I had the same problem until I read this .It might not solve all your questions but definetely sheds light to why whould a benevolant God let animals suffer ,let me know what you think:
In his book Nature Red in Tooth and Claw, Michael Murray explains on the basis of neurological studies that there is an ascending three-fold hierarchy of pain awareness in nature:
Level 3: Awareness that one is oneself in pain
Level 2: Mental states of pain
Level 1: Aversive reaction to noxious stimuli
Organisms which are not sentient, that is, have no mental life, display at most Level 1 reactions. Insects, worms, and other invertebrates react to noxious stimuli but lack the neurological capacity to feel pain. Their avoidance behavior obviously has a selective advantage in the struggle for survival and so is built into them by natural selection. The experience of pain is thus not necessary for an organism to exhibit aversive behavior to contact that may be injurious. Thus when your friend asks, “If you beat an animal, wouldn't it try to avoid the source of pain so that way 'it' wouldn't suffer? Isn't that a form of 'self-awareness?'," you can see that such aversive behavior doesn’t even imply second order pain awareness, much less third order awareness. Avoidance behavior doesn’t require pain awareness, and the neurological capacities of primitive organisms aren’t sufficient to support Level 2 mental states.
Level 2 awareness arrives on the scene with the vertebrates. Their nervous systems are sufficiently developed to have associated with certain brain states mental states of pain. So when we see an animal like a dog, cat, or horse thrashing about or screaming when injured, it is irresistible to ascribe to them second order mental states of pain. It is this experience of animal pain that forms the basis of the objection to God’s goodness from animal suffering. But notice that an experience of Level 2 pain awareness does not imply a Level 3 awareness. Indeed, the biological evidence indicates that very few animals have an awareness that they are themselves in pain.
Level 3 is a higher-order awareness that one is oneself experiencing a Level 2 state. Your friend asks, “How could an animal not be aware of their suffering if they're yelping/screaming out of pain?" Brain studies supply the remarkable answer. Neurological research indicates that there are two independent neural pathways associated with the experience of pain. The one pathway is involved in producing Level 2 mental states of being in pain. But there is an independent neural pathway that is associated with being aware that one is oneself in a Level 2 state. And this second neural pathway is apparently a very late evolutionary development which only emerges in the higher primates, including man. Other animals lack the neural pathways for having the experience of Level 3 pain awareness. So even though animals like zebras and giraffes, for example, experience pain when attacked by a lion, they really aren’t aware of it.
To help understand this, consider an astonishing analogous phenomenon in human experience known as blind sight. The experience of sight is also associated biologically with two independent neural pathways in the brain. The one pathway conveys visual stimuli about what external objects are presented to the viewer. The other pathway is associated with an awareness of the visual states. Incredibly, certain persons, who have experienced impairment to the second neural pathway but whose first neural pathway is functioning normally, exhibit what is called blind sight. That is to say, these people are effectively blind because they are not aware that they can see anything. But in fact, they do “see” in the sense that they correctly register visual stimuli conveyed by the first neural pathway. If you toss a ball to such a person he will catch it because he does see it. But he isn’t aware that he sees it! Phenomenologically, he is like a person who is utterly blind, who doesn’t receive any visual stimuli. Obviously, as Michael Murray says, it would be a pointless undertaking to invite a blind sighted person to spend an afternoon at the art gallery. For even though he, in a sense, sees the paintings on the walls, he isn’t aware that he sees them and so has no experience of the paintings.
Now neurobiology indicates a similar situation with respect to animal pain awareness. All animals but the great apes and man lack the neural pathways associated with Level 3 pain awareness. Being a very late evolutionary development, this pathway is not present throughout the animal world. What that implies is that throughout almost the entirety of the long history of evolutionary development, no creature was ever aware of being in pain.
Viewed theologically, this discovery magnifies the mercy and goodness of God. God has shielded almost the entire animal kingdom throughout its history from an awareness of being in pain! For those of us who are pet owners and lovers of animals, this is a tremendous comfort and a cause of praise to God for His goodness and wondrous, even ingenious, care of creation. Who would have guessed that God had done such a thing? These neurological insights, documented by Murray, greatly reduce the force of the problem of evil posed by animal suffering.
