One thing that has long been apparent to biologists, is the massive differences that exist between cells which have their DNA loose in the cell substance and those in which genetic material is protected by membranes inside a nucleus. The former are the prokaryotes (now called bacteria and archaea) and the others are the eukaryotes. The prokaryotes have tiny cells with a firm wall and no organized membrane-bound organelles. Everything happens in the cytoplasm. These consist of single cells with no differentiation between them. They do exhibit some very sophisticated metabolic capabilities however. In contrast, the eukaryotes are much larger cells which may exist as single cells (like protozoa and algae). However, many others develop into multicellular organisms with plenty of differentiation between kinds of cells, tissues, organs, and whole organisms.

Biologists continue to reflect on this situation, pointing out, for example that “The greatest evolutionary discontinuity between living organisms is that separating prokaryotic and eukaryotic cells.” [Rudolf A. Raff and Henry R. Maher.1972. The Nonsymbiotic Origin of Mitochondria. Science 177: 575-582 p. 575.] And more recently a scientific team wrote: “The origin and cellular complexity of eukaryotes represent a major enigma in biology….. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear.”    Furthermore they note that “The origin of the eukaryotic cell is regarded as one of the major evolutionary innovations in the history of life on our planet. Yet, the emergence of the complex and compartmentalized nature of the eukaryotic cell represents a major conundrum in modern biology.”  {Last 2 quotes Katarzyna Zaremba-Niedzwiedzka et al. 2017. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541:353-358.   Both p. 353].

Apart from superficial differences in appearance, the internal differences between the prokaryotes and eukaryotes are major. The existence of a defined nucleus is one obvious difference in the eukaryotes, but that nucleus can undergo not only an elaborate process of mitosis (which involves the appearance of spindle fibres and results in two identical daughter cells), but also many eukaryotes (if they achieve a diploid condition with two complete sets of chromosomes per cell) are able to undergo meiosis which involves spindle fibres and two successive divisions leading to four unlike haploid (one set of chromosomes each) daughter cells.

On the topic of the spindle fibres and other microtubules, one expert reflected: “Modern eukaryotic cells are reinforced by fibrous and tubular structures, often associated with tiny motor systems, that allow the cells to move around and power their internal traffic. No counterpart of the many proteins that make up these systems is found in prokaryotes. Thus, the development of the cytoskeletal system must have required a large number of authentic innovations. Nothing is known about these key evolutionary events, except that they most likely went together with cell enlargement and membrane expansion, often in pacesetting fashion.” [Christian de Duve. 1996. The Birth of Complex Cells. Scientific American. April. pp. 50-57 See p. 55.]

The list of major innovations in the eukaryotic cell goes on and on. The chromosomes, in eukaryotes, rather than consisting of one circle lying free in the cytoplasm as happens in the prokaryotes, exist as straight separate chromosomes in which the DNA is wound around histone proteins (nucleosomes) to form very condensed chromosomes. There are also numerous membrane systems in the cell, like golgi bodies and endoplasmic reticulum. Of course, the mitochondrion is also unique to eukaryotes. On the membranes inside the mitochondria, chemical energy is produced by oxidizing organic compounds. The end result is the high energy molecule ATP which provides energy to the processes of life.

Endosymbiosis is the main theory used to explain how the eukaryotic cell could develop spontaneously through evolutionary processes. That theory has major problems. The complexity of every cell including the eukaryotic cell and their irreducible complexity clearly testify to the work of God the Creator.