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.

That kind of lab work is so boring that we knew we wouldn’t survive it for long. We gravitated from the third flood of Coker Hall, where the young guns were forging ahead with all the new tech that they could get, upstairs to the fourth floor where the crusty old guard had their classical collections of specimens. That’s when we got into paleobotany.

We did a quick search on of our molecular lab professor Mark Chase, and we found this abstract from 2003 which summarizes 10 years of progress and ironically uses the phrase “tree of life“.


Over the past decade, botanists have produced several thousand phylogenetic analyses based on molecular data, with particular emphasis on sequencing rbcL, the plastid gene encoding the large subunit of Rubisco (ribulose bisphosphate carboxylase). Because phylogenetic trees retrieved from the three plant genomes (plastid, nuclear and mitochondrial) have been highly congruent, the ‘Angiosperm Phylogeny Group’ has used these DNA-based phylogenetic trees to reclassify all families of flowering plants. However, in addition to taxonomy, these major phylogenetic efforts have also helped to define strategies to reconstruct the ‘tree of life’, and have revealed the size of the ancestral plant genome, uncovered potential candidates for the ancestral flower, identified molecular living fossils, and linked the rate of neutral substitutions with species diversity. With an increased interest in DNA sequencing programmes in non-model organisms, the next decade will hopefully see these phylogenetic findings integrated into new genetic syntheses, from genomes to taxa.

– Mark Chase, A decade of progress in plant molecular phylogenetics

Phylogenetic analysis is only a description of the evolutionary relationships between organisms if you choose to believe that organisms evolved. This is called circular reasoning, or bootstrapping.

However, according to the currently accepted definition of evolution, it’s not evolution at all, it’s abiogenesis. Phylogenetic analysis reveals the systematic way in which God created terrestrial plants on the third day, fish and birds on the fifth day, and terrestrial animals on the sixth day. This is wisdom. This is understanding.

Archaeopteris and Devolution – Navigation

1Archaeopteris and DevolutionJeremiah 21:8
2Evolution Theory vs. Process1 Corinthians 1:19
Induction vs. DeductionTitus 3:9
3Cladistics and Circular Reasoning2 Corinthians 10:4-5
Coding a Character State MatrixLeviticus 19:36
A Phylogenetic Tree of LifeProverbs 4:5-7
What’s a Tarheel?Isaiah 29:14
Archaeopteris1 Timothy 6:20
Archaeopteris (1991) Term Paper(Further reading)
4Spherogenetic SystematicsEzekiel 38:20
Carl LinnaeusLuke 12:27
SalvationRomans 10:9-10
– Navigate your way around Archaeopteris and Devolution.

August 9th – Archaeopteris and Devolution

If we were created fully formed, then this should be coded as the ancestral or primitive state in a character state matrix for phylogenetic analysis.

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