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History of the Tree of Biological Life

Oak tree against the sky Image by Momentmal from Pixabay

[Excerpted from Darwin’s Tree Got Tangled. What Happened?]


Aristotle,Marble bust of Aristotle the 4th century B.C. Greek philosopher, is credited as the first to begin systematically ranking species on a “graded scale of perfection”—from simple to complex.

Aristotle’s purpose was to understand nature. Without specifically using the “tree of life” term, his ranking of nearly 500 species was published in his book, the History of Animals.

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His approach, known as natural philosophy, had a powerful and lasting influence on future generations of naturalists. Even though Aristotle did not include any illustrations, diagrams, tables, or graphs in his book, his system of unifying human knowledge set the stage for applying the “tree of life” metaphor to nature.

Logic is the instrument, Aristotle argued, to understand and gain knowledge using a what and why approach. Logical schemes represent the true nature of reality.

Aristotle’s system of logic built a gateway for the emerging theories of evolution—an approach embraced by Darwin. In a letter to his friend William Ogle, Darwin said his “two gods,” Carolus Linnaeus and Georges Cuvier, were “mere schoolboys to old Aristotle.”

“Tree of Life” Logic

In the first century A.D., Porphyry of Tyre, a Roman philosopher from Tyre, advanced Aristotle’s logic by publishing the “scale of being” in the work entitled Isagoge in 268–270 A.D. Porphyry was a defender of Paganism. The Greek manuscript was later translated into Latin in the 6th century by Boëthius, an influential Roman leader.

3 medieval drawings of "scale of life" or "porphyrian trees"Boëthius’s translation emerged as the standard textbook for teaching Aristotelian logic during the Middle Ages—even through to the late 19th century. During this time, Porphyry’s “scale of being” was eventually illustrated by unknown artists into different types of trees. These illustrations (pictured above) are known as the Porphyrian Trees.

In 1745, Swiss naturalist Charles Bonnet is credited as publishing a diagram—although, not a tree—illustrating an organized sequence of nature that was known as the “Great chain of being.”

This diagram demonstrates how Aristotle’s philosophical principles of evolution had already been incorporated into western academic circles more than a century before The Origin of Species was first published in 1859.

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Pre-Darwin “Tree of Life” Logic

Augier Tree of Life drawingThe earliest known biological “tree of life” illustration was of the plant kingdom published by Augustin Augier, a French botanist, in 1801. As a “figure like a genealogical tree,” Augier argued, “appears to be the most proper to grasp the order and gradation” of life. To Aristotle’s what and why logic approach, Augier argued:

It appears, and one can hardly doubt it, that the Creator, when making flowers, followed certain proportions and progressions in the number of their different parts.

Lamarck's chart showing progression and relationship of animal life 1815

Within ten years, Jean-Baptiste Lamarck, a French zoologist, published the first branching tree of animals (pictured left) in his Philosophie Zoologique in 1809. Unlike contemporary colleagues, including Darwin, since Lamarck did not believe in common ancestry, his graphic illustration did not include a trunk.

American geologist Edward Hitchcock published his first tree of life in 1840. The book, entitled Elementary Geology, was based on what he knew about fossils along with his geological observations.Edward Hitchcock two trees of life chart

In the editions published between 1840 and 1859, his “paleontological chart” included two trees (pictured above); one for plants and the other for animals. As a leading advocate of the gap theory, Hitchcock argued:

The gradual introduction of ‘higher races’ is perfectly explained by the changing condition of the earth which is being adapted for more perfect races Divine Wisdom introduced them.

Ironically, even though Hitchcock advanced a “higher races” theory and Darwin argued for the “preservation of favoured races,” Hitchcock opposed applying Darwin’s theory of natural selection to humans.

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Hitchcock was a Congregational pastor and professor of chemistry and natural history at Amherst College, Massachusetts. Subsequent editions of Elementary Geology were published without his once popular “paleontological chart.”

