I was asked recently how atheists account for and deal with such issues as illness, suffering, and grief. Here's my go at it:
Illness can be caused by pathogens, such as bacteria, viruses, or fungi, each eking out their own existence in this world, or it can be a natural by-product of the fact that our bodies are mortal animals, evolved from other animals, and are still links in the evolutionary chain.
Mutations, the cause of genetic illnesses, are also the source of variability. If your particular mutation had given you the ability to jump extra-high to escape predators, or nowadays to sit in an office chair for 15 hours without developing blood clots, then your genes may have been more represented in the next generation.
It's unfortunate when one person is damaged by deleterious mutations, but one must remember that evolution does not work on an individual level. Evolution works on the population level and is defined as the change in gene frequencies in a population over time.
Some genes that were previously very adaptive are now less so and even damaging. Examples: the cystic fibrosis gene, if you have two of them, causes CF. If you have one CF gene, you do not have CF, but you are freakishly resilient to typhoid and cholera. Having one sickle cell anemia gene does not cause sickle cell trait but does confer resistence to malaria. Personally, the genes that control my immune system are especially vigilant, and this was probably beneficial even a century ago. Now, however, with the advent of antibiotics to cure whatever bacteria ail me, my white blood cells are bored, and they tend to pick out random proteins in my body and produce antibodies to them, causing various autoimmune diseases.
Pain is an adaptive response to the environment. Fire is pretty, but playing with it hurts. Thus, people do not play with fire and cause large, open sores on their body. These breaches of the skin would soon by colonized by bacteria and the organism would die. People with genetic mutations that render them unable to feel pain sustain damage to their bodies, terrible damage, and generally die young. Thus, pain is an excellent adaptation and protective mechanism and is highly selected for.
Suffering, on the other hand, is a more intricate subject. We suffer because we are smart enough to. We recognize problems and ideal situations that do not or cannot exist.
Even suffering and depression may be evolutionarily adaptive. I've read papers (here's one, http://www.biopsychiatry.com/depression/evolution.html , though this is not the one I read previously,) that noted that depression is not unique to humans and may be a catalyst for changing maladaptive behavior. I have had some depression problems in my life, and I note that at the end of these I either was hit with a new autoimmune disease (and there's excellent evidence for an biochemical basis for depression mediated by inflammatory cytokines, so this makes sense, and see above for examples of biology and disease,) or I changed my life in major ways. The depressions were responsible for very positive changes that have ultimately made me very happy and helped me contribute to the world. I would not consider changing any of the decisions that were based in depression that have led me to my life, now.
On a personal philosophical note, while it may be difficult to remember at the time, suffering and obstacles are a chance to learn and to grow. You can choose what you want your life to be and how to react.
In a previous workplace, a particular woman was nasty to me while I was dealing with a major autoimmune thing, sniping behind my back, silent treatment, everything you would expect from a 13-year-old girl, not a 26-year-old woman. I thought about it, and I realized that she was a very sad person and had significant maturity problems. I exercised compassion. On a day-to-day basis, it was difficult to maintain equilibrium and be compassionate toward her, realizing that she was quite nuts, but I had chosen to deal with my autoimmune thing as quietly and privately as possible and I didn't want to compromise that, either.
Dealing with the autoimmune thing itself was easier: it's just something that happened. It was not personal. It's just a factor that I deal with as expediently as possible without recriminations toward myself or others. I'm also short. These are merely facets of my human body. They are not a punishment. I had no choice in the matter. I have a great choice, however, in my reaction to them and how I allow them to impact my life and my happiness.
Grief is another issue, especially grief caused by the death of a person that you loved. Grief is directly proportional to love. Serial killers feel no grief because they feel no love for other people.
Without getting too Tennyson on you, grief must be borne to have love in your life, and love for friends and family is worth the grief that comes afterward. As we are mortal, you have two choices: experience grief or die first.