Mitochondria certainly do show the markers of a being a cell within a cell. They have their own DNA and transcriptional machinery, they divide on their own, they have their own ribosomes, etc. However just because they have these things does not mean they are derived from some prokaryotic ancestor. What I would like to see in terms of more evidence is what changes these mitochondria have undergone relative to that ancestor and how those changes have taken place. For instance mitochondria do not have the ability to make most of the lipids they need to maintain the structural integrity of their membranes. Of course the prokaryotic ancestor would have had to do this. How then did the present day mitochondria lose this ability?
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