Tree of Life

Viruses

Viruses are by far the most abundant biological entities on Earth and they outnumber all the others put together. "The origins of viruses in the evolutionary history of life are unclear: some may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria." [2] "However, plasmids, like viruses, are not generally classified as life." [3] "A virus is a small infectious agent that replicates only inside the living cells of other organisms. Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea." [2] Scientists debate whether viruses are "organisms at the edge of life” even though they replicate and contain DNA/RNA. So in the above tree diagram, viruses are included by inference because they exist in all living cells of the three main divisions of life but, remember, are not included in most evolutionary tree of life diagrams, even though viruses outnumber all life forms combined; bacteria, archaea and eukaryote. The Tree of Life Web Project acknowledges viruses with a question mark in its diagram shown below:

The Tree of Life Web Project acknowledges, "The rooting of the Tree of Life, and the relationships of the major lineages, are controversial. The monophyly of Archaea is uncertain, and recent evidence for ancient lateral transfers of genes indicates that a highly complex model is needed to adequately represent the phylogenetic relationships among the major lineages of Life." The UCMP Phylogeny Wing explains, "A fourth group of biological entities, the viruses, are not organisms in the same sense that eukaryotes, archaeans, and bacteria are. However, they are of considerable biological importance."

Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more bacteriophages on the planet than every other organism on earth, including bacteria, combined and have been around for 3 billion years according to evolutionists. [4]

The Controversy

While most articles on the three domains give the impression this is a canonical belief among evolutionists, the fact is, not everyone accepts this classification. Classifying organisms has had a rich history of controversy, i.e., the Cuvier-Geoffroy debate (form vs function). [18] The classification of all living organisms into three domains is not without controversy, some scientists support a two domain classification. [19] Some biologists include the protista and fungi, i.e., Whittaker's five kingdoms. Explaining further about the controversy, one authority states, "a great deal of additional work has been done to resolve relationships within the Eukaryota. It now appears that most of the biological diversity of eukaryotes lies among the protists, and many scientists feel it is just as inappropriate to lump all protists into a single kingdom as it was to group all prokaryotes. Although many revised systems have been proposed, no single one of them has yet gained a wide acceptance." [12] Carl Zimmer, writing in National Geographic, writes that most experts favor the two-doman tree proposed by Martin Embley of the University of Newcastle and his colleagues., quoting James McInerney of the National University of Ireland as stating, “I’m pretty sure that the three domain hypothesis has been falsified.” [13][19] Even with the controversy, a $5.76 million grant from the U.S. National Science Foundation to create the Open Tree of Life is now an open source project. [14]

There is a "a great deal of heated debate between pheneticists and cladists, as both methods were initially proposed to resolve evolutionary relationships." Phenetics, Today, Wikipedia

An even more controversial subject is how life began from non living matter.

“The transition from non-living to living entities was not a single event, but a gradual process of increasing complexity that involved molecular self-replication, self-assembly, autocatalysis and cell membranes.” [5] This transition from non-living to living entities took place in a relative short period of time after the earth was born according to the evolutionists, when you consider the age of the earth and how long bacteria has been around.

Timeline for the Origin of Life

According to evolutionists, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats, forming a biomass which exceeds that of all plants and animals. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life and may play roles in both the carbon cycle and the nitrogen cycle and are also part of the human microbiota, found in the colon, mouth, and skin. "Although probable prokaryotic cell fossils date to almost 3.5 billion years ago, most prokaryotes do not have distinctive morphologies and fossil shapes cannot be used to identify them as archaea....Since the Archaea and Bacteria are no more related to each other than they are to eukaryotes, the term prokaryote's only surviving meaning is 'not a eukaryote', limiting its value." [6]

Eukaryotes represent a tiny minority of all living things.[8] However, due to their generally much larger size, their collective worldwide biomass is estimated to be about equal to that of prokaryotes. Eukaryotes evolved approximately 1.6–2.1 billion years ago, during the Proterozoic eon. ]7]

The age of the universe is generally accepted at 13.8 billion years, while the age of the earth is generally accepted to be 4.5 billion years. [8]

The last universal common ancestor (LUCA) "is estimated to have lived some 3.5 to 3.8 billion years ago in the Paleoarchean era, a few hundred million years after the earliest evidence of life on Earth,"

To simplify this timeline the following football field of 100 yards represents the age of the earth with the red H representing the birth of the planet, and the yellow V as the present day, with the timeline of 4.5 billion years. Each yard on this field equals 45,000,000 years (five yards equals 225 million years, ten yards equals 450 million years).

