Unintelligent Design

I'm taking some biology classes. From a engineer's point of view, living things are not intelligently designed. Vestigial organs, vestigial genes, and a multitude of other obvious design flaws litter the biological landscape. For instance, we havean ugly hack embedded in our DNA replication.

Telomeres are what is known in the software design world as a "hack" - they fix the immediate problem without correcting the underlying cause of the problem. To understand the problem that telomeres are meant to fix, you have to know a little about DNA and DNA replication. (I've attempted a terse explanation here, but there's always Wikipedia for a more thorough description.) DNA is a double helix consisting of two strands nucleotides. These nucleotides contain the familiar A, C, G and T bases that are held by 5-carbon sugar rings, and the rings are connected by phosphate groups. These sugars are asymmetrical, with an oxygen atom in one part of the ring, and a carbon atom sticking off the side. Biologists have labeled the carbons 1 - 5. The 3' carbon and the 5' carbon are the two that bond to the phosphate group, and to make a strand of DNA, you have to keep all the nucleotide lined up the same way: 3' - 5' - phosphate - 3' - 5' - phosphate and so on. So each double helix is made up of two nucleotide chains pointing in oposit directions.

When DNA is replicated, the enzymes that assemble new DNA strands can only add nucleotides to the 3' end, not the 5' end. The following video demonstraits how strand can be replicated continuously as it comes unwound, and the other must be copied backwards, one loop at a time, as it comes unwound.
That in it self is a bit of a hack. Why not just make an enzyme that can copy the nucleotide string going the other way? In fact, some viruses use such backwards-moving enzymes to replicate their own genetic code.

A larger problem occurs when the enzymes get to the end of the DNA strand. Because the copying enzyme is unidirectional, when it comes to replicating the final loop of the wrong-facing nucleotide strand, the enzyme attaches to the end of the strand and works back toward the copied section. But it cannot copy the spot where it attaches, only what is in front of it. That means there is a small part at the end of one strand of nucleotides that cannot be copied. Each time your DNA replicates, a piece on the end is lost. Since DNA is only stable with both complimentary strands, the corresponding bit on the other strand also falls off.

The patch that we use to compensate for the immediate problem is this: whenever you make a gamete (sperm or egg) a special enzyme adds telomeres - non-coding nonsense DNA - to the ends of all of your chromosomes. (Chromosomes are long, coiled and packed strands of DNA.) We are all conceived with telomeres on the ends of our DNA so that, as our DNA replicates and we loose little bits on the ends, we're only loosing nonsense... until our cells have replicated for many years. When humans were only living into their 40s, this wasn't so much of a problem. Now, this might be one of the causes of aging. You can think of it this way: if all of the important instructions on how to make your cells were held in a manual, telomeres would be blank pages at the front and the back of the book. Each cell needs it's own copy of the book, and each time the book is copied, it looses a few of the pages at the front and the back. If the book is copied enough times, it starts loosing valuable information.

Whereas a bad engineer might have come up with the temporary, wasteful fix of telomeres, a good engineer would have found a way to fix the underlying problem. As previously mentioned, she could have engineered an enzyme that could copy DNA in the other direction. This would solve two problems and make your DNA replication much more efficient, both in time and energy consumption. The second fix is already used by bacteria. If the DNA were stored in long rings, or just connected the ends during the final steps of replication, then there would be no "end", and our enzyme could copy the entire strand until it looped back upon itself. Bacteria store some or all of their DNA in rings, and those rings don't loose bits when they are copied because the DNA strands have no ends. An intelligent designer would have seen the problem, thought over possible solutions, and implemented a solution to permanently fix the problem. Evolution blindly fumbled around for whatever fixed the immediate problem, and we ended up with telomeres.