As stated, the pattern of nature seems to correspond very well with the old nineteenth-century typological model, which is mostly based on structure (morphology). Nearly all known groups appear to be isolated and well defined. Clear sequential patterns whereby one class is linked to another through transitional forms, as evolution would require, are virtually unknown.
However, no matter how much the diversity of nature may appear to conform to the theory of types at a morphological (= structural) level, there is no way of quantifying such conclusions. Judging relationships in terms of morphological characteristics is bound to involve an element of subjectivity. It was not until the advances in molecular biology that we were finally able to quantitatively describe the relationship between different organisms at a biochemical level.
In the late 1950s it was found that the sequence of a particular protein, hemoglobin for example, was not fixed but varied considerably from species to species. The amino acid sequence of a protein from two different organisms can be readily compared by aligning the two sequences and counting the number of positions where the chains differ. The differences between two proteins can be quantified exactly and the results of these measurements can provide an entirely novel approach to measuring the differences between species.
As work continued in this field, it became clear that each particular protein had a slightly different sequence in different species and that closely related species had closely related sequences. When the hemoglobin sequences in different mammals, such as man and dog, were compared, the sequential divergence was about twenty percent. When the hemoglobin in two dissimilar species such as man and carp were compared, the sequential divergence was found to be about fifty percent.
These results showed that not only did organisms vary at a morphological level in terms of their gross anatomy, but that they also varied at a molecular level as well. It became increasingly apparent as more and more sequences accumulated that the differences between organisms at a molecular level corresponded to a large extent with their differences at a morphological level.
Armed with this new technique, biology at last possessed a strictly quantitative means of measuring the distance between two species and of determining the patterns of biological relationships. If it is true, as typology implied, that all the members of one type always conform exactly to the basics of their type, all possessing equally all the defining character traits of their type and all standing equidistant from the members of other types, then these molecular studies should bear that out.
Conversely, this new molecular approach could potentially have provided very strong, if not irrefutable, evidence supporting evolutionary claims. All that was necessary to demonstrate an evolutionary relationship was to examine the proteins in the species concerned and show that the sequence could be arranged into an evolutionary series.
The prospects were very exciting to evolutionary biologists. Where the fossils had failed and morphological considerations were at best only ambiguous, perhaps this new field of comparative biochemistry might at last provide objective evidence of sequence and of the connecting links which these evolutionary biologists had long sought.
Unfortunately for the evolutionist, as more protein sequences began to accumulate during the 1960s, it became increasingly apparent that the molecules were not going to provide any evidence of sequential arrangements in nature. Instead, they reaffirmed the typological view. In fact, the divisions turned out to be more mathematically perfect than even the most die-hard typologists would have predicted !
In his book, Evolution: A Theory in Crisis, (1), Michael Denton used data from the Dayhoff Atlas of Protein Structure and Function (3), which compiles and compares various amino acid sequences for hundreds of species. The data is presented in the form of a percent sequence difference. Upon examination, it was found that the groups correspond precisely to the groups arrived at on traditional morphological grounds. (4)
It also became apparent that the sequential divergence becomes greater as the taxonomic distance between organisms increases, as typologists would have predicted. For example, one would expect the divergence to be greater between a horse and a fruit fly (two animals) than between a horse and a dog (two mammals), and this is exactly what was found.
The most striking feature is that each identifiable subclass is isolated and distinct. Every sequence can be unambiguously assigned to a particular subclass. No sequence or group of sequences can be designated as intermediate with respect to other groups. All the sequences of each subclass are equally isolated from the members of other groups. Transitional or intermediate classes are completely absent. (5)
For example, Denton provides a chart showing the percent of sequence divergence of a specific cytochrome C protein between a bacteria and a wide variety of eukaryotic organisms (organisms whose cells possess a nucleus). (6) Bacteria do not possess a nucleus, whereas all other organisms have a nucleus, hence they are two fundamentally different types of organisms.