We have been discussing lately the idea that mutations, rather than being haphazard, may actually be directed by cellular machinery. In a recent volume of the Annals of the New York Academy of Sciences, several scientists presented evidence in favor of this view. One of these scientists has a paper on what he calls “mutation protocols” – that is, repeated patterns of mutations whose behavior is not only physical, but also logical. In other words, the pattern that the mutation follows is consistent with the overall architecture of the organism. You might call these design-consistent mutations.
In any case, David King gives us examples of two mutation protocols – cut-and-paste functional segments, and tuning knobs.
Tuning knobs are generally implemented in the cell through short sequences of repetitive DNA (called SSRs) — one of the types of DNA previously thought to be junk. The idea was, if it is the same, short DNA sequence over and over again, how can it be useful? If mutations are likely to increase or decrease copy number, aren’t the copies just the result of random copying errors? But it turns out that these short sequences are actually usable *because* they mutate by adding/removing copies, and because of their special placement. These sequences act as “tuning knobs” for the genome. Adding copies is like turning a volume knob one way, and removing copies is like turning it the other. You can also tell that these are specially placed, because if a mutation creates an SSR where there wasn’t one to begin with, this often leads to diseases and even cancer.
So, by having certain sequences signal to the genome “hey I’m a tuning knob”, the mutation system can easily and fairly safely adjust organismal parameters across generations.
The second mutation protocol discussed by King is the copy-and-paste protocol implemented by Transposable elements. These were previously considered “genomic parasites”, but have recently been shown to play a role in providing robust variation in organisms. In other words, transposons can import necessary functions into new sites.
But, what’s even more amazing, is that the functions that the transposons import may themselves have tuning knobs! So, not only is it importing function, it is importing a function with control knobs!
The author also makes an interesting observation – mutations have historically (and in fact still are) described in textbooks to be copying errors, while sexual recombination – which is in fact a mutation – has not been considered in the category of “mutation” because the organism expends considerable energy to accomplish it, and it is so useful for the longevity of the organism. In other words, it wasn’t considered an “error” since it seems to be a part of the design. Likewise, we are finding more and more mutations to actually be part of the design rather than being “errors”.
Of course, this is why I proposed a second-level classification of mutations. A while ago, I proposed separating mutations out into design-consistent and design-inconsistent mutations, and described how one might be able to classify these empirically. I still think this is a useful road to follow.