The LUCA (blue L) would be placed on this timeline around the ten yard line near the red H with the prokaryotes showing up immediately following. The eukaryotes show up in the timeline around the 45 yard line on the yellow V side of the field. Therefore, according to the evolutionists life emerged rather quickly over a period of about 500 million years after the birth of the earth.

The vertebrates show up during the timeline in the Cambrian period which is just shy of the ten yard line which is known as the 'Cambrian Explosion' that "produced the first representatives of all modern animal phyla." [9]

All three divisions of life have extant organisms living today that are represented in the fossil record which is a timeline written in stone, a more reliable time line than any other. Some of the life forms found in the fossil record show extinct life forms, but many ancient life forms of plants and animals are extant and look exactly like those shown in the fossil record and are said to be billions of years old because the bacteria found in the fossil record are extant today. The tree diagram on this page [Wikimedia Commons Neomuratree.svg] at Wikipedia depicts how archea and eukarya are more closely related to each other than to bacteria. Of course, there is no fossil record of the LUCA ever found, so it is presumed to have existed. Microbial mat fossils have been found in 3.48 billion-year-old sandstone from Western Australia, while biogenic graphite has been found in 3.7 billion-year-old metamorphized sedimentary rocks from Western Greenland. Recent studies have tentatively proposed evidence of life as early as 4.28 billion years ago. [10]

Why No Transitional Fossils?

A fundamental central thesis of evolution is the assumption of the descent of all living species from a common ancestor depicted in many of the published evolution tree of life diagrams. Usually the reason proposed by evolutionists why there are no fossil records of the transitions from the LUCA to the three major domains, not to mention the major transitions from fish to amphibian to reptile to birds and mammals, are simply excuses, since evolutionists point out they have evidence of bacteria fossils that are nearly 4 billion years old. Why are there no transitional fossils during this 4 billion year record? Evolutionists quickly point to the bacteria fossils as evidence of evolution. There are fossils in the Cambrian period of soft bodies like jellyfish, coprolites, earthworms, flatworms, priapulids, flowers, plants, and the list goes on. Why are there not any fossils before or during the Cambrian period indicating transitions? Why the Cambrian Explosion? The missing transitional fossils are the proverbial missing link. The fossil record simply does not indicate proof of the central concept of evoluton that all three domains of life originated from a common ancestor.

Tree of Life Ladder

The tree of life diagrams that evolutionists use illustrate 'a ladder-like progression from lower into higher forms of life.' i.e., LUCA > Prokarya and Eukarya [see Figure 2] and a typical tree diagram shown below [Figure 5] in a biology textbook shows this lower to higher forms of life:

The diagram above [Figure 5] shows a timeline starting at 550 mya to the fossils of mammals and birds, 400 million years, which is shown on the Figure 4 football field diagram in the yellow line from the eleven yard line to the three yard line. During these 400 million years there are no transitional fossils between these major life forms. Why are these transitional fossils missing? When a timeline is written in stone, the record stands out and speaks for itself. Another tree diagram example is below [Figure 6]:

When you look at the above tree [Figure 6] it is assumed that the branches and leaves connected to the trunk extends its roots to the eukaryote which shows up in the fossil record in Figure 4 near the 45 yard line (yellow side of the football field) without any fossil transitions connecting to the LUCA. Some transitional fossils may be proposed but they are debated by scientists whether they are the transitions hoped for. There is no consensus among evolutionists on how the fossil record supports the central fundamental assumption of the descent of all living species from a common ancestor. The only consensus among evolutionists is the belief in the LUCA, without any evidence to support this belief using the fossil record. In fact, the fossil record supports the conclusion that life forms emerge from non living matter independently and completely separate from previous life forms. If evolutionists accept the concept of abiogenesis [5] with the LUCA, why couldn't this happen with all major organism taxa?

