I would like first to welcome Charney's target article. It is an excellent introduction to those genetic mechanisms that are most relevant for behavioral genetics, and it provides a first-class overview of the recent advances in genetics concerning the weight of epigenetic processes. I agree completely with Charney in his view that “the biological worldview of postgenomics is characterized by extreme complexity, variability, multilevel reciprocal interactionism, and stochasticity as an inherent property of biological systems, which all contribute to what might be called the blurring of boundaries, in particular, the boundary between genes and environment” (sect. 1). I also agree that the new epigenetics is changing the way we must understand the relationship between the genotype and the phenotype. I have myself tried to transmit the idea for a long time, with very little success, that this is a fact to be assumed in cognitive neuroscience (Hilferty & Vilarroya Reference Hilferty and Vilarroya2002; Reference Hilferty, Vilarroya, Fank, Dirven, Ziemke and Bernárdez2008; Hilferty et al. Reference Hilferty, Valenzuela and Vilarroya1998).

However, if we take that the aim of the article is to convince the reader that we are in front of a paradigm shift, then I think that Charney misdirects his efforts. A paradigm shift implies a replacement of the theoretical framework and the methodologies of a discipline by new ones, such as heliocentric cosmology did to its precedent geocentric cosmology. All the mechanisms that Charney reviews are extremely relevant developments and imply important improvements in genetics theory and methodology, but they do not replace genetics with a new discipline; rather, they enrich it. These improvements are part of the normal dynamics in the development of a young discipline. In science, there are many assumptions that are modified in the course of new findings. Genetics is a growing discipline, and as such, it has undergone a great deal of change in its short life. Raising its working assumptions to the status of a dogma is, in my opinion, an exaggeration. For one thing, the idea that the genotype is not sufficient to predict phenotype, or that biological causation runs upwards and downwards, can be accommodated by a genetics framework understood as a set of scientific, and thus flexible, assumptions (e.g., Fusco & Minelli Reference Fusco and Minelli2010).

My impression is that Charney has created a straw man out of the myth of an immutable genetics. First, he pictures genetics as embodying a fixed dogma, and then he assumes that new developments in epigenetics count as a paradigm shift. For example, he argues that the causes of phenotypic variation are attributed to genetic or environmental parameters, or to the interaction of the two, and then he advances that “the neogenome constitutes a class of heritable agents that do not fall into either category” (sect. 6). I believe that extant genetics is confidently accommodating this new notion (e.g., Bell et al. Reference Bell, Finer, Lindgren, Wilson, Rakyan, Teschendorff, Akan, Stupka, Down, Prokopenko, Morison, Mill, Pidsley, Deloukas, Frayling, Hattersley, McCarthy, Beck and Hitman2010; Caldji et al. Reference Caldji, Hellstrom, Zhang, Diorio and Meaney2011; Cherry & Daley Reference Cherry and Daley2012; Gershon et al. Reference Gershon, Alliey-Rodriguez and Liu2011; Hamm & Costa Reference Hamm and Costa2011; Oh & Petronis Reference Oh and Petronis2008; Pike Reference Pike2011; Rutten & Mill Reference Rutten and Mill2009). Second, he creates artificial categorical assumptions, which later can be easily refuted with evidence. For example, the qualifications of “all” and “never” in the description of the central assumptions for twin study methodology are not common qualifications in science, nor are they a reasonable attribution to genomics. Finally, Charney reverses the burden of proof by asking extant genomics methodologies to prove their soundness. For example, Charney asserts that “although employing statistical analysis, biometric genetics must make contact with the natural world at some point” (sect. 6.1.1). It is difficult for me to see the point of such a claim. The challenge is either trivial or highly argumentative. How does one independently assess biometric genetics contact with the natural world?

Additionally to creating a straw man, I believe that some of Charney's conclusions are non sequiturs. In some places he is carried away by his paradigm shift momentum. For example, considering that the DNA is no longer privileged as the sole carrier of information does not grant the idea that the DNA is no longer a privileged carrier of information, as Charney seems to imply. In other places, he presents contentious argumentations. For example, he argues that “if MZ [monozygotic] twins are concordant for [a specific] trait to a greater extent than DZ [dizygotic] twins, this greater concordance cannot confidently be attributed to genetic concordance, since they may be genetically discordant” (sect. 6). In view of all the evidence that Charney has brilliantly presented in his target article, we can all agree that MZ twins may be genetically discordant, but it doesn't follow that we cannot confidently attribute trait concordance to genetic concordance. The issue cannot be all or nothing; rather, it is a question of degree. Finally, and perhaps most important, the target article seems to convey the corollary that heritability studies and gene association studies are no longer valid as methodologies. For example, Charney argues that “the cumulative evidence of recent discoveries in genetics and epigenetics calls into question the validity of two classes of methodologies that are central to the discipline: Twin, family, and adoption studies, which are used to derive heritability estimates, and gene association studies, which include both genome-wide and candidate-gene association studies.” My view is that the evidence presented by Charney does not support such a strong contention. It is one thing to hold that the interpretation of gene association and heritability findings should be modified, but a very different thing to aver that such methodologies are no longer valid as research tools. I think that heritability studies and gene association studies have still a role to play, albeit assuming improvements (e.g., Gershon et al. Reference Gershon, Alliey-Rodriguez and Liu2011).