(3) The genome organization
The bacterial genome consists of a single circular DNA molecule, where all genes carry real information and are arranged one after the other without interruptions. Such an organization is surely very efficient, but precisely for this reason it could not have been present at the beginning. A genome which consists of many, open-ended, DNA molecules, is definitely more primitive that a bacterial one, and it is also more likely that the first chromosomes did not contain only nuclei acids but other molecules as well.
As anyone can see, the features that we can reasonably attribute to the common ancestor are not bacterial ones, but the very features that later, in a more complex form, will be found in eukaryotes. The separation between transcription and translation, the use of stable messengers, and a genome organized in linear chromosomes, are all typical eukaryotic features, and yet they are also intrinsically primitive features.
The last common ancestor did not have the impressive structures that we usually associate with eukaryotes – it did not have a nucleus, a cytoskeleton, mitochondria, chloroplasts, mitosis, meiosis and sexuality – and yet it did already have the basic features that deep down characterize the eukaryotic cell. Despite the lack of a nucleus, in conclusion, the last common ancestor was not a bacterium, because it did not have the functional features that are specific of bacteria.

The origins of bacteria

The primitive oceans had the consistency of a “diluted broth”, and it is only too likely that their organic molecules were used by the first cells as nutrients. Such a large food store, however, was inevitably destined to become extinguished, and this created the conditions for the appearence of two very different survival strategies. Some cells adapted their metabolism to smaller and smaller starting molecules, and eventually learned to perform all metabolic reactions from inorganic compounds. In this way they ceased to be consumers, and became producers of organic matter (and when this happened, the risk that life could become extinct by lack of food was finally avoided).