".....But my correspondent asked about an argument in favor of common ancestry he had heard that basically went like this:
organisms that don't fit neatly into a phylogenetic tree. Or, what happens is evolutionary biologists attempt to force-fit organisms into the tree only by invoking processes like convergent evolution and loss of traits. In other words, evolutionary biologists are forced to propose that an organism's traits did not arise through common ancestry, because common ancestry fails to explain the data.
Does this mean that evolutionary biologists reject common ancestry when they find data that doesn't fit a tree? No, because they assume common ancestry; they aren't interested in testing it. So when they find data that doesn't fit a tree, they just find ways to force-fit the data into the tree. Here's what's going on:
The first and primary assumption of all evolutionary phylogenetic classification methodologies is that common ancestry is true. This assumption nearly always goes unquestioned, even when the data doesn't support it. As Elliott Sober and Michael Steele explain, "It is a central tenet of modern evolutionary theory that all living things now on earth trace back to a single common ancestor," and "This proposition is central because it is presupposed so widely in evolutionary research." They acknowledge that cladistics assumes that a tree exists, and common ancestry is correct:
Sahelanthropus tchadensis is widely touted as a human ancestor that lived about 6-7 million years ago, sometime very soon after the supposed split between the human line and the chimp line. But it's rarely mentioned that this specimen doesn't fit into the standard hominin tree at all. Why? Because it has a flat face, a humanlike quality, which shouldn't exist that far back:
Another good example of an organism whose genome posed problems for phylogenetic classification after it was sequenced is birds. As we reported last December, the sequencing of various bird genomes led to the unexpected conclusion that many types of birds that were previously thought to be closely related -- water birds, birds of prey, and songbirds -- evolved their groups' defining traits convergently. As Nature put it, "the tree of life for birds has been redrawn" by this study. The problem was, once genomic data was sequenced and understood, many basic habits and lifestyles of birds no longer fit into a nested hierarchy." EvolutionNews&Views
...and every winged fowl after his kind:
and God saw that it was good.
Genesis 1:21
All life forms fall within a nested hierarchy. Of the hundreds of thousands of specimens that have been tested, every single one falls within a nested hierarchy, or their evolutionary phylogenetic tree is still unknown and not sequenced yet.This claim (which he wasn't making, by the way) is far from true. We constantly find
Does this mean that evolutionary biologists reject common ancestry when they find data that doesn't fit a tree? No, because they assume common ancestry; they aren't interested in testing it. So when they find data that doesn't fit a tree, they just find ways to force-fit the data into the tree. Here's what's going on:
The first and primary assumption of all evolutionary phylogenetic classification methodologies is that common ancestry is true. This assumption nearly always goes unquestioned, even when the data doesn't support it. As Elliott Sober and Michael Steele explain, "It is a central tenet of modern evolutionary theory that all living things now on earth trace back to a single common ancestor," and "This proposition is central because it is presupposed so widely in evolutionary research." They acknowledge that cladistics assumes that a tree exists, and common ancestry is correct:
Whether one uses cladistic parsimony, distance measures, or maximum likelihood methods, the typical question is which tree is the best one, not whether there is a tree in the first place.Likewise, the assumption is made explicit, and primary, in the UC Berkeley Museum of Paleontology's introductory page on cladistics:
(Elliott Sober and Michael Steele, "Testing the Hypothesis of Common Ancestry," Journal of Theoretical Biology 218 (2002): 395-408 (emphasis added).)
What assumptions do cladists make? There are three basic assumptions in cladistics:One textbook cited by Stephen Meyer in Darwin's Doubt concurs about this assumption:
1.Any group of organisms are related by descent from a common ancestor.
The key assumption made when constructing a phylogenetic tree from a set of sequences is that they are all derived from a single ancestral sequence, i.e., they are homologous.Together, these authorities make a crucial point: cladistics and other phylogenetics methods do not demonstrate common ancestry; they assume it. Thus, Michael Syvanen -- a rare evolutionary biologist who is open to the possibility that universal common ancestry is false -- laments the pro-tree biases of treebuilding algorithms:
(Marketa Zvelebil and Jeremy O. Baum, Understanding Bioinformatics (New York: Garland Science, 2008), p. 239.)
Because tree analysis tools are used so widely, they tend to introduce a bias into the interpretation of results. Hence, one needs to be continually reminded that submitting multiple sequences (DNA, protein, or other character states) to phylogenetic analysis produces trees because that is the nature of the algorithms used.Common ancestry, therefore, is a starting assumption about the data -- not a conclusion from it.
(Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, 46:339-356 (2012) (emphases added).)
Sahelanthropus tchadensis is widely touted as a human ancestor that lived about 6-7 million years ago, sometime very soon after the supposed split between the human line and the chimp line. But it's rarely mentioned that this specimen doesn't fit into the standard hominin tree at all. Why? Because it has a flat face, a humanlike quality, which shouldn't exist that far back:
If we accept these as sufficient evidence to classify S. tchadensis as a hominid at the base, or stem, of the modern human clade, then it plays havoc with the tidy model of human origins. Quite simply, a hominid of this age should only just be beginning to show signs of being a hominid. It certainly should not have the face of a hominid less than one-third of its geological age. Also, if it is accepted as a stem hominid, under the tidy model the principle of parsimony dictates that all creatures with more primitive faces (and that is a very long list) would, perforce, have to be excluded from the ancestry of modern humans."
(Bernard Wood, "Hominid revelations from Chad," Nature, 418 (July 11, 2002):133-35.)
Another good example of an organism whose genome posed problems for phylogenetic classification after it was sequenced is birds. As we reported last December, the sequencing of various bird genomes led to the unexpected conclusion that many types of birds that were previously thought to be closely related -- water birds, birds of prey, and songbirds -- evolved their groups' defining traits convergently. As Nature put it, "the tree of life for birds has been redrawn" by this study. The problem was, once genomic data was sequenced and understood, many basic habits and lifestyles of birds no longer fit into a nested hierarchy." EvolutionNews&Views
...and every winged fowl after his kind:
and God saw that it was good.
Genesis 1:21