Physiology or Medicine was awarded to scientists studying the genetic regulation of fruit fly development and another was awarded in 2002 to scientists studying the genetic regulation of nematode development. Nonetheless, Explore Evolution repeats Wells-like denials of the scientific consensus that genes carry instructions for embryonic development.

From Explore Evolution:

Also, on the cutting edge of research is the noteworthy claim that genes may not do as much as scientists previously thought.
Explore Evolution, p. 109
But some scientists contend that while the genes in DNA carry assembly instructions for building proteins out of amino acids, they do not carry the assembly instructions for building organs out of proteins or for building whole creatures out of organs or other body parts.
Explore Evolution, p. 110
many biologists (embryologists in particular) are beginning to think that genes do not (by themselves) carry the instructions for building a whole organism or animal.
Explore Evolution, p. 110
Scientist are not entirely sure where these higher-level assembly instructions are stored. However, these instructions are clearly necessary, and many scientists doubt that they are stored in DNA alone.
Explore Evolution, p. 111

Explore Evolution ignores the fact that DNA does significantly more than code for proteins, it has regulatory information (such as cis-regulatory elements) that controls when and where genes are expressed. More seriously, Explore Evolution ignores the fundamental unit of life, the cell, when it claims that genes "do not carry the assembly instructions for building organs out of proteins". In order to raise questions about the plausibility of morphological evolution, Explore Evolution must shield students from the uncomfortable fact that critics of a gene-centric view of biology propose viable alternative scientific explanations that are fully compatible with evolutionary biology.

References in the quotations above cite the Origination of Organismal Form, edited by Gerd Muller and Stuart Newman, to assert that DNA: "does not carry out the assembly instructions for … building whole creatures." Muller and Stuart's essay is an introduction, giving an overview of the various issues that the research published in the rest of the book will address. Muller and Newman write:

Organismal evolution is nowadays almost exclusively discussed in terms of genetics. But are genes determinants of form? … The chapters of part III [Relationships between Genes and Form] provide viewpoints on several of the problems that will have to be taken into account in future modeling approaches.
G. Muller and S. A. Newman (2003) The Origination of Organismal Form pp. 5-6

Explore Evolution asserts that the "mutation argument" has serious problems since DNA (alone) does not carry assembly instructions and "scientist are not entirely sure where the higher level assembly instructions are stored," therefore calling into question whether morphological evolution is possible. However, these claims are not supported by Origination of Organismal Form. As the book's back cover explains, the goal is not to remove gene sequences and gene expression from biological consideration, but to introduce another set of factors into biology's toolkit.

By placing epigenetic processes, rather than gene sequence and gene expression changes, at the center of morphological origination, this book points the way to a more comprehensive theory of evolution.
The Origination of Organismal Form, Back Cover

Each paper in Part III of Origination of Organismal Form discusses other factors besides genes which are important for generating form. Mina Bissell and colleagues argue that the 3-D organization of a tissue in the extracellular matrix is important for cellular differentiation. Roy Britten argues that molecular interactions as opposed to "global control mechanisms" are responsible for embryonic development. Scott Gilbert explains that genomes have been selected to respond to environmental cues during embryonic development. Finally, Ellen Larson summarizes how changes in cellular behaviors in development facilitates morphological evolution. Larson explains:

1. Rates of morphological evolution depend upon changes in the coordination of developmental processes

2. The hierarchical organization of biological systems facilitates relatively rapid evolution and change because developmental systems are modular.

3. At the molecular level, surprisingly few genetic changes may lead to change in coupling between genes and their regulatory signal.

4. Genes affect morphogenesis by affecting cell behaviors, including cell behaviors that modify morphogenetic fields.

5. At the tissue level, cell-autonomous genetic behavior in two-dimensional sheets may permit large and evolutionarily rapid changes in morphogenesis, compared to changes in interacting tissues that probably require complementary changes in both interacting tissues to achieve change.

