Dramatic advances in the field of developmental biology have in fact revealed a "prodigious biological phenomenon" of precisely this sort -- but since this represents something known rather than unknown to science, Le Fanu prefers to see it as a problem rather than a solution.
[W]hen it takes six thousand genes to build a heart, what chance was there that a 'random mutation' in any one of them might generate a beneficial variation in favour of the heart's further perfection? Perhaps there were some 'mastermind' switching genes, turning the others 'on and off' according to some preconceived plan. . . . And sure enough, in the late 1980's, . . . the Swiss biologist Walter Gehring discovered two clusters of those master genes. These Hox genes, as they are known, determine the three-dimensional organization of the front and back half of the fly respectively . . . (p. 140)What Le Fanu is referring to is the discovery, not only of the Hox genes, but a group of genes with very special functions, pertaining not to the transmission of specific traits, but controlling the development of the organism during various stages of its life. The study of such genes has given rise to the field of Evolutionary Developmental Biology, described as follows in Wikipedia:
The developmental-genetic toolkit consists of a small fraction of the genes in an organism's genome whose products control it's development. These genes are highly conserved among Phyla. Differences in deployment of toolkit genes affect the body plan and the number, identity, and pattern of body parts. The majority of toolkit genes are components of signaling pathways, and encode for the production of transcription factors, cell adhesion proteins, cell surface receptor proteins, and secreted morphogens, all of these participate in defining the fate of undifferentiated cells, generating spatial and temporal patterns, which in turn form the body plan of the organism. Among the most important of the toolkit genes are those of the Hox gene cluster, or complex. Hox genes, transcription factors containing the more broadly distributed homeobox protein-binding DNA motif, function in patterning the body axis. Thus, by combinatorial specifying the identity of particular body regions, Hox genes determine where limbs and other body segments will grow in a developing embryo or larva. A paragon of a toolbox gene is Pax6/eyeless, which controls eye formation in all animals. It has been found to produce eyes in mice and Drosophila, even if mouse Pax6/eyeless was expressed in Drosophila .The existence of these "toolkit" genes goes a long way toward explaining not only organs such as the heart, lungs, kidneys, etc., but the famous problem of the eye, which troubled not only skeptics such as Le Fanu, but Darwin himself. For Le Fanu, however, the glass is not half full, but half empty:
This is, in fact, a legitimate puzzle, and a legitimate concern, expressed in the Wikipedia article as follows:
But when Gehring and his colleagues pursued this extraordinarily important discovery further, they found something yet more astonishing still . . . : that precisely the same 'master' genes mastermind the three-dimensional structures of all living things: frogs, mice, even humans (p. 140).
Among the more surprising and, perhaps, counterintuitive (from a neo-Darwinian viewpoint) results of recent research in evolutionary developmental biology is that the diversity of body plans and morphology in organisms across many phyla are not necessarily reflected in diversity at the level of the sequences of genes, including those of the developmental genetic toolkit and other genes involved in development. . . The finding that much biodiversity is not due to differences in genes, but rather to alterations in gene regulation, has introduced an important new element into evolutionary theory. Diverse organisms may have highly conserved developmental genes, but highly divergent regulatory mechanisms for these genes. Changes in gene regulation are "second-order" effects of genes, resulting from the interaction and timing of activity of gene networks, as distinct from the functioning of the individual genes in the network.
For Le Fanu, the fact that the same "toolkit" genes regulate the development of so many different creatures, from fruit flies to mice to humans, presents an insurmountable obstacle to Darwinian evolution, which, as he sees it, has no other choice but to concede defeat. For Ernst Mayr, however, the same evidence has a very different meaning: "Mice and flies share 6 Hox genes, which the common ancestor of Protostomia and Deuterostomia already must have had." In other words, "Everything indicates that the basic regulatory systems are very ancient and were later coopted for additional functions when these were acquired" (What Evolution Is, p. 110).
Le Fanu has forgotten a basic principle of Darwinian evolution: descent from a common ancestor. If the same gene (or system of genes) is found among a great many different creatures, that tells us that all these creatures may well have inherited it from the same ancestor, even if that ancestor may have lived hundreds of millions of years ago. And if that gene must have had a different function in that long lost ancestor, that tells us that genes can change their function in different settings, and thus be "coopted" to adopt Mayr's term. Truth can often be far stranger than ficiton -- and science far stranger than skeptics such as Le Fanu can imagine.
But we have yet to consider the greatest puzzle of them all: the human mind.