August 09 – The Naked Prophet

August 9, 2020May 2, 2022

Spherogenetic Systematics

So that the fishes of the sea, and the fowls of the heaven, and the beasts of the field, and all creeping things that creep upon the earth, and all the men that are upon the face of the earth, shall shake at my presence, and the mountains shall be thrown down, and the steep places shall fall, and every wall shall fall to the ground.
(Ezekiel 38:20) KJV

In the book of Jonah it’s said that the Lord prepared a great fish to swallow up Jonah. In the book of Matthew, Jesus describes Jonah spending three days and three nights in the belly of a whale. Is this a problem?

August 9, 2020August 9, 2021

Carl Linnaeus

Consider the lilies, how they grow: they neither toil nor spin; and yet I say to you, even Solomon in all his glory was not arrayed like one of these.
(Luke 12:27) NKJV

The classification of plants animals and minerals is called taxonomy or systematics. Our scientific background is plant systematics. The modern age of systematics is based on comparing DNA sequences.

August 9, 2020May 2, 2022

Coding a Character State Matrix

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.

August 9, 2020March 1, 2021

A Phylogenetic Tree of Life

Get wisdom! Get understanding! Do not forget, nor turn away from the words of my mouth. Do not forsake her, and she will preserve you; Love her, and she will keep you. Wisdom is the principal thing; Therefore get wisdom. And in all your getting, get understanding.
(Proverbs 4:5-7) NKJV

Back in the early days of DNA sequencing in systematics, when PCR machines (polymerase chain reaction) were cool new toys, the data was fragmentary. We were a grad student in one of the molecular labs sequencing plant DNA.

August 9, 2020May 2, 2022

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?

August 9, 2020May 17, 2022

Induction vs. Deduction

But avoid foolish questions, and genealogies, and contentions, and strivings about the law; for they are unprofitable and vain.
(Titus 3:9) KJV

In the scientific method there’s a lot philosophy involved in constructing a logical framework which should produce an experimental result which is free from bias.

August 9, 2020August 9, 2020

What’s a Tarheel?

And the Lord said:
“Because this people draw near with their mouth
and honor me with their lips,
while their hearts are far from me,
and their fear of me is a commandment taught by men,
therefore, behold, I will again
do wonderful things with this people,
with wonder upon wonder;
and the wisdom of their wise men shall perish,
and the discernment of their discerning men shall be hidden.”
(Isaiah 29:13-14) NKJV

In the fall of 1990 we began the graduate program in Plant Biology at the University of North Carolina at Chapel Hill. On our first day we were shown around Coker Hall by a senior graduate student, Victor Albert.

August 9, 2018August 9, 2021

August 9th

Archaeopteris and Devolution

“Now you shall say to this people, ‘Thus says the LORD: “Behold, I set before you the way of life and the way of death.
(Jeremiah 21:8) NKJV

We (me and the Holy Spirit) didn’t realize it at the time, but the first nail we hammered into the coffin lid of our scientific career was a paper about using cladistic phylogenetic analysis to study the fossil Archaeopteris.

July 29, 2018September 21, 2021

Archaeopteris

O Timothy! Guard what was committed to your trust, avoiding the profane and idle babblings and contradictions of what is falsely called knowledge—by professing it some have strayed concerning the faith. Grace be with you. Amen.
(1 Timothy 6:20-21) NKJV

We’re critical of the philosophical construction of the scientific method because it’s been meticulously crafted to exclude any possibility that the truth can be either an acceptable premise, or a possible conclusion.

October 21, 2016May 19, 2022

Archaeopteris (Dawson): A case study in the applicability of phylogenetic analysis to fossil taxa

We didn’t realize it at the time, but the first nail we hammered into the lid on the coffin of our scientific career was a paper that we wrote about using cladistic phylogenetic analysis to study the Devonian fossil Archaeopteris.