The original meaning of a gene was simply a heritable unit. This was long before the discovery of DNA. The theory was based on phenotype, i.e., observable characteristics. What they didn’t know and what still doesn’t often get acknowledged is that much gets inherited from parents, especially from the mother. This includes everything from epigenetics to microbiome, the former determining which genes express and how they express while the latter consists of the majority of genetics in the human body. The fetus will also inherit health conditions from the mother, such as malnutrition and stress, viruses and parasites — all of those surely having epigenetic effects that could get passed on for generations.
Even more interestingly, DNA itself gets passed on in diverse ways. Viruses will snip out sections of DNA and then put them into the DNA of new hosts. Mothers, including surrogate mothers, can gain DNA from the fetuses they carry. And then those mothers can pass that DNA to any fetus she carries after that, which could cause a fetus to have DNA from two fathers. Fetuses can also absorb the DNA from fraternal twins or even entirely absorb the other fetus, forming what is called a chimera. Bone marrow transplantees also become chimeras because they inherit the stem cells for blood cells from the donor, along with inheriting epigentics from the donor. These chimeras could pass this on during a transplantee’s pregnancy.
We hardly know what all that might mean. There is no single heritable unit that by itself does anything. That is not the direct source of causation. A gene only acts as part of DNA within a specific cell and all of that within the entire biological system existing within specific environmental conditions. The most important causal factors are various. What is in DNA only matters to the degree it is expressed, but what determines its expression will also determine how it expresses. Evelyn Keller Fox writes that, “the causal interactions between DNA, proteins, and trait development are so entangled, so dynamic, and so dependent on context that the very question of what genes do no longer makes much sense. Indeed, biologists are no longer confident that it is possible to provide an unambiguous answer to the question of what a gene is. The particulate gene is a concept that has become increasingly ambiguous and unstable, and some scientists have begun to argue that the concept has outlived its productive prime” (The Mirage of a Space between Nature and Nurture, p. 50). Gene expression as seen in phenotype is determined by a complex system of overlapping factors. Talk of genes doesn’t help us much, if at all. And heritability rates tells us absolutely nothing about the details, such as distinguishing what exactly is a gene as a heritable unit and causal factor, much less differentiating that from everything else. As Fox further explains:
“It is true that many authors continue to refer to genes, but I suspect that this is largely due to the lack of a better terminology. In any case, continuing reference to “genes” does not obscure the fact that the early notion of clearly identifiable, particulate units of inheritance— which not only can be associated with particular traits, but also serve as agents whose actions produce those traits— has become hopelessly confounded by what we have learned about the intricacies of genetic processes. Furthermore, recent experimental focus has shifted away from the structural composition of DNA to the variety of sequences on DNA that can be made available for (or blocked from) transcription— in other words, the focus is now on gene expression. Finally, and relatedly, it has become evident that nucleotide sequences are used not only to provide transcripts for protein synthesis, but also for multilevel systems of regulation at the level of transcription, translation, and posttranslational dynamics. None of this need impede our ability to correlate differences in sequence with phenotypic differences, but it does give us a picture of such an immensely complex causal dynamic between DNA, RNA, and protein molecules as to definitely put to rest all hopes of a simple parsing of causal factors. Because of this, today’s biologists are far less likely than their predecessors were to attribute causal agency either to genes or to DNA itself— recognizing that, however crucial the role of DNA in development and evolution, by itself, DNA doesn’t do anything. It does not make a trait; it does not even encode a program for development. Rather, it is more accurate to think of DNA as a standing resource on which a cell can draw for survival and reproduction, a resource it can deploy in many different ways, a resource so rich as to enable the cell to respond to its changing environment with immense subtlety and variety. As a resource, DNA is indispensable; it can even be said to be a primary resource. But a cell’s DNA is always and necessarily embedded in an immensely complex and entangled system of interacting resources that are, collectively, what give rise to the development of traits. Not surprisingly, the causal dynamics of the process by which development unfolds are also complex and entangled, involving causal influences that extend upward, downward, and sideways.” (pp. 50-52)
Even something seemingly as simple as gender is far from simple. Claire Ainsworth has a fascinating piece, Sex redefined (nature.com), where she describes the new understanding that has developed. She writes that, “Sex can be much more complicated than it at first seems. According to the simple scenario, the presence or absence of a Y chromosome is what counts: with it, you are male, and without it, you are female. But doctors have long known that some people straddle the boundary — their sex chromosomes say one thing, but their gonads (ovaries or testes) or sexual anatomy say another. Parents of children with these kinds of conditions — known as intersex conditions, or differences or disorders of sex development (DSDs) — often face difficult decisions about whether to bring up their child as a boy or a girl.”
This isn’t all that rare considering that, “Some researchers now say that as many as 1 person in 100 has some form of DSD.” And, “What’s more, new technologies in DNA sequencing and cell biology are revealing that almost everyone is, to varying degrees, a patchwork of genetically distinct cells, some with a sex that might not match that of the rest of their body. Some studies even suggest that the sex of each cell drives its behaviour, through a complicated network of molecular interactions. Gender should be one of the most obvious areas to prove genetic determinism, if it could be proven. But clearly there is more going on here. The inheritance and expression of traits is a messy process. And we are barely scratching the surface. I haven’t seen any research that explores how epigenetics, microbiome, etc could influence gender or similar developmental results.