In 1844, Robert Chambers, a Scottish journalist, anonymously published an international best seller entitled the Vestiges of the Natural History of Creation. The book was wildly popular with contemporary radicals, yet, even Prince Albert is reported to have read it to Queen Victoria. The book included a diagram indicating how the evolutionary path of fish, reptiles and birds ascended to the formation of mammals.

By 1859, evolution was as controversial then as politics are today. In the words of Darwin, “evolution was in the air” as the book sales demonstrated. All 1,250 copies of the book released by the publisher were sold on the first day—a publisher’s dream.

Darwin’s Perfect Timing

“It was just enough, in the right form, at the right time,” said Quammen. “It presented the theory as ‘one long argument,’ not with a bare syllogism, and with oodles of data but many footnotes. It was plain spoken, and readable by any literate person.”

“The affinities of all the beings of the same class,” Darwin had argued, “have sometimes been represented by a great tree… all animals of [the] same species are bound together just like buds of plants.”

The Origin of Species gained immediate global recognition. In Darwin’s lifetime, the book was translated into Danish, Dutch, French, German, Hungarian, Italian, Polish, Russian, Serbian, Spanish, and Swedish.

When goodreads, a literary group managed by Amazon, asked members to rate “the most influential books in history,” Darwin’s Origin of Species was rated second only to the King James version of the bible.

The theory gained notoriety, but only as a scientifically untested theory. Not until the biotechnological advances developed in the 20th and early 21st century have scientists had the tools to validate Darwin’s “one long argument” theory.

Molecular Biology Revolution

Biomolecular technologies developed during the 20th century unleashed a revolution in molecular biology. Laboratory equipment, instruments, computer hardware and software, once unimaginable in the 19th century, revolutionized the scientific approach to validate the theory of evolution.

Scientists, since the publication of The Origin of Species, had been searching for the type of evidence that could be tested and re-tested to scientifically validate the theory. Molecular biology is exactly that type of evidence.

DNA Xray, photo credit: NIHIn 1953 while working at the Cavendish Laboratory at the University of CambridgeFrancis Crick, a British molecular biologist using x-ray technology, co-authored the paper proposing that the molecular structure of inheritance was a double helix structure (pictured right).

Subsequent testing quickly validated that the DNA molecule was a double helix structure – as predicted from their objective evidence. For the finding, Crick was jointly awarded the Nobel Prizein 1962. Amazingly, Darwin’s long-standing unsolved mystery – inheritable variations – was finally solved at his alma mater; Cambridge University.

In 1957, Crick presented at the Society for Experimental Biology symposium a revolutionary vision finally linking molecular biology to the secrets driving evolution. Crick explained:

Biologists should realize that before long we shall have a subject which might be called ‘protein taxonomy’ – the study of amino acids sequences of the proteins of an organism [products of DNA and RNA] and the comparison between species … The vast amount of evolutionary history may be hidden away within them.

Linking changes in molecular biology to genetic inheritance is now argued as the primary mechanism driving evolution. Discoveries in the field of molecular biology were anticipated to reveal and retrace the mysterious steps of evolution molecule-by-molecule.

The bet was on. Questions regarding the scientific validity of evolution were anticipated to be finally solved. Giuseppe Sermonti, an Italian geneticist said:

It seemed as though life could be disassembled and reassembled like a child’s blocks.

At a subsequent 1964 symposium at Rutgers UniversityEmile Zuckerkandl along with Francis Crick and Linus Pauling, argued that

the branching of molecular phylogenetic trees should in principle be definable in terms of molecular information alone.

Laboratories in the subsequent decades produced unprecedented scientific breakthroughs. With the accuracy and speed of testing dramatically improving, the rate of new scientific breakthroughs gave rise to the Genomic Revolution.

By the turn of the century, the FDA had approved the safe and effective use of more than 125 genetically engineered drugs in healthcare.

