Even though endosymbiosis is called a theory does not mean that it is completely accepted. There is evidence for but there is also against the theory. The double membrane that is usually an argument for the endosymbiotic theory but some argue it because the differences between the mitochondrial membranes and the membranes of bacteria are different. Another point that is argued is the form of replication that mitochondria have begins at a different location than in bacteria. The largest argument against the theory is the lack of a good mechanism for how gene transfer could have occurred between the organelle and the cell, especially during the beginning of the process.
I find it interesting how there can be a universally accepted theory that can still be debated. There are arguments for and against. I would go with the proendosymbiosis theory but i enjoyed learning about arguments against the theory.
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http://www.evolutionnews.org/2012/01/on_the_origin_o054891.html
http://learn.genetics.utah.edu/content/begin/cells/organelles/
http://www.biology.iupui.edu/biocourses/N100/2k2endosymb.html
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