Anyone who regularly reads this page will know we have been highly critical of phylogenetics as a method of evolutionary proof. We have found it inconsistent, circular, and bereft of the evolutionary explanatory power it pretends to have. Evolutionists have long quibbled over which method of phylogenetics to use and whether phylogenetics needed to assume evolution to work. However, a recent study has begun to question applications of phylogenetics. They do not directly challenge the premise of phylogenetics, but do admit that there are significant issues.
The paper, soon to be published in Nature, does not look specifically at the phylogenetic foundations. Instead, what it looks at is how some phylogenetic trees are used. This is a key distinction. Phylogenetic trees can be used to infer time. These types of phylogenetic trees are called timetrees. These timetrees are essentially drawn to fit the evolutionary time scale. The goal of a timetree is to track the diversification of organisms over time. They are most commonly used in paleontology, as paleontology has no real-time way to track diversification. Instead, they must infer a pathway of diversification over the past time. They are used in other applications in phylogenetics as well, however. When extant organisms are shown on the tree, they all by definition have the same branch lengths.
This recent study throws a monkey wrench into the use of timetrees to interpret fossils or any other diversification. The researchers tested the accuracy of timetrees by looking into the models that generated them. Since we lack much information about both the fossil record and modern organisms rates of speciation and extinct, when researchers attempt to build a time tree, they assume a particular model of evolution to build it. Turns out, using phylogenetics an infinite number of timetrees can be generated, all of which are equally likely. This is a huge problem, because it means that you cannot generate an accurate model of evolution using timetrees. While the author propose a solution to this issue, the solution is largely still dependent on the assumption of evolution.
Phylogenetics has had this problem for a long time. There are large numbers of underlying assumptions which, while some may be accurate, undermine the validity of their results. We’ve dealt with these assumptions previously but it bears repeating here. Phylogenetics assumes a known rate of speciation, which, in most instances, we haven’t got the faintest notion what it is. In fact, science can’t even tell us what a species is, which makes it very difficult to determine rates of speciation. It also assumes you are able to trace differentiation by means of traits. This assumption is wrong because traits can be passed non-linearly due to recessive traits. Also, some traits can be lost with time, due to extinction or just loss of information. Given that phylogenetics assumes no extinctions, it will always be highly unlikely and unrealistic.
Phylogenetics has other issues which are independent of timetrees or any other model The first is character selection. Characters are the traits that the phylogenies are built upon. The problem is, who defines a character? What makes something a character? These questions are fundamental to building any phylogenetic tree and are rarely addressed. Worse, because phylogenies are so character dependent, changing even one or two characters in analysis can return strange results. Of course, unless you’ve personally tested their phylogenetic methods, you won’t know that because they do not report aberrant results and only rarely discuss them in the literature, generally to point out that their method is better than their rival’s method.
Character selection is not the only issue. Phylogenetic methods are grossly contradictory. One method will claim one line of ancestry, while another will claim another based on the same data. No wonder the evolutionists are constantly revising their timelines. The timelines are derived from phylogenetic timetrees which are constantly being revised by methods using the same data and coming to different conclusions.
While it is encouraging to see the evolutionists challenge phylogenetics in public, no creationist should get their hopes up that the evolutionists will give up using the method. That is not going to happen. Phylogenetics is far too useful to them. Despite the fact that the method is simply unworkable, evolutionists will continue to use it as long as it gives them the results they want.
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