Indeed, a New York Times Magazine article, states, "The tree of life is not a tree." This article is about Carl Woese who is famous for defining the archaea and pioneered the work of molecular phylogenetics which Woese described in 1969 as an 'internal fossil record' and together with Charles E. Fox redrew the taxonomic tree into the three-domain system, based on phylogenetic relationships rather than obvious morphological similarities. The result of all this after many years of studying horizontal gene transfer is an unusual tree diagram [Figure 7] shown below:

Abiogenesis

The deeper issue to the fundamental central thesis of evolution and the assumption of the descent of all living species from a common ancestor is whether the LUCA originates from abiogenesis and what causes abiogensis? If evolutionists believe that the LUCA orginated not on earth but somewhere in outer space, then you push this deeper issue so farther out that is beyond the reach of any scientific method to analyze. One article on this subject states, "some scientists contend that abiogenesis was unnecessary, suggesting instead that life was introduced on Earth via collision with an extraterrestrial object harbouring living organisms, such as a meteorite carrying single-celled organisms; the hypothetical migration of life to Earth is known as panspermia." [11]. It is of interest to note, that while three nucleobases (adenine, guanine and uracil) have been discovered on meteorites, cytosine and thymine have not. Does it really make any sense to speculate that the five known nucleobases must have originated from outer space when all five exist on planet earth without any doubt? What caused the abiogenesis to occur way out in outer space?

If the abiogensis of the LUCA originated here on planet earth what caused this to occur? And what evidence is there that this cannot happen again and again with different life forms? In one article on abiogenesis it states, "Some scientists have proposed that abiogenesis occurred more than once." [11] Why does the evolutionist phylogenetic tree of life always assume a common ancestor? Why couldn't there be multiple trees of life? Is it because the evolutionists can't see the forest for the trees?

A Forest of Trees of Life

There are many biologists and scientists who have a forest of trees showing where life originated, i.e., example below [Figure 8]:

Morphology vs Phylogeny

The classification of living forms of life has been around a long time, as well as debated on how this should be done. For a long time morphology was king when it came to classifying life forms. In 1977 when Carl Woese defined the archaea, creating a new domain of life using phylogenetic taxonomy of 16S ribosomal RNA, phylogeny has now become the king when it comes to classifying life forms due to the evolutionary assumption of the descent of all living species from a common ancestor which is the motive behind phylogeny. The definition of phylogeny presupposes evolution. [15] Nevertheless, morphology is still a basic scientific concept widely accepted and evolution is not presupposed in its definition. [16] You can clearly see how phylogeny has influenced the taxa. In its article on taxonomy, Wikipedia states:

"Taxonomy is the identification, naming and classification of organisms. It is usually richly informed by phylogenetics, but remains a methodologically and logically distinct discipline. The degree to which taxonomies depend on phylogenies (or classification depends on evolutionary development) differs depending on the school of taxonomy: phenetics ignores phylogeny altogether, trying to represent the similarity between organisms instead; cladistics (phylogenetic systematics) tries to reproduce phylogeny in its classification without loss of information; evolutionary taxonomy tries to find a compromise between them."

"In biology, phenetics (Greek: phainein - to appear) /fɪˈnɛtɪks/, also known as taximetrics, is an attempt to classify organisms based on overall similarity, usually in morphology or other observable traits, regardless of their phylogeny or evolutionary relation....Phenetics has largely been superseded by cladistics for research into evolutionary relationships among species." Phenetics, Wikipedia

Cladistics (/kləˈdɪstɪks/, from Greek κλάδος, cládos, "branch") is an approach to biological classification in which organisms are categorized in groups ("clades") based on the most recent common ancestor. Wikipedia

Yale University, explains, "Remember, 'phylogenetic relationship' refers not to the similarities and differences among organisms, but to the relative times that they shared common ancestors in the past." [17]

From the above, you can see that originally morphology (or phenetics) does not assume evolution as the motive for the classification of life and still is a valid scientific method, while plylogeny (or cladistics) does assume evolution as the motive for the classification. Assuming evolution happened with the belief that all life springs from a common ancestor continues to influence the drawing of the tree of life diagrams into so many variations that continue to cause debates among the scientific evolution community.

