Welcome to the Molecular Machines

The Blind Watchmaker Gives Us the Easy Ones

If you have been following along, you have learned two important things about the blind watchmaker behaving as a designer-mimic.

1. Since designers are limited by their building material; the blind watchmaker (as designer-mimic) is likewise limited by its building material.

2. The blind watchmaker makes things that are simply “good enough” – kluges – a clumsy or inelegant solution to a problem that gets the job done, but not necessarily in the best way possible.

The latter point is has been driven home by recent research on a very simple system:

Special Stop Codons

We’ve seen that the genetic code channels cytosine deamination (one of the most common mutations) such that a rather random pool of amino acids is converted to a cluster of hydrophobic residues while at the same time is quite exceptional at buffering against deleterious mutations. But let’s consider the three termination codons that function as stop signals during the synthesis of proteins.

The three stop codons are as follows:

UAA

UAG

UGA

The first thing to note about all three stop codons is that none of them contain cytosine (C). In other words, these three are perfectly immune to cytosine deamination.

But remember that DNA is double-stranded. Is the complementary sequence on the other strand of DNA likewise immune to cytosine deamination?

Kluge: Hallmark of the Blind Watchmaker

Perhaps it would help to pause and define a kluge (often spelled as kludge). Let me quote from Gary Marcus, who defines it as follows:

A kluge is a clumsy or inelegant solution to a problem that gets the job done, but not necessarily in the best way possible.

Good definition. And note the vital ingredient as far as the blind watchmaker is concerned – “gets the job done.” That is all that is needed. As long as a solution gets the job done (and getting the job done is simply about reproductive success), it gets selected. The blind watchmaker is blind because it cannot see if a solution is clumsy, inelegant or entails an immediate payoff at a future cost; it only sees whether or the not the immediate job is done. This is why we expect kluges from the blind watchmaker.

But let’s add more.

An Exceptional Code

The genetic code is universal. While there are some variants of the code, these variants, which tweak at the periphery, arose after the universal code was established. The universality of the code means that all of evolution has been under the constraint and influence of the genetic code.

The genetic code was originally thought to be a frozen accident. Murray Gell-Mann explains the concept as follows:

Now, most single accidents make very little difference to the future, but others may have widespread ramifications, many diverse consequences all traceable to one chance event that could have turned out differently. Those we call frozen accidents. I give as an example the right-handed character of some of the molecules that play important roles in all life on Earth though the corresponding left-handed ones do not. People tried for a long time to explain this phenomenon by invoking the left- handedness of the weak interaction for matter as opposed to antimatter, but they concluded that such an explanation wouldn’t work. Let’s suppose that this conclusion is correct and that the right-handedness of the biological molecules is purely an accident. Then the ancestral organism from which all life on this planet is descended happened to have right-handed molecules, and life could perfectly well have come out the other way, with left- handed molecules playing the important roles.

Yet this original explanation has been effectively falsified as scientists analyzed the code in more depth.

Evolution makes do with ‘good enough.’

Gary Marcus explains how the blind watchmaker designs:

Evolution is often likened to a process of climbing a mountain. If one follows the strategy of taking small steps, only going up (never down) and is willing to keep at it long enough, one will inevitably make it to the top of the mountain.

Alas, the strategy of small upward steps can only take a mountain climber so far. If the mountain is a single smooth surface with just one peak (like Mount Fuji), all is well. But if the mountain range looks more like the Himalayas, rough, uneven and full of peaks and valleys, there’s a distinct chance of getting stuck on a low peak that is by no means the highest peak in the range.

Neither evolution nor Darwin ever promised anything like perfection. Evolution is not about creating perfect or optimal creatures, which would require forethought, but only about the fact that the genes of creatures with modest advantages (“fittest” among those that happen currently to be alive) tend to spread throughout the population.

Darwin’s theory of natural selection tells us that a one-eyed creature may outcompete a blind creature, but that doesn’t mean that a creature with two eyes couldn’t come along later.

This seemingly subtle difference — between “fittest among the choices that happen to be lying around” and “fittest imaginable” — makes all the difference in the world.

Biologist PZ Myers agrees: “evolution does not produce rational, perfect, finely-tuned beings. It makes organisms that are good enough.”

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?

Designer-Centrism

Many people subscribe to this notion that we must have independent and objective knowledge about the designers in order to make a reasonable inference of design. Typically, we are told that evidence of the designer’s motives, methods, techniques, history, psychology, etc. are all necessary requirements before inferring design. This form of extreme requirement is something I call designer-centrism.

In my book, I have no problem with making some modest assumptions about the designer, since, as I have explained, detecting design requires that we extrapolate from our own subjective and objective experience with human design. But the demand for such extensive and independent knowledge is a completely different thing. How is one supposed to obtain this independent information about the designer?

RecA – The Evolution Gene

Introduction

In his book Endless Forms Most Beautiful, Sean Carroll explains the role of tool kit genes in the development of organisms. Tool kit genes express products that in turn regulate whether or not other genes are turned on during embryological development. As such, most of them are transcription factors that bind to regulatory regions of a gene, regions Carroll refers to as switches. What thus determines whether or not a particular gene is expressed during development is the combination of activated and repressed switches as a consequence of the composition of the tool kit gene products available.

The teleological echo of all this can be seen from more than one angle. For example, Carroll writes:

The distribution of the genes in the tool kit tells us that the tool kit is ancient and was in place prior to the evolution of most types of animals. (p. 79)

Such observations clearly fit into the hypothesis of front-loading evolution I’ve been discussing for some time, something I hope to further explore for years to come. But there is also something more subtle.

DM Outline III

My continuing effort to organize blog entries into an outline so readers can better connect the dots (a consilience of clues).

A. Detecting Design

1. Science and Design

a. Outline the common definitions of ‘subjective’ and ‘objective.’

b. Identify problems with common definitions and propose George Cooper’s definition of objective - that which can be measured by all parties who should obtain the same result given an appropriate range of accuracy.

c. Draw upon the wisdom of one the great biologists, Jacques Monod, to explain why science cannot determine whether or not life was designed.

d. Demonstrate how archeology and forensics fail to give us reason to think that science can determine whether or not life was designed.

e. Explain how most proponents and critics of design are likely to think alike on one issue – they will find it uncomfortable to acknowledge that science cannot determine whether or not life was designed.