Use of these technologies emerged as a standard of practice in biological science laboratories – and in the laboratories dedicated to studying the theory of evolution. As Quammen noted,

This was a whole new way of sketching those trees which rose and spread their branches as the clock ticked.

Revolutionary Outcome

Towards the end of the 21st century’s first decade, scientists began to evaluate the newly emerging biomolecular data to review the potential implications. Molecular biology was expected to overcome the theories long-lasting scientific issues.

Stephen Jay Gould, an evolution paleontologist at Harvard University and a long-time critic of Darwin’s tree, wrote:

The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils.

By the end of the first decade, since integrating the emerging molecular evidence into the standard theory [known as Neo-Darwinism or Modern Synthesis] was becoming increasingly problematic, The Royal Society invited internationally recognized evolution scientists to a 3-day meeting in November 2016, stating:

Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution, although the issues involved remain hotly contested.

At the conclusion of the contentious meeting, the attendees could not develop a consensus on any revisions. Huffington Post journalist, Suzan Mazur, asked:

Why is it so difficult to pull together the most compelling ideas in evolutionary biology and come up with an approximate understanding of how it all works?

Eugene Koonin,  head of the Evolutionary Genomics Group, National Center for Biotechnology Information, National Institute of Health, noted:

The public is already extremely skeptical about the value and the scientific nature of evolutionary biology… The genomic revolution… effectively overturned the central metaphor of evolutionary biology, the Tree of Life.

After 150 years, evolution theorists seem to have exhausted conceivable natural mechanisms. Lynn Margulis, evolution theorist awarded the National Medal of Science Award, and a long critic of Darwin’s tree, pointed out the problem:

The notion is that if we accumulate enough gene change, enough genetic mutations, we explain the passage from one species to another. This is depicted as two branches in a family tree that emerge from one common ancestor to the two descendants. An entire Anglophone academic tradition of purported evolutionary description was developed quantified, computerized based on what I think is a conceptual topological error.

“The tree of life is an artifact of some early scientific studies that aren’t really holding up… So there is not a tree of life,” noted Craig Venter,  an American biotechnologist, biochemist, geneticist, and businessman known for leading the first draft sequence of the human genome.

Italian geneticist Giuseppe Sermonti explains that a “genealogical tree that shows forms gradually varying and diverging—the ‘fact’ for which Darwinism proposed its revolutionary explanation—is nowhere to be found.” Not surprisingly:

Science has taken on the great wager… and lost.


Beginning in Genesis, the “tree of life” phrase has signified new beginnings prospering in peace and harmony throughout the centuries of human history. The beginning of all that is good originates from the Bible. In using the “tree of life” phrase far removed from it’s original purpose, Darwin’s tree got tangled – and lost. That’s what happened.

Advanced technologies, while continuing to undermine the theory of evolution, continue to generate scientific evidence that is increasingly compatible with the Genesis record written by Moses.

Nicholas Copernicus (1473-1543), a Renaissance mathematician and astronomer, proposed that Earth rotates around the Sun. The theory, known as a heliocentric theory eventually upended the once accepted geocentric model of our solar system commented on our Creator:

To know the mighty works of God, to comprehend His wisdom and majesty and power; to appreciate, in degree, the wonderful workings of His laws, surely all this must be a pleasing and acceptable mode of worship to the Most High, to whom ignorance cannot be more grateful than knowledge.

Biological evolution exists only as a philosophy; not as a scientific fact.

Richard William Nelson

Written by Richard William Nelson

Richard William Nelson earned a Doctor of Pharmacy degree from the University of Southern California following graduation from the University of California, Irvine, with a Bachelor of Science degree in biochemistry. For more than a decade Dr. Nelson has been writing and speaking on the scientific merits of biological evolution. Dr. Nelson has spoken nationally and internationally to audiences in churches, schools, universities, and community organizations. As the author of the book entitled Darwin, Then and Now, The Most Amazing Story in the History of Science using more than 1,000 documented references, Dr. Nelson advocates using the scientific method to assess the merits of the theory of evolution.

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