In the 2nd version of the model, all genes start as individually replicating and there are no chromosomes in any of them.
Specialized enzymes do not evolve in protocells with individually replicating genes and random assortment (no chromosome case) even if there are only three reactions to catalyze.
In the individually replicating ribozymes case (version 1), whenever the cumulative flux exceeds a value (C I dd = 6.7) a new replicator is added to the protocell till the number of independent replicators reaches the threshold (ncrit = 15) value.
Thus if we assume that the system with individually replicating genes can exist (which is an interesting question in its own right!), then the one with linkage does not need significantly more enzymes (see our discussion).
However, when replicators replicate individually then there is intragenomic conflict [ 25], as the fastest replicator tends to dominate the system, thereby causing the loss of other replicators, and thus information.
After an overnight fast, subjects consumed a light breakfast (normal breakfast was replicated, with individually different food items, but only given 50%) to prevent the stage of prolonged fasting (Hojlund et al. 2001) and fasted again for at least 4 h during the remainder of the morning until the MR examination.
We implemented three separate versions of the model: in one (version 1), ribozymes replicate individually, in the second (version 2) chromosomes sometimes form, but genes mostly replicate individually; and in the third (version 3), genes are permanently linked together in a chromosome.
Xenopus were exposed individually at 25°C in 1 L glass jars protected from the light (3 individual replicates by time and exposure conditions).
For each chip feature, significance of difference between control and experimental conditions was tested by applying an error model-based hypothesis test to all control replicates as a group versus each treatment replicate individually.
Confirmed associations were then genotyped in the individual Belgian samples, and replicated results further validated in the US samples, also by typing each DNA individually.
