Homology and Homoplasy (from Uncommon Descent)

All credit for the following goes to Barry A- one author on the blog Uncommon Descent. I thought this topic required seeing that Zachriel is bringing up homology in reference to cetacean "hands":

Homology and Homoplasy

Here is the standard Neo-Darwinian explanation of homology and homoplasy:

Suppose two organisms have a similar feature. The features are “homologous” if they were inherited by the organisms from a similar feature in a common ancestor. In other words, the features are homologous if they result from a shared genetic ancestry. Bat wings and human arms are homologous because they are similar structures inherited from a shared mammalian ancestor.

On the other hand, the features are not homologous, but “homoplasious” if they were not inherited by the organisms from a similar feature in a common ancestor. In other words, the features are homoplasious if they did not result from a shared genetic ancestry. Homoplasious structures evolved independently more than once in a process known as convergent evolution. Bird wings and insect wings are homoplasious; they are similar and perform the same function, but they do not result from common genetic ancestry. Homoplasious features are also called “analogous features.”

The difficulty is determining whether similar structures are homologous or homoplasious, because similarity, does not necessarily imply common ancestry. As Gavin De Beer points out:

“Homologous structures need not be controlled by identical genes, and homology of phenotypes does not imply similarity of genotypes.” Gavin De Beer, Homology, an Unsolved Problem (London: Oxford University Press, 1971), 16.

Roger Lewin adds: “The key issue is the ability correctly to infer a genetic relationship between two species on the basis of a similarity in appearance, at gross and detailed levels of anatomy. Sometimes this approach . . . can be deceptive, partly because similarity does not necessarily imply an identical genetic heritage: a shark (which is a fish) and a porpoise (which is a mammal) look similar.” Roger Lewin, Bones of Contention: Controversies in the Search for Human Origins (New York: Simon and Schuster, 1987), 123.

Scientists attempt to determine homology through “outgroup comparisons.” An “outgroup” is a group of organisms (a taxon) that diverged from two other groups (taxa) before they diverged from one another. In other words, two of the taxa are more closely related to each other than they are to the third group, because they share a common ancestor with each other that they do not share with the outgroup. The more closely related groups are called the “ingroup.” Outgroup organisms are thus near relatives of ingroup organisms but not part of the ingroup.

Researchers use outgroup comparisons to determine the “polarity” (that is the direction) of evolution. Because the ingroup branched off from the common ancestor after the outgroup, scientists can assume that any character the ingroup shares with the outgroup must have been inherited from the ingroup’s common ancestor. In other words, a character state that is present in both the outgroup and the ingroup is ancestral, and a character state that is in the ingroup only is not ancestral but derived.

Now the problem with using homology to show common ancestry is that it is quite circular. Jonathan Wells points this out:

“Many biology textbooks define homology as similarity due to common ancestry, yet claim that it is evidence for common ancestry. For example, Starr and Taggart’s Biology: The Unity and Diversity of Life (8th Edition, 1998) states that the “pattern of macroevolution–that is, change from the form of a common ancestor–is called morphological divergence…. Homology [is] a similarity in one or more body parts in different organisms that share a common ancestor…. Homologous structures provide very strong evidence of morphological divergence.” (pp. 318-319) In a section on “The Evidence for Evolution” in the teacher’s edition of Johnson’s Biology: Visualizing Life (1998), students are told that “homologous structures are structures that share a common ancestor,” and an accompanying note tells the teacher that “such structures point to a common ancestry.” (p. 178) According to Campbell, Reece and Mitchell’s Biology (5th Edition, 1999), “similarity in characteristics resulting from common ancestry is known as homology, and such anatomical signs of evolution are called homologous structures. Comparative anatomy is consistent with all other evidence in testifying [to] evolution.” (p. 424) Raven and Johnson’s Biology (5th Edition, 1999), in a section titled “The evidence for macroevolution is extensive,” includes the following: “Homology: Many organisms exhibit organs that are similar in structure to those in a recent common ancestor. This is evidence of evolutionary relatedness.” A few pages later, the same textbook explicitly defines homologous structures as “structures with different appearances and functions that all derived from the same body part in a common ancestor.” (pp. 412, 416) Audesirk, Audesirk and Byers’s Life On Earth (2nd Edition, 2000) calls homology “evidence of relatedness” in a section titled “Comparative Anatomy Provides Structural Evidence of Evolution.” The textbook tells students: “Internally similar structures are called homologous structures, meaning that they have the same evolutionary origin despite possible differences in function. Studies of comparative anatomy have long been used to determine the relationships among organisms, on the grounds that the more similar the internal structures of two species, the more closely related the species must be, that is, the more recently they must have diverged from a common ancestor.” (p. 236)”

edit:

The original reason this was posted on UD was because of the Matzke et al. paper pertaining to homologs and the bacterial flagellum. This blog demonstrates that what may appear as a homolog may actually not be. Homologs are usually assumed. And homolgy of proteins that make up the bac flag does NOT explain the assembly instructions- what protein goes where and in what amount- nor does it explain the command and control center required to use it-> the bac flag can turn CW, CCW and at varying speeds. It can also stop turning or when it is turning in one direction, regardless of the speed, it can stop and change directions within a quarter of a turn! Evolutionitwits never address any of that.