Reasons to Believe

Why Do Mitochondria Have DNA?

Whenever I speak on university campuses, students challenge me with the endosymbiont hypothesis. This hypothesis is an important facet of the evolutionary paradigm, presumably providing an explanation for the origin of eukaryotic (or complex) cells.

First-year biology students learn about the endosymbiont hypothesis and its attending evidence, and many find it compelling, consequently accepting the evolutionary explanation for the origin, history, and design of life. But even though the evidence for the endosymbiont hypothesis may seem compelling, it is equally reasonable to view eukaryotic cells (and therefore life) as the product of a Creator’s handiwork, as demonstrated by recent work from scientists in the United States and the United Kingdom.1

The Endosymbiont Hypothesis

Evolutionary biologists believe that eukaryotic cells originated through a process known as endosymbiosis (or symbiogenesis). According to this idea, complex cells originated through symbiotic relationships among single-celled microbes when free-living bacterial and/or archaeal cells were engulfed by another microbe. The ingested cells are referred to as endosymbionts.

This theory suggests that organelles, such as mitochondria, were once endosymbionts. Once taken inside the host cell, the endosymbionts presumably established a permanent symbiotic relationship with the host, with one cell growing and dividing inside the other. Over time the endosymbionts (engulfed microbes) and the host became mutually interdependent, with the endosymbionts providing a metabolic benefit for the host cell. Eventually, the host cell evolved the machinery to produce the proteins needed by the endosymbionts and to transport those proteins into their interior.

According to this evolutionary model, the endosymbionts gradually evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from the endosymbionts’ genomes were transferred into the genome of the host organism. During the transformation from endosymbiont into organelle, the genome reduction was extreme. For example, mitochondrial genomes are around 20,000 base pairs in size, encoding about 35 to 40 proteins, while the group of bacteria that biologists think gave rise to mitochondria has a genome of over 1 million base pairs in size.

Evidence for the Endosymbiont Hypothesis

One of the main lines of evidence for the endosymbiont hypothesis is the similarity between organelles and bacteria. For example, mitochondria—which are believed to be descended from a group of bacteria called Rickettsiales—are about the same size and shape as a typical bacterium and have a double membrane structure like Rickettsiales. These organelles also divide in a way that is reminiscent of bacterial cells.

Another piece of evidence for the endosymbiont hypothesis is the presence of DNA in mitochondria. Evolutionary biologists view the existence of the diminutive mitochondrial genome as a vestige of this organelle’s evolutionary history. Additionally, the biochemical similarities between mitochondrial and bacterial genomes are taken as further evidence for the evolutionary origin of these organelles.

The partial genomes of mitochondria could be viewed as transitional in nature. Given more time, some biologists believe the transfer of genes into the host cell’s nucleus will presumably be completed. In support of this view, they point to other organelles such as mitosomes and hydrogenosomes, which completely lack genomes. Apparently, the gene transfer process has reached fruition in these endosymbionts-turned-organelles.

Maintaining organellar genomes is a costly prospect for the host cell. Typically, a couple hundred proteins are needed to support the production of proteins encoded in mitochondrial genomes. This appears to be an unnecessary feature of the cell’s biochemistry because it would be more efficient to produce all the proteins in the cytoplasm and then transport them to the organelles. This inefficiency and waste seemingly supports the evolutionary origin of these organelles.

A Creation Model Perspective on Mitochondria

In spite of the apparent evidence for the endosymbiont hypothesis, it is reasonable to view eukaryotic cells as the work of a Creator. The shared similarities between mitochondria and Rickettsiales, for example, may actually reflect common design rather than common descent.

However, to legitimately interpret mitochondria from a creation model perspective, there must be a rationale for why mitochondria have their own genomes. And recent work by a team of US and UK scientists has proved helpful in providing an explanation.

Why Do Mitochondria Have DNA?

To determine if there is a rationale for mitochondrial genomes, the team of scientists developed an algorithm that would allow them to identify common features in mitochondrial genomes. By surveying over 2,000 mitochondrial genomes representing a wide range of eukaryotic organisms, they discovered three properties that are common to the genes found in these organelles.

1. Proteins encoded by mitochondrial genomes are associated with the organelle’s membranes, consisting of a large number of hydrophobic amino acids. If these proteins were encoded in the nuclear genome and produced in the cytoplasm—instead of the lumen of mitochondria—the proteins would be misdirected to the endoplasmic reticulum (ER) instead of the mitochondria. The cell’s machinery that directs proteins to the ER can’t discriminate between the proteins of the ER and a select number that should be targeted to mitochondria. To avoid misdirection, these proteins must be produced in the interior of mitochondria.2

2. Proteins encoded by mitochondrial genomes form the core components of the electron transport chain (ETC). The ETC is part of an elaborate biochemical operation that takes place in the inner membranes of mitochondria. This process harvests energy for the cell’s usage. Encoding ETC proteins within the mitochondrial genome, instead of the nuclear genome, affords the cell more efficient regulatory control over its energy metabolism than if this process was regulated globally, which would be the case if ETC proteins were encoded within the nuclear genome.

3. Protein-coding genes in mitochondrial genomes have a high GC content (or guanine-cytosine content). The higher the GC content of a region of DNA, the more stable it is. Since the interiors of mitochondria are harsh environments, the greater GC content of mitochondrial genes serves as an elegant design feature, ensuring their durability in the presence of reactive oxygen species that are by-products of energy metabolism.

In other words, there is a rationale for why mitochondria have DNA. An exquisite biochemical logic undergirds the structure and function of mitochondrial genomes. In light of this new insight, it is reasonable to view organelles, such as mitochondria, as the Creator’s handiwork. Like most biological systems, this organelle appears to be designed for a purpose.

Subjects: Design, Bad Designs

Dr. Fazale Rana

In 1999, I left my position in R&D at a Fortune 500 company to join Reasons to Believe because I felt the most important thing I could do as a scientist is to communicate to skeptics and believers alike the powerful scientific evidence—evidence that is being uncovered day after day—for God’s existence and the reliability of Scripture. Read more about Dr. Fazale Rana


  1. Iain G. Johnston and Ben P. Williams, “Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention,” Cell Systems 2 (February 2016): 101–11, doi:10.1016/j.cels.2016.01.013.
  2. I have written about this idea in a previous article: “Mitochondrial Genomes: Evidence for Evolution or Creation?,” Today’s New Reason to Believe (blog), Reasons to Believe, August 27, 2015,