This question is explored in Nick Lane's book Power, Sex, Suicide. Eukaryotes are indeed unusual. They alone have ascended above the simple constraints of bacterial life.
Bacteria remain simple because natural selection keeps them simple. Unlike eukaryotes, most bacteria have no junk DNA at all. Copying the genome takes time. When bacteria are dividing, those that are fastest will quickly take over. Therefore, junk DNA is quickly discarded. Any gene that is not absolutely essential will be lost over time. Bacteria are very thrifty in this way and this keeps complexity in check and keeps their genome trim. Another constraint is size. Bacteria respire through their cell membrane. If a bacterium were to increase in size, it's surface area with respect to volume quickly plummets. This makes it hard to generate the energy that it needs. Therefore, it is not possible for bacteria to achieve the complexity of eukaryotes through the gradual Darwinian process of natural selection even over the billions of years they have existed. Bacteria remain eternally bacteria.
As I discussed in an earlier post, eukaryotes escaped these bonds through symbiosis. Our mitochondria freed us from a bacterial prison. With mitochondrial to power us, cells could get bigger increase in complexity.
So what is so special about mitochondria? Are bacteria really eternally doomed? Some bacteria have infolded cell walls to increase surface area, why couldn't this have gradually led to eukaryote-like complexity? I will tackle these questions and more next time!
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