For example, prokaryotes completely lack membrane-bound organelles, yet eukaryotes are dependent on them for survival. Prokaryotes lack a cell nucleus, while eukaryotes have one. Prokaryote DNA is largely free-floating within the nucleoid, while eukaryote DNA is stored carefully in the nucleus. All prokaryotes are single celled, while some eukaryotes are able to be multicellular. While these may seem like insignificant changes, at a molecular level, they are massive.
The biggest and most obvious problem for the transition from LUCA to FECA is the emergence of membrane-bound organelles like the mitochondrion and chloroplast. Usually, this is explained by an appeal to the endosymbiont theory. According to the theory, a prokaryote ingested another prokaryote. Instead of digesting the newly ingested prokaryote, prokaryote 1 allowed prokaryote 2 to continue living inside it. Eventually, prokaryote 2 lost the ability to be free-living and developed a mutually beneficial living arrangement with prokaryote 1. While being given a safe home to live in, prokaryote 2 would perform important cellular functions like providing energy and nutrients. All this took place before the transition to FECA, according to the model.
Evidence for this model of origins of membrane-bound organelles comes largely from phylogenetic comparisons of gene sequence similarities. However, these phylogenetic trees disagree with species trees, meaning the evolutionists must reconcile them using algorithms.
Since mitochondria are assumed to be descended from prokaryotic bacteria, it is reasonable to assume they would be similar to bacteria, and there are some similarities. Mitochondrial DNA is circular like bacterial DNA, they have similar membranes, and they are around the same size as bacteria. Despite these superficial similarities, there are crucial differences. Mitochondria have vastly different ribosomes, manufacture proteins differently, and are more structurally complex than bacteria. Furthermore, mtDNA genomes have much reduced genome sizes compared to their supposed bacterial relatives.
Other differences confound the LECA expectations. The model is riddled with assumptions. It is assumed prokaryote 1 did not digest prokaryote 2 for an unknown reason. It is further assumed that prokaryote 1 was autotrophic. It further assumes that prokaryote 2 could survive not being free-living. It further assumes that when prokaryote 1 replicated, prokaryote 2 did so as well. Wild replication times are tough to get for bacteria, but estimates range from 1.1 hours (Vibrio cholerae) to 25 hours (Salmonella enterica) for a population to double.
---What this means is any endosymbiont has a very short time to completely adapt to the life cycle of its host. If the first endosymbiont did not adapt quickly and divide on cue with its host, there would be no eukaryotes today.
---Keep in mind that the evolutionists argue that the transition from prokaryote to modern eukaryote took at least one billion years."
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