In the old Pixar movie; Monsters Inc. The monsters fear nothing more than human children, this is because the children are supposedly toxic. Its found out that this isn't true at the end, but what if it was? What biological reasons would a species have for fearing its own children?
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I wrote down my few thoughts on the topic ranging from most to least likely.
- Growth; Maybe in this species they live very dangerous lives and thus they need to be able to grow quickly. Instead of developing the brain and intelligence first this species would want to become big and active quicker. Thus for the first 1-4 years they are little more than animals. An example of this is in the fictional species Triaformica, a three sexed worm-like species; except instead of fearing the kids they pen them up like dogs.
- Puberty; Perhaps when this species goes through puberty they become extremely violent and attack anything they perceive as a threat, thus a larger version of themselves (adults) would be considered a threat.
- Cannibalism; Perhaps this species follows the design used by the artificial creatures created by Pea in The Games, were the parents give birth to children only for the purpose of eating them. In the games the children simply run away after being born but the children may eventually evolve to be toxic to their parents. Alternatively the species may contain 2 subspecies each of which eat the others young, thus being toxic to the other would be beneficial.
The children eat their parents.
In some species of spiders, the newborn young hatch and immediately eat their mothers. This pattern of behavior could easily lead to a race fearing its children.
A simple extension of this pattern of behavior could be that the young won't just eat their parents, but any adult individual that they come across. Eggs could hatch into huge swarms of tiny offspring that cooperatively hunt adults. In a protein-poor environment, for a species in which the adults do not aid in raising children, this could be the only method by which the young can grow large enough to fend for themselves.
In the latter scenario, it's likely that parents would have some pheromone which would protect them from their own children, but the children of any other adult would be terrifying.
Many creatures in nature have weird built in pheromones systems. There can't be two queens in a beehive for example. So a species can fear their children because of this biology need to challenge the alpha-leader. So maybe in a story the children once they reached puberty would migrate away and form new tribes and clans with their own leadership structure. But with space limited the children might challenge the old generations simply because it's there pubertal desire to rule.