A) I see no reason to assume that altruistic actions cannot be instinctive, so saying that something is instinctive is not, to me, a defeater of the notion that it is altruistic.
2) Altruistic actions can be beneficial to the gene pool. If one's actions contribute to the survival of one's children or even of one's siblings or one's siblings' children they can contribute to the survival of one's genome.
Faldage, altruism can be instinctive and contribute to the survival of siblings and their children. This version of it is called, "Reciprocal Altruism". Worker honey bees are a classic case in point. Since they themselves are sterile, by looking after the inhabitants of the hive, they increase the chances of propagating their gene copies (75% true) which they share with siblings.
As for parents protecting their young and thus increasing survival. It is a question of interpretation again. I think I wrote about individual(species)/gene perspectives in the thread on memes. The same thing applies here. It depends on whether you look at it from the point of view of the bird or from that of the bird's gene.
Behaviour: Bird protecting young from predator
Effect: Offspring survive
Bird: Altruism
Bird's Gene: Selfish
Observable altruistic behaviour in an individual, is just selfishness on the part of the gene. Where observable altruistic behaviour is *known to be inherited, as in bird alarm calls, the genes are clearly in charge there and so, it is interpreted as innate selfishness. Where a genetic link is not ascribable to behaviour and the trait seems more cultural, there is a great deal of restraint exercised before theories are floated. In fact, the science of animal behaviour, intelligence and cognition is deeply bogged down by this caution. Morgan's Canon is one such tenet that restricts a scientist from acribing a higher mental ability to an animal's behaviour wherever a simpler explanation can be utilised. Critics (and I veer towards their point of view) view this approach as reductionist.
