The theory of Endosymbiosis explains the origin of chloroplasts and mitochondria and their double membranes. This concept assumes that chloroplasts and mitochondria are the result of years of evolution initiated by the endocytosis of bacteria and blue-green algae. According to this theory, blue green algae and bacteria were not digested; they became symbiotic instead. Endocytosis is when a substance gains entry into a cell without passing through its cell membrane. A cell's plasma membrane encloses and fuses to lock foreign material inside. An intracellular vesicle is formed as result .The ribosomes of the inner structure in chloroplasts and mitochondria resemble prokaryotic ribosomes. Evolutionist Lynn Margulis proposed the idea in the late 1960’s. In 1970 she published her argument in The Origin of Eukaryotic Cells. The controversy surrounding theory is that it is not a fact. The endosymbiotic theory is that it proposes no real process and most textbooks show the simple picture of a cell that swallows another cell that becomes a mitochondrion. There is a difference between the process of endosymbiosis and its incorporation in the germ line, necessitating genetic changes. One of the controversies stated by Albert de Roos: What were those changes? What was the host? Was it a fusion, was it engulfment, how did the mitochondrion get its second membrane, how did two genomes in one cell integrate and coordinate? The theory is also strongly teleological, illustrated by the widely used term "˜enslavement'. But how do you enslave another cell, how do you replace its proteins and genes without affecting existing functions? The existence of obligate bacterial endosymbionts in some present eukaryotes is often presented as a substitute for a mechanism, but they remain bacteria and give not rise to new organelles. So, before we can speak of the endosymbiotic as a testable scientific theory, we need a mechanistic scenario which is lacking at the moment.
Another controversy was it was inconsistent with an accepted theory such the theory of evolution. At the time many biologist believed that genetic mistakes were an important mechanism in evolution. They thought all evolution occurred as a result of the gathering of small mutations over time. Scientist did not want to spend money on a new idea when they had the evolution theory that already had supporting ideas. Extra evidence was needed to convince the scientist that the evolutionary theory had to make room for additional changes. http://telicthoughts.com/a-critique-on-the-endosymbiotic-theory-for-the-origin-of- mitochondria/ http://biology.kenyon.edu/HHMI/Biol113/the%20endosymbiotic%20theory.htm
http://undsci.berkeley.edu/lessons/pdfs/endosymbiosis.pdf