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Homology and similarity

Summary of problems:

Despite using the term in the title of two chapters, and using the word "homology" or "homologous" over 80 times, EE never provides a clear and consistent definition of homology. Their usage is inconsistent and vague, promoting confusion and obscuring the actual ways in which scientists use the term. Furthermore, the focus on "homology," as opposed to terms and concepts with clearer meanings and less historical baggage, introduces confusion to the discussion of the morphological evidence of common descent.

Full discussion:

In the glossary, "homologous structure" is [mis]defined as "a body part that is similar in structure and position in two or more species but has a different function in each; for example, the forelimbs of bats, porpoises and humans" (EE, p. 146). "Molecular homology" is defined in the glossary as "similarity of the nucleotide sequences of DNA or RNA molecules, or the amino acid sequences of proteins." In the text of this chapter, homology is never explicitly defined, but is referred to in the context of "similarities," without any restrictions regarding function. As discussed below, similarity of developmental pathways is treated as a requirement of anatomical homology, but is not included in any definitions. None of these definitions match the actual way scientists define and use the term homology, let alone how scientists evaluate the anatomical evidence for common descent.

To choose a trivial example, evolutionary biologists agree that the hooves of a cow and the hooves of a deer are homologous. By the definition EE offers, they could not be homologous structures since they share the same function. Badly misdefining the term that is central to two chapters, and then using it inconsistently throughout, is not a good way to increase student comprehension.

The glossary in Futuyma's Evolutionary Biology defines homology as "Possession by two or more species of a trait derived, with or without modification, from their common ancestor." West-Eberhard defines it as "similarity due to common descent," but adds that "homology, like 'fitness' and 'species', is an elusive concept. There is unceasing debate within evolutionary biology regarding its meaning and use" (M. J. West-Eberhard, 2003, Developmental Plasticity and Evolution Oxford University Press:Oxford. p. 485 of 794).

While the first mistake Explore Evolution makes in this chapter is its failure to define "homology" (correctly), the far greater error is that they do not engage with the ways that modern evolutionary biologists use the concept, and the ways in which the term "homology" has been superseded by clearer concepts.

Here is how biologist Günter Wagner explained the situation in 1989:

Among evolutionary biologists, homology has a firm reputation as an elusive concept. Nevertheless, homology is still the basic concept of comparative anatomy and has been used successfully in reconstructions of phylogenetic history. A large number of characters are certainly derived from the same structure in a common ancestor and are therefore undoubtedly homologous. One simply cannot escape the conclusion that the brain of a rat and a human are actually the "same" in spite of their obvious differences.
G. P. Wagner (1989) "The biological homology concept." Annual Review of Ecology and Systematics. 20:51–69

The phenomenon is real, but teasing out how to identify "homology" has proven difficult. As EE mentions, "homology" was originally coined by Robert Owen to describe a sort of Platonic ideal which individual species drew upon to produce their forms. This non-evolutionary treatment of the concept can promote confusion when thinking about a structure that evolved in stages, and various of those stages are still present. For an example, see our discussion of eye evolution below.

A term that many scientists prefer is "synapomorphy," or "shared, derived characteristic." This concept was crafted by Willi Hennig specifically to describe a trait of an organism which is shared by all of the descendants of a common ancestor, and which is not shared with other groups — it is newly derived within that lineage. Examining the pattern of shared, derived traits allows scientists to develop hypotheses about common descent, and examining additional traits allows scientists to test those ideas.

Tetrapod limbs provide an example of the way that scientists develop and test hypotheses about synapomorphy. Many different aspects of tetrapod limbs unite tetrapods as the descendants of a species like Tiktaalik (discussed in the critique of chapter 3). Such a species possessed certain novel traits that were passed on to their descendants. Within the various lineages, those traits changed, and those changes were passed on to their descendants. Using only synapomorphic concepts, we can make the following observations and hypotheses:

  1. Observation: Bats, seals, and birds are tetrapods (have four limbs) and the particular bones in their limbs share many of the same traits.
  2. Hypothesis: Bats, seals, and birds share a common ancestor.

  1. Observation: Bats share more limb traits with seals than they do with birds. The limb traits that bats share with birds are the same traits that seals share with birds.
  2. Hypothesis: The common ancestor of bats and seals is more recent than the most recent common ancestor of bats, seals, and birds.

The examination of limb morphology allows scientists to propose an hypothesis about the evolution of the groups which possess those limbs. That hypothesis can be tested by examining other traits, such as skull morphology, or DNA sequences. The hypothesis of common descent allows scientists to predict that the hierarchal arrangement of novel traits in each part of the organism should match the pattern derived from the other parts. Hypotheses about the synapomorphy of a trait can be tested by examining that trait in additional species which share the same common ancestor, as discussed below in the context of eye evolution.

By omitting any discussion of the way that scientists propose and test evolutionary hypotheses, Explore Evolution obscures the ways in which scientists actually use concepts like "homology" and "synapomorphy." Misdefining "homology" in the glossary is bad scholarship or an attempt to further confuse the issue at hand.