Hypotheses don’t get many more bonus points-or any bonus points- if what’s being predicted is something we already knew anyways (i.e. something that is already part of our background knowledge). For example, we already know that gravity exists so that hardly confirms (or more strongly confirms) a newly proposed hypothesis. One of the reasons evolution is so well-confirmed is not just because Darwin made predictions before those predictions were confirmed as being true. Rather, his theories proposed things that weren’t already part of our background knowledge. Darwin made ‘risky’ predictions that were specific and ‘surprising’. The surprising data point is surprising by itself because that same data wasn’t part of our knowledge; however, the surprising data was expected (and not surprising) under Darwin’s theory of evolution. Therefore, the surprising data confirmed (to a very large extent) Darwin’s theory because the data was expected under Darwin’s theory.
The problem of evil has been around far before Darwin. If you were to ask somebody, before Darwin, whether certain facts like animals suffering for millions of years would lower the probability of theism even further than general suffering, they should have said yes. Animals suffering for millions of years was something that was not always common knowledge-it was or would be surprising data taken alone. It would, also, be very surprising data on the hypothesis of theism, which means that the data of animal suffering we’re looking at counts as very strong evidence against the existence of God. (1) (2). It’s not just that the fact that animals suffering for millions of years (and most species going extinct) is incredibly unexpected given the hypothesis of theism, there’s also the fact that this piece of data wasn’t always something that was obvious and ‘trivial’. Since the data of animal suffering was something that was not always part of our background knowledge, and since it wasn’t something that was just expected to show up, and since the data is extremely surprising on theism, then that clearly counts as more confirmation that theism isn’t true… when taking in facts about suffering. One could chalk up all the animal suffering/extinction to God’s mysterious ways. But we all know the simpler explanation: nature doesn’t care whether we suffer or not.
But suppose I’m wrong: suppose that there aren’t any “bonus points” in this way. Nevertheless, evolution still makes the problem of evil worse for theism in different senses. For one, it increases the amount and intensity of suffering in the world. And secondly, evolution is more expected under naturalism than under theism. That’s because on theism, evolution is highly optional, and because special creationism is a possible/plausible hypothesis under theism (but impossible under naturalism). Thirdly, as mentioned before, naturalism is a simpler hypothesis than theism when it comes to explaining suffering; that’s because theism needs the additional assumption that God has unknown/known reasons for suffering. In addition, naturalism doesn’t need to introduce an entirely new ontology in order to explain suffering (this would also mean that theism faces the charge here of being ad hoc, if there is little or no independent evidence for theism). Fourthly and finally, evolution brings up many new and puzzling facts that are very hard or impossible to explain under theism (e.g. even if humans have to suffer, why do animals have to suffer? And why did animals have to suffer for so long? Why millions of years of suffering instead of hundreds? Why is the suffering so intense? Also, what’s up with all the unfair competition and extinction?)
Notes
(1) The problem, then, is not just whether theism is false, but also the problem is whether evil renders theism irrational.
(2) One might try and appeal to some evidence in favor of theism to offset the data of evil. This evidence, though, must be very strong; we must also know whether the data point is actually something that manifests in the world. Additionally, many arguments for God’s existence aren’t actually arguments for traditional theism, instead, they are arguments for a deism of some kind. Finally, there is also other data that counts against the existence of God: divine hiddenness, religious diversity, mind-brain dependency, dysteleology, moral disagreement, etc.
Philosophy of Religion blog 
A brilliant observation! I myself have considered this when reading various theodicies, such as the free will defence, and the ability to engage in the virtues like empathy and compassion. It is not at all clear how these theodicies explain the brutal nature of natural selection amongst animals. Of course this is an argument for the evidential, not logical, problem of evil. It is nonetheless compelling.
I’m a little confused here. There really is no “problem of suffering” for the theist, though people do talk about it as if there is one. Suffering came into the world because of sin. IE, suffering is humankind’s responsibility.
Actually atheists have the problem: what explains suffering in their worldview?
Becky
“Suffering came into the world because of sin. IE, suffering is humankind’s responsibility.”
How could this possibly work? Under Christianity, God has designed and created everything, including human nature. If human beings want to disobey God, then it is God’s responsibility for designing us in such as way as to have that want. We cannot choose our wants. In fact, I would say it’s impossible for God to create anything for which he has no responsibility, unless he has no choice over his actions. If you deliberately do something (like creating easily-tempted human beings in a situation containing a huge temptation) and know what will happen as a consequence (because you have omniscience) then you’re responsible for the consequences.
Becky is right. It’s a major theological and philosophical mistake to assume the suffering of animals existed as a(n a priori) feature of the creation.