The Evolution of Homoplasies

It is one of the fundamental concepts of, and evidences for, evolution: similarities found in different species. These similarities, or lack thereof, are used to construct evolutionary trees which show how the species are evolutionarily related. Species sharing many similarities are close neighbors while species sharing fewer similarities are distantly related. And according to textbooks such relationships are obvious. Those textbooks show clean and compelling illustrations of evolutionary trees. But the biological data are not so cooperative. One problem is the many uncanny similarities found in what otherwise must be, according to evolution, more distant species.

Similarities in otherwise distant species are known as homoplasies. They are, as one paper explained, not the expected outcome:

Phenotypes and taxa are expected to diverge as evolution proceeds. Thus, when divergent lineages are found to be morphologically similar, explanation is needed. Homoplasy is similarity that is the result not of simple ancestry, but of either reversal to an ancestral trait in a lineage or of independent evolution. …

However, one does not seek homoplasy—it “finds” the researcher and compels one to ask appropriate questions.

Of course evolutionists have answers for those questions. These unexpected similarities may have independently evolved from scratch. Or perhaps the trait disappeared in one lineage, only to later reappear much later. To elucidate such details evolutionists construct evolutionary trees. As the paper explains:

Phylogenetic analysis is necessary to show that derived similarity is not the simple result of common ancestry of taxa being compared.

But the process of constructing evolutionary trees, using phylogenetic analysis, presupposes that evolution occurred. In other words, in order to demonstrate that a trait independently evolved in different lineages, evolutionists begin by assuming evolution. This assumption, however, is implicit rather than explicit. It is unspoken. When reporting that they have discovered that a trait, such as the vision system, independently evolved several times, evolutionists do not explain that they began by assuming evolution is true. Without that assumption there is no scientific reason to think these homoplasies evolved—independently or otherwise.

In fact, there are plenty of scientific reasons to think they did not evolve. Specific designs, where many are possible, are not likely to repeatedly arise by chance (no, selection does not help).

In some cases these homoplasies develop in the embryonic stages via similar pathways. For instance, the Pax6 master control gene plays an important role in the development of the different vision systems that are supposed to have independently evolved. This means that Pax6 must predate the evolution of these different vision systems. This is yet another example of the serendipity that pervades evolutionary theory. In this case, we must believe that genes such as Pax6 first evolved when no vision system existed. Then later it enabled such phenomenal designs to arise:

The image-forming eyes of invertebrate and vertebrate taxa are convergent organs that share some core developmental genetic mechanisms that exemplify deep homology. All eyes, invertebrate and vertebrate, develop through a cascade of similar transcription factors despite vast phylogenetic distances. These networks include genes (e.g., Pax6) that have been deployed in different ways at different times, and specific pathways that have re-evolved in different lineages by mutation, gene duplication, and intercalary evolution. The networks and cascades, which contain homologous genes and members of the same gene families, are not genetically identical. Thus, the end phenotypes might be general homologs at a deep hierarchical level but convergent with respect to end phenotype and phylogeny. Indeed, what has historically been termed “convergence” and attributed to independent evolution in unrelated taxa has a common genetic system associated with trait development.

Such pre adaptation narratives are ubiquitous in the evolution literature. All kinds of profoundly complex designs arise only much later to be recruited as a crucial component in some even more complex design.

Plant and animal defense systems

Or consider the striking similarities in how plants and animals defend against pathogens. In this case various homoplasies are found, calling for various evolutionary explanations. As one paper explained, a clear, irrefutable picture has emerged. “Plants and animals use similar types of cell surface sensors to detect conserved microbial signatures.”

These different types of cell surface sensors work rather well in helping to defend against pathogens. This is why they evolved independently according to evolutionists. But in fact what such findings reveal is the tight design requirements. Apparently only a limited set of cell surface sensors can do the job.

This runs counter to the typical evolutionary explanation that the impossible probabilities they must surmount don’t really matter because there must be a great many different, as yet unknown, designs that evolution could have luckily hit upon. Yes, the chances of any one design is remote, but there must be a great many different designs that all could do the job. Apparently not in the case of these cell surface sensors.

Evolutionary trees are not the clean, compelling result as they too often are represented to be. Homoplasies, which strain the evolutionary probabilities even further, are yet another example of this. Yes the similarities between the species can be modeled with evolutionary trees, but such a conclusion has substantial scientific problems.