6. Because there are alternative routes to achieve a morphology using different cellular behaviors, the likelihood of having sufficient genetic variation for selection is increased.

E. Larson, (2003), "Genes, Cells and Form" in The Origination of Organismal Form p. 126

Far from denying the importance of DNA, this is an acknowledgment of the importance of genes, and an exploration of the ways that genes vary. Explore Evolution is wrong to offer this book as evidence that biologists do not thing DNA is crucial in establishing morphology. The same passages in Explore Evolution mischaracterize teh views of Alessandro Minelli. Minelli also acknowledges that embryonic development is influenced by genes, but argues that there is too much an emphasis placed upon morphological changes in embryos as a means to generate adults. As with Stuart Newman, Minelli does not think that his arguments are anti-evolutionary.

Development, even in its simplest forms … is the complex networking of cellular behaviors and mechanisms influenced by the expression of all these genes …All of these behaviors, mechanisms, and genes are not there to ensure the deployment of wonderfully complex shapes of living beings. Much more modestly, they are simply there and consequently affect other behaviors, mechanisms or genes and set in place those forms of self-regulation that are the key to avoid developmental bankruptcy.
Alessandro Minelli (2003) The Development of Animal Form pp. 4-5
The non-adultocentric view of development I am advocating here is perfectly compatible with most views of development and evolutionary biology – for example, with the concept of the developmental module, a local cell population with its own developmental dynamics, but also interacting with other modules in a kind of metapopulation of cells (the biological individual or colony).
Alessandro Minelli (2003) The Development of Animal Form, p. 6

In claiming compatibility with "most views of development and evolutionary biology," Minelli is surely not supporting the anti-evolution arguments of Explore Evolution, nor its particular claim that Minelli claims DNA is not crucial to "building whole creatures out of organs and other body parts."

Explore Evolution also wrongly claims support from a paper by Brian Hall, a developmental biologist with a long-standing interest in evolution who thinks that cellular behaviors play an important role in morphogenesis. Is "DNA demoted" according to Brian Hall?

By emphasizing the role of cells, I want to be very explicit and not misunderstood. I am not downgrading the role of genes, either in development or in evolution.
B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219

The diagram below, based upon Figure 8 of Hall (2003), shows how Brian Hall views the relationship between genes (genotype) and organismal structure (phenotype). Notably, these "higher-level assembly instructions" consist of interactions of genes as networks and cascades, and the interactions of cells in aggregation and communication which are fully able to "translate the effects of mutations into phenotypic change."

Genotype to Phenotype: Figure 8 from B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219Genotype to Phenotype: Figure 8 from B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units." Biology and Philosophy, 18, p. 219
This modular and hierarchical cellular organization allows like cells to receive the intra- and extra-organismal environmental and epigenetic signals that allow organisms to develop, adapt to their environment, modify their development and translate the effects of mutations into phenotypic change on both developmental (including regeneration) and evolutionary (including asexual reproduction) time scales.
B. Hall (2003) "Unlocking the Black Box between Genotype and Phenotype: Cell Condensations as Morphogenetic (modular) Units."Biology and Philosophy, 18, p. 219

Another reference in the quotations above cites a 1990 essay by Fred Nijhout as an example of a scientist who now doubts that "higher-level assembly instructions" are stored in DNA alone. Undoubtedly, Nijhout expresses clear reservations about a gene-centric approach to biology.

The reason that pattern and form exhibit heritability is that they develop under a specific and restricted set of physical circumstances. When these circumstances are altered whether by changes in gene products or by changes in the environment a different pattern, equally heritable, develops. Changes in the heritable phenotype that are cause by changes in the environment are referred to as norm of reaction and have occasionally have been studied from the evolutionary perspective. Since gene do not 'code' for form, but form emerges out of an interaction of gene product and environment, it is clear that the norm of reaction deserves more wide spread study.
F. Nijhout (1990) "Metaphors and the Role of Genes in Development," Bioessays 12, p. 445

Despite this, Nijhout's research can hardly be said to reject DNA's role in morphology. In a recent Science paper, Suzuki and Nijhout show how a mutation in a gene affecting the hormonal regulatory pathway increases the environmental sensitivity to moth larval coloration and the origination of an new adaptive phenotype.

