The theory of endosymbiosis says that eukaryote cells have evolved from a symbiotic relationship of several prokaryotes. Specifically, the mitochondria and chloroplast organelles of eukaryotic cells are thought to have evolved this way. The evidence that supports this piece of modern evolutionary theory is astounding. We can build a positive case for endosymbiosis, while creationists can only reply with "Well, God decided to create the molecular structure of eukaryotes in a way that just so happens to look like the cell formed via endosymbiosis."

There is quite a bit of molecular evidence for endosymbiosis, including:

A. Both mitochondria and chloroplasts divide inside the eukaryotic cell by binary fission, as bacteria do. Normal eukaryotes do not divide this way (Lynn Sagan 1967).

B. Mitochondria and chloroplasts both have double-layer membranes which are chemically similar to eubacteria membranes (Lynn Sagan 1967).

C. Both mitochondia and chloroplasts have circular DNA, similar to that of prokaryotes and unlike the nuclear DNA of eukaryotes (Lynn Sagan 1967).

D. Mitochondrial ribosomes are similar to those from bacteria in terms of size and structure (O'Brien 2003).

D. Phylogenetic studies of mitochrodria link them closely to alpha-proteobacteria (Sicheritz-Ponten, Kurland, and Andersson 1998). Phylogenetic studies of mtDNA confirm common descent

MtDNA is the DNA which is passed down by mitochondria of eukaryotes. Because mitochondria have very little effect on the overall phenotype in metazoa, and because they aren't largely affected by the surrounding environment, there is no reason disregarding common descent to assume that similar metazoa would have similar mtDNA. For example, there is no serious reason to think that humans and chimpanzees would share more similar mtDNA than humans and horses, or humans and birds. Except, of course, for common descent, which predicts this.

The following tree was created using BLAST and the mitochondrial DNA of 15 organisms. Again, the prediction posed byMolecular Phylogenetics of Mastodon and Tyrannosaurus rex

A phylogenetic analysis of protein fragments recovered from fossils confirmed that mastodons are closely related to elephants, and T. rex to birds. This confirmed a simple prediction of evolution (Organ et al. 2008).

Evidence of jerry-rigged design on the molecular scale

Nuclear porecComplexes, or NPCs, are large proteins which stretch across the nucleus membrane in a cell. They allow molecules to transfer in and out of the nucleus. Vesicle coat proteins are also proteins which transfer molecules in a different and simpler way. Brohawn et al. 2008 found that the molecule ACE1 has been jerry-rigged for similar purposes in both NPCs and vesicle coat proteins. There is no particular reason for the reuse of the exact same molecule in both; however, it strongly supports the evolutionary hypothesis that NPCs and vesicle coat proteins once shared a common molecular ancestor, and diverged as separate structures with substantial differences over time.

The Roots Of Archea And Eukaryota

The Three-domain system of life was first proposed by Carl Woese in 1990, and is now generally accepted and used throughout the scientific community. This proposed classification divides life into three domains: Bacteria, Eukaryota, and Archea. What exactly are each of these domains? Bacteria includes Eubacteria, which are basically all of the bacteria you are familiar with: everything from E. coli to Yersinia pestis. Eukaryota includes the eukaryotes, which are all multicellular life. Archea is the rarest and possibly most interesting of the domains: Archeabacteria are rare, odd bacteria which in many cases have adapted to extreme conditions.

As can be seen in the tree above, Archeabacteria and Eukaryota are more closely related than bacteria; this was determined by comparing genetic similarities between the three domains. Thus, several billion years ago, Archea and Eukaryota shared a common ancestor- however, what was this ancestor like?

Well, morphologically primitive relatives of this ancestor still exist today, according to an article from November in Science Magazine, and they are known as Planctomycetes, Verrucomicrobia, and Chlamydiae. According to the article, these phyla share features of both archea and eukaryota, showing us that chemically, an ancestor of these domains could have existed with a similar mosaic of features. Below is a list of these physical features.

This find helped confirm a successful prediction of the three-domain system of life and the common ancestry of Archea and Eukaryota.

Cellular systems appear to have been created by natural selection.

A recent study published in the Proceedings of the National Academy of Sciences found that mitochondria protein transport machines have primitive component homologues in α-proteobacteria, from which they are thought to have evolved. A simple series of beneficial mutations could convert these components into protein transport systems (Clements et al. 2009).

evolution has been verified: an mtDNA phylogenetic analysis shows a tree of life identical to the tree we find with other types of evidence.