Pseudogenes in the Matrix

Over at BioLogos, Dennis Venema and Darrel Falk have written a nice summary of pseudogenes and how they relate to our understanding of common descent.  But we can take their discussion to a deeper level to help you better appreciate pseudogenes from a teleological perspective.

The Rational Essence of Proteins and DNA

In my previous essay about proteins-as-design-material, I noted:

This all raises some interesting questions. For example, without proteins, and their manufacturing process, what becomes of the blind watchmaker? Without proteins, and the latent functions contained within, might not the blind watchmaker exist as the impotent, crippled, blind watchmaker with no one to notice its existence? If so, how much credit does the blind watchmaker really deserve?

The vast and immense Tree of Life is a protein-dependent output. Point to some evidence of evolution and I’ll point to the proteins that underlie it. Without proteins, would there be a Tree of Life 3.5 billion years after the RNA world took root? How do we know? If we believe so, would the Tree be as immense and vast as it is today? A life form composed of nucleic acids, carbohydrates, and lipids would suffice for the purposes of the blind watchmaker. But could the blind watchmaker turn this material into something that is analogous to an Ash tree filled with squirrels, beetles, and birds?

Genetic Cross-Talk

Bacteria can do tricks that your dog cannot do. A bacterium can acquire DNA from another completely unrelated species of bacteria just by living in the same area. For example, if you take cyanobacteria, a type of bacteria that normally live in the oceans and carry out photosynthesis, and mix them in a test tube with a population of E. coli, the bacteria that normally live in your large intestines, something odd can happen. If you let them sit together overnight, some of the E coli cells will link up with the cyanobacteria using a microscopic hose and then transfer some of their DNA into the cyanobacteria [1]. Once the E. coli DNA is inside the cyanobacterium, the cellular machinery will then splice the E. coli DNA into the chromosome. This would be like your dog somehow acquiring cat DNA and the ability to purr simply by sleeping on the same bed with the cat!This process of acquiring foreign DNA is known as lateral gene transfer (LGT) or horizontal gene transfer(HGT). A large number of scientists consider LGT to be a powerful force in bacterial evolution.

Cytosine Deamination and Evolution

It has been argued that no engineer would have used cytosine as part of the genetic material because of its predisposition for deamination. But it’s exactly this predisposition that might cause an engineer of evolution to include it.

Life itself appears to have been designed to minimize errors. The universal nature of the proof-reading/repair machinery, the optimized genetic code, and the G/C:A/T parity code all converge on this point. Yet despite this design logic, there is the interesting fact that cytosine is especially prone to deamination, where the removal of its exocyclic amino group converts it into uracil (a base normally found in RNA). Uracil does not exist in DNA, thus it can be effectively detected and removed by repair enzymes. However, if not detected and repaired, it can base pair with adenine, meaning that it would specify adenine during DNA replication. In a subsequent round of replication, the adenine in turn would specify thymine. The bottom line is that spontaneous deamination of cytosine can lead to a base substitution known as a transition, where C is replaced by T (and G is replaced by A on the other strand of DNA). We might expect such mutations to be quite common, as the rate constant for cytosine deamination at 37 degree C in single stranded DNA translates into a half-life for any specific cytosine of about 200 years. In fact, such high rates of deamination led researchers Poole et. al to complain of “confounded cytosine!” [1]

We would thus seem to have two contradictory lines of evidence. On one hand, there is the growing list of evidence to support the hypothesis that error correction was an important principle guiding the design of life. Yet the incorporation of cytosine works against such efforts, given its predisposition to spark a mutation. In fact, Poole et al. go so far as to argue, “Any engineer would have replaced cytosine, but evolution is a tinkerer not an engineer.” From a design perspective, how might these contrary dynamics be reconciled? That is, given the emphasis on error correction, why would an engineer include cytosine?

The Rational Essence of Proteins and DNA

In my previous essay about proteins-as-design-material, I noted:

This all raises some interesting questions. For example, without proteins, and their manufacturing process, what becomes of the blind watchmaker? Without proteins, and the latent functions contained within, might not the blind watchmaker exist as the impotent, crippled, blind watchmaker with no one to notice its existence? If so, how much credit does the blind watchmaker really deserve?

The vast and immense Tree of Life is a protein-dependent output. Point to some evidence of evolution and I’ll point to the proteins that underlie it. Without proteins, would there be a Tree of Life 3.5 billion years after the RNA world took root? How do we know? If we believe so, would the Tree be as immense and vast as it is today? A life form composed of nucleic acids, carbohydrates, and lipids would suffice for the purposes of the blind watchmaker. But could the blind watchmaker turn this material into something that is analogous to an Ash tree filled with squirrels, beetles, and birds?