So I reread The Last Days of Foxhound for the third time. I finish the whole thing, and start thinking about Psycho Mantis, both in-comic and in-game, in particular Mantis' death scene, where he says he's helping someone for the first time in his life, and that "[I]t feels kind of... nice...". I then think of someone pointing out once that Mantis was actually continuing with the overall plan when he did this in the game. Now, think of this within the context of the comic - Mantis was becoming friends with and actually trusting Liquid. He was tired of being controlled by Ocelot, the Patriots, and Solidus. He started obeying Liquid, wearing clothing that Liquid suggested, and calling him Boss. When he told the ninja to kill as many people as possible, he said he was doing it out of a desire to kill as many people as possible. When he helped Snake continue down the right path for the plan, he was helping Liquid fufill his dream of a better world. The line "It feels kind of... nice..." suddenly carries a lot more weight, now that we've seen where it came from.
The scene where Liquid beats Mantis by letting Big Boss take control of him makes perfect sense considering how Mantis is beaten in the actual game. Liquid switched his controller.
Genetic and recessive traits (as far as they exist) can both be good or bad. But if genes were as simple as dominant and recessive, then for every gene that the person you're 'cloning'note of course, if you mess about with the genes they aren't really a clone is heterozygous for, the dominant allele corresponds to the trait they actually express - and if they are a perfect specimen of whatever you're trying to produce, then that should a 'good' trait. Of course it doesn't get around the fact that the dominant-recessive thing isn't really true, or that Big Boss and his three clones are said several times to be genetically identical, and sometimes it's essential to the plot, or that a lot of Big Boss' super-soldier traits ought to be more down to his upbringing than his genes. But one out of four ... is pretty terrible actually. But better than none.