Reasons to Believe

Mitochondrial Genomes: Evidence for Evolution or Creation?

Little kids love to ask, “Why?” So do skeptics; however, their “why” questions aren’t asked to gain insight. Instead, they are rhetorical—posed to highlight inconsistencies between the way the world actually is and the ideal that arises out of the Christian worldview. In this vein, skeptics object to the notion of creation and intelligent design by asking, “If God is responsible for creating life, why are there so many ‘bad designs’ in nature?”

Even though biological systems appear to be designed for a purpose, skeptics are quick to point out features that appear to be cobbled together by evolutionary processes from preexisting structures. They assert that poorly designed systems aren’t what anyone would expect if an all-powerful, all-knowing, and all-benevolent Creator brought life into existence. On the other hand, marginally designed systems—which appear to be kludged together—are exactly what one would assume if evolutionary processes are responsible for life’s origin, history, and design.

One example of intracellular biological structures that seem to be kludged together is organelles, such as mitochondria and chloroplasts. Life scientists point to the genomes found in these organelles as evidence for their evolutionary origin. Each of these subcellular components possesses a small, circular piece of DNA housed within its interior (the lumen). Mitochondrial genomes are around 20,000 base pairs in size, encoding about 35 to 40 proteins. Chloroplast genomes are around 120,000 base pairs in size, encoding between 60 and 100 proteins. For reference, the smallest known genome—found in the bacterium Mycoplasma genitalium—is comprised of about 480,000 genetic letters, specifying around 500 proteins.

Evolutionary biologists believe that these two organelles originated through a process known as endosymbiosis. According to this idea, complex eukaryotic cells originated through a symbiotic relationship among single-celled microbes when free-living bacteria and archea were taken inside another cell as an endosymbiont. Presumably, mitochondria are derived from Rickettsiales, and chloroplasts from cyanobacteria. Once taken inside the host cell, these microbes established a permanent symbiotic relationship with the host, with one cell living inside the other. After this event occurred, the endosymbiont (engulfed microbe) and the host became mutually interdependent, with the endosymbiont producing food for the host cell. According to the endosymbiotic hypothesis, over time the endosymbionts evolved into organelles through a process referred to as genome reduction. This reduction resulted when genes from the endosymbiont’s genome were transferred into the genome of the host organism. Eventually, the host cell evolved the machinery to produce the proteins needed by the endosymbiont to transport those proteins into the endosymbiont’s interior. During the transformation from endosymbiont into organelle, the genome reduction was extreme. For example, a typical cyanobacterium has over 2,000 genes, easily 10 times the number of genes found in a chloroplast.

In light of these processes, the presence of reduced genomes in mitochondria and chloroplasts seemingly represents the vestiges of the evolutionary origin of these two organelles. This begs the question: Why haven’t all of the genes in these organellar genomes been transferred to the host genome? According to some evolutionary biologists, the partial genomes of these organelles could be viewed as transitional in nature. Given more time, the transfer will eventually become complete. In support of this view, they point to other organelles such as mitosomes and hydrogenosomes, which completely lack genomes. Presumably, the gene transfer process has been completed in these endosymbionts-turned-organelles. They also point to the fact that mitochondrial genomes from different organisms possess a differing number of genes, connoting that gene transfer is in differing stages in these organisms.

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 chemistry because it would be more efficient to produce all the proteins in the cytoplasm and then transport them to the organelles. Evolutionary biologists take this inefficiency and waste as added support for the evolutionary origin of these organelles.

Skeptics versed in biology reasonably ask why an all-knowing, all-powerful, and all-benevolent Creator would produce organelles with genomes. Recent work by investigators from Sweden provides an answer to this question.1 Their research supplies a reason for why organelles possess genomes and why these genomes must encode proteins—albeit, a limited number.

The researchers demonstrated that the proteins encoded by mitochondrial and chloroplast genomes have distinct structural features. (Namely, they are proteins associated with the organellar membranes, comprised 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 and chloroplasts, as they actually are—the proteins would be transported to the endoplasmic reticulum (ER) instead of the mitochondria and/or chloroplasts. 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 and chloroplast because of the common structural features these two groups of proteins share. Therefore, to ensure that the appropriate proteins wind up in the membranes surrounding mitochondria and chloroplasts, these biomolecules must be produced in the interior of these organelles. This requirement entails that these organelles have genomes within their lumen to encode the information needed by the organelle’s machinery to make these specialized membrane proteins.

So, a biochemical logic undergirds the structure and function of mitochondrial and chloroplast genomes. The existence of this rationale makes it reasonable to view organelles, such as the mitochondria and chloroplasts, as the Creator’s handiwork. Like most biological systems, these organelles appear to be designed for a purpose. So when a skeptic asks why organelles have genomes, creation and intelligent design proponents now have a ready answer.

Subjects: 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. Patrik Björkholm et al., “Mitochondrial Genomes Are Retained by Selective Constraints on Protein Targeting,” Proceedings of the National Academy of Sciences, USA (June 2015), doi:10.1073/pnas.1421372112.