The two possible hierarchies, one formed by comparing morphology (the physical appearance of the organisms) and the other formed by comparing molecular data (genotype of the organisms), would be expected to be congruent if all life had originated via evolution from a common ancestor. While there are certainly discrepancies between the two nested hierarchies, the two trees certainly show an amazing degree of similarity.
Of course, based upon the fact that the genes of an organism determines the morphology of the organism, one may expect the two trees would share a certain degree of resemblance. However, the biochemical analyses can also look at things that have very little or no influence on morphology, such as non-functional DNA or the sequence of metabolic enzymes, and end up with the same results. Also, there is no reason to assume that similar morphology demands similar genetics, as convergent evolution of marsupials and eutherian mammals will attest. Creatures such as the marsupial mouse and the eutherian mouse look very similar, but they differ a great deal in their genetics and biochemistry. This is because there are many ways for DNA to encode for the same proteins or the same regulatory elements, thus resulting the same morphology with different genetics. Therefore while common design would not predict such a congruence between trees, common descent would. Thus, common descent is greatly corroborated by such congruence.http://evolutionwiki.org/wiki/Nested_Hierarchy
Above is a quote from evolution wiki. This directly contradicts Tertius assertion that evolution is not based on “similarities”, since even the nested hierarchies are based on similarities. Interestingly, the similarities chosen for the nested hierarchies tend to be fewer for the families and more for the species. This would be essential in order to develop a nested hierarchy. Using an analogy, we would see that we could divide things into buildings and vehicles. Buildings then would be divided into houses, offices, factories and churches. Vehicles could be divided into wheeled and non-wheeled, and wheeled divided into two-wheeled and more than two wheeled, and more-than-twowheeled into trucks, trains, cars, tractors. We have a type of morphological and functional hierarchy. This obviously does not show evolution, except for an evolution of design.
However, does the examination of the genomes show this self-evolution required for evolutionary theory? It seems to, but does it not depend primarily on the assumptions made?
Common design not does prevent a similarity between genomes for similar morphologies. Nor does it prevent using dissimilar genome for similar morphologies. I do not really see a limitation for common design in this way. However, the common similarities do support a common design, but not that common design is limited by limitations that we might impose. We might one day build a bicycle out of steel, and another day out of wood or titanium. The design is common, but the materials are different. The design might even be different somewhat, but not so different that we would not call them all bicycles. Thus there is no justification for saying that Common design would be invalid under the present evaluation of genetics.
Does common descent provide a better explanation than common design? Keeping in mind that common descent is somewhat speculative; in other words, beyond observing actual instances of genome changes in the present, and observing the potential to interfere in natural selection based on random mutations, we are speculating that our definition of nested hierarchies relates to a progression in time over millenia. Simple genetics does not seem to provide this progression intuitively. In other words, I wonder what we see as viable forward progression, could genetically be just as viable in reverse.
In addition, I see some problems with nested hierarchies in this: If we divide everything into single cells and multi-celled organisms, we have separated and divided organisms into “nests”. What justification do we use to assume that single celled organisms caused multi-celled organisms outside of their “nest”? Or the reverse… that multi-celled did not devolve into single celled? And if both happened, then how does that justify the validity of using nested hierarchies in this way?