Round and Round We Go—Proposed Evolutionary Relationships Among Archaea, Eubacteria, and Eukarya

by Dr. Georgia Purdom on October 4, 2006

Many scientists are desperate to find evidence to support their theory or to make the current evidence fit their theory rather than admitting their theory is wrong.

The following quote from a recent review article on this topic sums up the status of evolutionary thought in this field.

There are no obvious precursor structures known among prokaryotes from which such attributes [eukaryotic flagella, Golgi, endoplasmic reticulum, etc.] could be derived, and no intermediate cell types known that would guide a gradual evolutionary inference between the prokaryotic and eukaryotic state. Accordingly, thoughts on the topic are diverse, and new suggestions appear faster than old ones can be tested.1

Even with that being said, scientists spend pages and pages of scientific journals discussing the possibilities of eukaryotic (protists, fungi, plants, animals and humans) origins from the combination of “simple” eubacteria (true bacteria or prokaryotes) and archaea (bacteria-like organisms that live in extreme environments). Many of these scientists are desperate to find evidence to support their theory or to make the current evidence fit their theory rather than admitting their theory is wrong.

Archaea—common ancestor of life?

For many years scientists believed there were only two domains of life: eubacteria and eukaryotes. One of the major distinguishing characteristics between these two groups was the absence of nuclei in eubacteria. In 1977 Carl Woese first identified what he called a third domain of life, one based on ribosomal RNA sequence comparisons (ribosomes are the protein-making factories of the cell).2 The archaea do not have a nucleus, like eubacteria, but tend to live in more extreme environments such as hot springs and extremely saline environments.3 Scientists believed such extreme environments were present on the early earth, which is why these organisms were named archaea.3

Their extreme habitats and bacteria-like nature led many to believe that archaea was a candidate for a common ancestor of eubacteria and eukarya. However, further analyses of archaea showed them to be genetically and biochemically quite different from eubacteria; thus, they are no longer believed to be an ancestor of eubacteria. Archaea are actually more genetically similar to eukaryotes than eubacteria and are often represented as a “sister” to eukarya on evolutionary trees of life.4

Ring of life

Which came first—archea, eubacteria or eukaryotes?

The problem comes down to which came first. The archaea genome is described as a combination of operational (metabolic) genes from eubacteria and informational (RNA-forming, protein-making, etc.) genes from eukaryotes.3 The eukaryotic genome is described as a combination of operational genes from eubacteria and informational genes from archea.1 Which came first—archea, eubacteria or eukaryotes? The problem was claimed to be at least partially solved in 2004 when a Nature article first described the “ring of life.”5 A ring has no beginning or end and so the problem of which came first is lessened. The authors believe that archea and eubacteria may have been involved in a symbiotic (mutually beneficial) relationship that eventually led to endosymbiosis. Endosymbiosis is a process in which one organism engulfs its symbiont but does not digest it. According to this view, the genomes of both organisms eventually fused, possibly via lateral gene transfer (genetic swapping between genomes). In addition to other proposed endosymbiotic events, like those giving rise to the mitochondria and plastids, the eukaryotes were formed. The authors published what they believed was genetic evidence demonstrating the origin of eukaryotes.

But just because archea, eubacteria and eukaryotes have genome similarities is not necessarily evidence that they evolved from each other. It depends on your starting point—belief in a common ancestor or belief in a common designer. In fact, even Nature magazine refuses to give the ring of life or other similar theories their vote of confidence: “To this day, biologists cannot agree on how often lateral gene transfer and endosymbiosis have occurred in life’s history; how significant either is for genome evolution; or how to deal with them mathematically in the process of reconstructing evolutionary trees.’6 Regardless of the lack of evidence, the editorial boards of most scientific journals believe that life evolved from a simple, common ancestor, so they publish articles that supposedly support their beliefs.


Scientists involved in this area of research seem to have more questions than answers. The articles they publish are riddled with words and phrases like “unknown,” “obscure,” “uncertain,” “far more complicated” and “fraught with difficulties.” One review article summarized it this way:

The available phylogenetic findings from genomes are not fully consistent with any current hypothesis for eukaryote origins, the underlying reasons for which—biological, methodological or both—are as yet unclear. Genomes must truly bear some testimony to eukaryotic origins, but new approaches and more rigorous attention to the details of phylogenetic inference will be required to decipher the message.1 (emphasis added)

The genomes of eukaryotes (and archea and eubacteria) bear testimony to the Creator God as their Designer, and only when one uses the Bible as the foundation can the message be properly deciphered.


  1. T. Martin Embley and William Martin, “Eukaryotic Evolution, Changes and Challenges,” Nature 440 (March 30, 2006): 623–630, doi:10.1038/nature04546.
  2. Carl R. Woese and George E. Fox, “Phylogenetic Structure of the Prokaryotic Domain: The Primary Kingdoms,” Proceedings of the National Academy of Sciences USA 74, no. 11 (November 1977): 5088–5090,
  3. Thorsten Allers and Moshe Mevarech, “Archaeal Genetics—the Third Way,” Nature Reviews Genetics 6, no. 1 (January 2005): 58–73, doi:10.1038/nrg1504.
  4. Carl R. Woese, Otto Kandler, and Mark L. Wheelis, “Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya,” Proceedings of the National Academy of Sciences USA 87 (June 1990): 4576–4579,
  5. Maria Rivera and James Lake, “The Ring of Life Provides Evidence for a Genome Fusion Origin of Eukaryotes,” Nature 431 (September 9, 2004): 152–155, doi:10.1038/nature02848.
  6. William Martin and T. Martin Embley, “Evolutionary Biology: Early Evolution Comes Full Circle,” Nature, 431 (September 9, 2004): 135–137, doi:10.1038/431134a.


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