Molecular phylogenetic trees provide an increasingly robust view of the early course of evolution and the three lines of descent that emerged from the origin of life, >3.8 billion years ago. We can now begin to interpret the results and there are many questions and frank paradoxes. How do we know where the universal common ancestor is located in the molecular tree of life? What was the nature of that earliest biology? How was it that chemiosmosis arose before the biological membrane? How can we peer deeper than the last universal ancestral state? How is it that some of the results refute basic textbook teachings on early evolution? What do the results say about the origin of eukaryotes? In the light of pervasive lateral transfer of genes between different organisms, is there any meaningful molecular tree at all? These and other questions will be addressed by fact and “reasonable” speculation.