Previous entry, Unintelligent Design #2: Help Me Invent This Protein.
Multicellular organisms are treasure troves of food and breeding space for replicators with bad intentions. (Don't knock me for speaking teleologically, you know I'm being figurative.) This is why we have immune systems. But the trick is for your immune system to figure out what's supposed to be there, and what's not. Sometimes it misses things that don't belong, and you get sick. Less often it attacks things that do belong, and you get an autoimmune disease. It's not perfect.
One of the ways your immune cells sort the good from the bad is with unique tags: proteins on the surfaces of cells that not only say, "This is supposed to be here", but that are constantly presenting ground up bits of their innards to passing immune sentries. (These are the HLA Markers of the title.) That way, if some smartass bad guys try to hide inside a cell where the guards can't see them, eventually it will get caught in the conveyor of ground of protein and get presented on the outside. The immune cell sees it and says, "This looks funny. I'm going to kill this whole cell."
It's really a pretty cool system, though subject to the kinds of arms races you often see in nature - there are viruses that throw a wrench into the ground-up protein conveyor belt so they don't end up on the surface. So to compensate for that, your cell has another protein that makes the immune system attack if it's not there - and so on. Not surprising that there are these layers of tricks for a war that's been going on for over a billion years.
Because humans around the world face different bugs that get into their cells and have to get ground up, we have different surface marking proteins that do a better job of presenting bits of the bugs that our ancestors tended to see more of Africa or Germany or wherever. In fact the HLA genes are the most diverse of any on the planet. For most genes there's only one functional version. For a few, like hair color, there are several. For these there are hundreds.
And here's the problem: this means if you need a kidney, and I give you one, your immune system sees weird HLA tags, and it attacks - this is why organs get rejected, and why organ donations have to be matched, often to a family member. If you need bone marrow replacement, and I donate it, the immune cells developing in my bone marrow emerge into your blood stream and see themselves as surrounded by what is to them an army of foreign cells - this is graft-versus-host disease, where the transplant attacks you.
One esteemed immunologist* put it like this: why would the Intelligent Designer make it that way? That is, why not give us interchangeable parts in anticipation of the day we'd get smart enough to share organs? As opposed to forcing us to load people up with all kinds of immunosuppressants that put them at risk for infection, cancer, and metabolic problems - which is what we have to do?
I was indirectly inspired to post this by the blog The Chirurgeons Apprentice, which celebrates the joys of surgery prior to anesthesia (probably not a lunch-time kind of website; H/T Boing Boing). Things have indeed improved, owing to sober-minded incremental improvements from science, not because of people praying (they'd had many centuries to do that). Anesthesia is not even a century and a half old! Think about that for a second. A hundred and fifty years ago during the American Civil War, if you needed a limb amputated, it was done with whiskey and strong men holding you down. Don't even ask about sterile technique. You could call this Unintelligent Design #3A: an off-switch for pain or consciousness (even a very limited one) would've been great, not just for surgery before anesthesia, but for all of existence for all animals.
Conclusion: either we're not intelligently designed, or we are designed, but the designer does not have moral intentions, in any way that humans can understand. If it's the second option, that's a tough sell if you're telling people how we should live our lives.
*Rational Thought @ UCSD members will be able to guess who this esteemed immunologist was, because he's been kind enough to do several events for RT@UCSD. His answer to "Why is it this way" was "I don't know, I only work here."