phylogenetic – The Naked Prophet

August 10, 2021August 10, 2021

Sharks and Bony Fish

So God created great sea creatures and every living thing that moves, with which the waters abounded, according to their kind, and every winged bird according to its kind. And God saw that it was good. And God blessed them, saying, “Be fruitful and multiply, and fill the waters in the seas, and let birds multiply on the earth.”
(Genesis 1:21-22) NKJV

Sedimentary deposits containing sharks and bony fish can be assigned to the Mississippian because of how the evolution narrative, of development from primitive to advanced, overlays with the geological timescale.

August 9, 2021August 9, 2021

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.

August 7, 2021

Diversification of Vascular Plants

And for this cause God shall send them strong delusion, that they should believe a lie: That they all might be damned who believed not the truth, but had pleasure in unrighteousness.
(2 Thessalonians 2:11-12) KJV

“Diversification of vascular plants: all major groups except flowering plants present by end of Devonian“. This demonstrates how inductive reasoning is used to account for evidence.

May 20, 2021July 19, 2021

Fish Or Whale?

May 20

Now the LORD had prepared a great fish to swallow up Jonah. And Jonah was in the belly of the fish three days and three nights.
(Jonah 1:17) KJV

For as Jonas was three days and three nights in the whale’s belly; so shall the Son of man be three days and three nights in the heart of the earth,
(Matthew 12:40) KJV

Was Jonah in the belly of a fish or a whale? Is this a contradiction in scripture? Unbelievers hoot with delight at contradictions in scripture because a whale isn’t a fish. Or is it?

May 3, 2021July 20, 2021

Bats are Birds

May 3

“And these you shall detest among the birds; they shall not be eaten; they are detestable: the eagle, the bearded vulture, the black vulture, the kite, the falcon of any kind, every raven of any kind, the ostrich, the nighthawk, the sea gull, the hawk of any kind, the little owl, the cormorant, the short-eared owl, the barn owl, the tawny owl, the carrion vulture, the stork, the heron of any kind, the hoopoe, and the bat.
(Leviticus 11:13-19) ESV

People have found some ingenious reasons to reject the truth of the Bible. There are some others which aren’t ingenious, not by a long shot.

March 16, 2021March 16, 2021

The Fish’s Belly

Then Jonah prayed unto the LORD his God out of the fish’s belly, And said, I cried by reason of mine affliction unto the LORD, and he heard me; out of the belly of hell cried I, and thou heardest my voice.
(Jonah 2:1-2) KJV

Jonah woke up in a dark, cramped, smelly, moist place not knowing where he was. He’d been resurrected after a harrowing experience in the interior of the Earth. That’s not the only thing that’s odd about this verse.

September 3, 2020September 3, 2021

Species Concepts

(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

Understanding how the process of evolution incorporates into the creation narrative solves a lot of issues, not the least of which is the potential space problem on Noah’s ark.

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.