Cladistics and Circular Reasoning

(For the weapons of our warfare are not carnal, but mighty through God to the pulling down of strong holds;) Casting down imaginations, and every high thing that exalteth itself against the knowledge of God, and bringing into captivity every thought to the obedience of Christ;

(2 Corinthians 10:4-5) KJV

Despite the rigorous application of philosophical ploys to guard against circular reasoning in cladistic analysis it’s a poster boy for circular reasoning because it’s based in a paradigm which is the result of personal bias. In this case the personal bias is: do you love or hate God?

The development and use of cladistic phylogenetic analysis (CPA) is something that we have personal experience with. We learned CPA using parsimony at Duke in 1991. We’ve posted a link to our term paper where we attempted to apply the technique to the fossil taxa Archaeopteris. We learned a lot which we didn’t fully understand until recently.

We can say that a whale isn’t a fish if we use a phylogenetic system of classification. However, we’ve pointed out that God’s process of creating, though systematic, wasn’t phylogenetic. Phylogenetic is based on changes at the genetic level which are passed from generation to generation. The taxa being analyzed must be related through ancestry and descent. However, there were no successive generations of offspring in the creative process. God created sequentially more complex iterations of beings.

What we learned is a version of the old computer programming adage: garbage in = garbage out. A computer, no matter how sophisticated, only knows what you tell it. If we want to use a computer to analyze specimens of some kind then the specimen has to be described to the computer in a way that it can understand. For simplicity this is a binary matrix. The idea is that we can identify groups of organisms based on their shared derived characteristics and then code these as a binary matrix from which the computer plots a tree. It’s surprisingly simple, but it immediately butts up against this reality: we’re going to code the matrix according to what we already believe about the organisms.

Here are some direct quotes from our paper in 1991:

• … representing this variation as a series of species concepts is highly misleading.
• … a barrier to phylogenetic analysis is the poignant lack of character data.
• … this has become a case of using parsimony to do phenetic (not phylogenetic) analysis.

Our conclusion was that a computer can only give you a restatement of the hypothesis that you used to code your character state matrix. That means that if you assume that the taxa in the study are the product of evolution, the computer will show you how they evolved.

Archaeopteris and Devolution – Navigation

Section	Title	Scripture
1	Archaeopteris and Devolution	Jeremiah 21:8
	What’s a Tarheel?	Isaiah 29:14
2	Archaeopteris	1 Timothy 6:20
	Archaeopteris (1991) Term Paper	(Further reading)
3	Carl Linnaeus	Luke 12:27
	Salvation	Romans 10:9-10

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