That animals help each other is far from a new observation, but it's puzzling nonetheless. If all that matters is survival of the fittest, shouldn't animals refrain from anything that fails to benefit themselves? Why help another get ahead? There are two main theories: First, that such behavior evolved to help kin and offspring, hence individuals who are genetically related. This promotes the helper's own genes as well. This "blood is thicker than water" theory explains, for example, the sacrifice of bees, who give their lives for their hive and queen when stinging an intruder. The second theory follows an "If you scratch my back, I'll scratch yours" logic: if animals help those who return the favor, both parties stand to gain. Mutual aid can explain political alliances, such as between Nikkie and Yeroen, who supported one another and shared the gains in power and sexual privileges.
Both theories concern the evolution of behavior, but neither tells us much about actual motives. Evolution depends on the success of a trait over millions of years; motives spring from the here and now. For example, sex serves reproduction, yet when animals couples, it's not out of a desire to reproduce. They don't know the connection: sexual urges are separate from the reason sex exists. Motivations lead a life of their own, which is why we describe them in terms of preferences, desires, and intentions, rather than survival value.
Image source: monkey pictures dot net
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Hmm.... seems to me this focuses on kinship-benefiting altruism and reciprocal altruism while disregarding both group selection (which, although problematic because it requires little to no migration between groups at first and then migration later, is a valid theory) and honest signalling, which seems to me the most promising candidate for explaining the evolutionary occurance and stability of altruism.
The main point is true though - individual motivation does not factor into these explanations. It doesn't have to. For cognizing beings capable of strategic planning and linguaform thought, we may explain motivation at least partially by invoking explicit means-ends cognition and cost-benefit thinking. But while these may be "implicit" 'free-floating rationales' in most animals, the primary motivation seems to be impulsive, instinctive. But I don't see a problem with that, nor in general the fact that motivation is divorced from the explanation for evolutionary occurence and stability of altruism.
I think this is less of a puzzle if you are not focussed on genes as essential. Evolution does not know about mechanisms - only about solutions. It just goes with what works. If this means genetic change (and a lot of the time it does), then that's what works. But ANY other stable mechanism of transmission can work too. In more complex organisms behaviour can be generated and transmitted (culture) and, in doing so, have genetic consequences (for example, if a cultural preference for cooperativeness arises even by accident, then it becomes - for that group - the norm, and non-cooperative members will be selected against as "deviant". If some minimum group size is necessary for survival then would not the pressure be quite strong?