Polyphenisms are adaptations in which a genome is associated with discrete alternative phenotypes in different environments. Little is known about the mechanism by which polyphenisms originate. We show that a mutation in the juvenile hormone-regulatory pathway in Manduca sexta enables heat stress to reveal a hidden reaction norm of larval coloration. Selection for increased color change in response to heat stress resulted in the evolution of a larval color polyphenism and a corresponding change in hormonal titers through genetic accommodation. Evidently, mechanisms that regulate developmental hormones can mask genetic variation and act as evolutionary capacitors, facilitating the origin of novel adaptive phenotypes.
Y. Suzuki and F. Nijhout (2006) "Evolution of a Polyphenism by Genetic Accommodation," Science, 311, p. 650

Science journalist Elizabeth Pennisi explains how the study of reaction norms supports role of mutations in evolution, contrary to the claim Explore Evolution advances.

The study demonstrates how species can mask effects of genetic mutations until an environmental trigger reveals them, an adaptive mechanism that may help organisms survive changing conditions. The work "is a tour de force of experimental evolutionary biology," says Mary Jane West-Eberhard, an evolutionary biologist at the University of Costa Rica. "It [begins] to answer a question of fundamental importance: How does a novel, environmentally sensitive trait originate?"
E. Pennisi (2006) "Hidden Genetic Variation Yields Caterpillar of a Different Color,"Science, 311, p. 591

Explore Evolution also cites a book by Lenny Moss, entitled What Genes Can't Do, published in the MIT Press's Basic Bioethics Series. Moss promotes the ideas of two embryologists, John Gerhart and Marc Kirschner, to explain the formation of multicellular organisms. Gerhart and Kirchner's explanation emphasizes the ways that modular processes can be linked together to generate novelty in evolution.

The evolution of complex, internally differentiated, and yet globally coordinated life forms, including Homo sapiens, was not achieved by the elaboration of a master code or script, but by the fragmentation of functional resources of the cell into many modular units whose linkages to one another have become contingent (Gerhart & Kirschner, 1997). The more contingently uncoupled the molecular and multimolecular constituents of the cell become, the greater becomes the subset of potential specializations that can be achieved.
Lenny Moss (2004) What Genes Can't Do., pp. 188-189

The critique by Gehart and Kirschner provides no support for Explore Evolution's claim that mutations are insufficient to produce morphological change, simply showing that a full understanding of the evolution of morphology will require other levels of explanation beyond stating that a gene was mutated.

Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits.
J. Gerhart and M. Kirschner (2007) "The Theory of Facilitated Variation," PNAS 104, p. 8582
Although recent insights in developmental biology and physiology deepen the understanding of variation, they do not undermine evolutionary theory. Laws of variation begin to emerge, such as regulatory change as the main target of genetic change, the means to minimize the number and complexity of regulatory changes, and the regulatory redeployment of conserved components and processes to give phenotypic variations and selected traits.
J. Gerhart and M. Kirschner (2007) "The Theory of Facilitated Variation," PNAS 104, p. 8588
This is a new and active field of research, and an inquiry-based textbook could take advantage of the field's new results to encourage student exploration. Instead, as elsewhere in Explore Evolution, students are encouraged to treat unanswered questions as unanswerable, as chances to stop investigating. Students are given neither the conceptual background nor the scientific resources to engage with the ideas introduced here, and the book's approach is to encourage intellectual surrender, giving up whenever scientists seem to disagree or scientific questions are unresolved. This is not "inquiry-based," and is not good science.