Just balances, just weights, a just ephah, and a just hin, shall ye have: I am the LORD your God, which brought you out of the land of Egypt.(Leviticus 19:36) KJV
When you use a computer to analyze data it has to be coded in a form that the computer can understand. This is where personal bias and circular reasoning starts: not in the analysis, in the coding.
When it comes to specimens of fossilized plants, animals or human remains we have to describe them to the computer in a way that the computer can work with. The simplest computer language is binary. Every entry has to be either a  or , it’s the basis of how computers work.
If we want a computer to analyze human skulls and give us an output which shows us how they compare to each other, then we have to encode each specimen as a series of characters in a binary matrix. This is called a character state matrix. The computer can’t tell us how the specimens relate to each other until after we’ve coded our matrix. A character could be something like the size of the cranium. The character state is: large or small? The bias is, which state is primitive  and which state is advanced ? The difference between what we code as  and what we code as  is based our belief about the relationships between the specimens.
A good example of how personal bias affects cladistic phylogenetic analysis is the supposed evolution of the Hominid series. How are we going to code data if we believe in the evolutionary origin of humanity?
If we believe that humans evolved then we’re going to encode the skull of Homo sapiens as the advanced state: . Anything else is less advanced and so it will have an increasing number of s in the character state matrix depending on how primitive we think it is. Our decision about how to code the specimens is based on our belief that humans evolved. The output from the computer is going to be that humans evolved. In computer lingo it’s called garbage in = garbage out.
If, on the other hand, we believe that humans were created, then Homo sapiens is the ancestral condition and would be coded . Everything else, including the Neanderthal, is derived from it because of how human groups split up and spread out after the tower of Babel. As such, our character state matrix will be the exact opposite of the one coded by someone who believes that we evolved. The computer will give us an output confirming our hypothesis that H. sapiens is the ancestral state.
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