Trees of Life

While the first tree of life is mentioned at Genesis 2:9, the last book mentions trees of life at Revelation 22:2.

End Notes

[1] Tree of Life, Wikipedia

Darwin and the Tree of Life: the roots of the evolutionary tree, Nils Petter Hellstrom, Archives of natural history 39.2 (2012): 234–252 Edinburgh University Press

[2] Virus, Wikipedia

[3] Plasmid, Wikipedia

[4] Bacteriophage Evolution and the Role of Phages in Host Evolution, Robert W. Hendrix, ASM Science

[5] Abiogenesis, Wikipedia

[6] Archea, Wikipedia

[7] Eukaryote, Wikipedia

[8] WYHAT (see end notes 3 and 4)

[9] Cambrian, Wikipedia

[10] LUCA, Wikipedia

[11] Abiogenesis, Encyclopedia Britannica

[12] UCMP Phylogeny Wing

[13] Redrawing the Tree of Life, Carl Zimmer, Science and Innovation, The Loom, National Geographic, December 2012

[14] "Synthesis of Phylogeny and Taxonomy Into a Comprehensive Tree of Life," C. Hinchliff et al. Proceedings of the National Academy of Sciences (PNAS Sept. 18, 2015. DOI: 10. 1073/pnas.1423041112, ‘TREE OF LIFE’ FOR 2.3 MILLION SPECIES RELEASED

[5] Phylogeny is another word for "phylogenetics," the study of evolution, diversity, and the way different organisms and species are related to each other. The German biologist Ernst Heinrich Haeckel was the first to use the word phylogeny, in 1866, and Darwin used it soon after. It combines the Greek phylos, "race," with geneia, "origin."

Phylogeny, or phylogenetics, is the study of the evolutionary development of organisms and relationships between them. vocabulary.com

Whats the difference between taxonomy, binomial nomenclature, and phylogeny?, Socratic

[16] Morphology is "the branch of biology that deals with the structure of animals and plants." vocabulary.com

Morphology is a branch of life science dealing with the study of gross structure of an organism or taxon and its component parts. Wikipedia

[17] What is a Phylogenetic Relationship?, Travels in the Great Tree of Life, Peabody Museum of Natural History, Yale University

[18] Wikipedia comments that "Geoffroy's philosophy is seen as early support of evolution theory and parts of the theory of the "unity of composition" are generally more accepted over Cuvier's fixed species philosophy." However, Valerie Racine, in her essay, The Cuvier-Geoffroy Debate (The Embryo Project Encyclopedia), states, "Historical interpretations of the debate, including E.S. Russell’s Form and Function (1917), often stress the divergence between Cuvier’s teleological or functional approach to comparative anatomy and Geoffroy’s emphasis on morphology......Cuvier was dismissive of the issue [the possibility of the transformation of species, i.e. evolution] as he tended to view it as merely another problematic corollary of Geoffroy’s penchant for unbridled theorizing." This debate took place 29 years before Darwin's book, Origen of Species was published. Racine comments, "It was evident, to Cuvier, that nature was purposeful in its designs." Racine further comments, "Geoffroy’s pre-Darwinian understanding of the similarities in the connection of anatomical features in different species did not assume common descent." It should be noted that Geoffroy's emphasis on 'analogues' (evolutionists refer to as 'homology') was to establish this new concept as a doctrine or a philosophy. Racine clearly points out that Geoffroy's focus was "the philosophical and methodological implications of their divergent views, declaring in his [Geoffroy's] memoir: 'It is a question of philosophy that divides us.' " Racine comments that Geoffroy's principle of unity of composition, the theory of analogies, the theory of arrests of development and the search for homologies "reflected a particular metaphysical view of life and a philosophy of anatomy." Evolutionists align themselves with Geoffroy.

[19] "As early as 2010, the major competitor to the three domains scenario for the origin of eukaryotes was the "two domains" (2D) scenario, in which eukaryotes emerged from within the archaea. A 2016 study supports the 2D view. Its "new view of the tree of life" shows eukaryotes as a small group nested within Archaea, in particular within the TACK superphylum. However, the origin of eukaryotes remains unresolved, and the two domain and three domain scenarios remain viable hypotheses" Neomura, Two Domain View, Wikipedia