Allen MacNeill has taken of the challenge of falsifying the objection to evolution usually framed, “How can random mutation” produce enough variation for evolution?” or “It’s only random mutation and natural selection.” In debate, random mutation is often assumed to be the substitution of one single amino acid for another, in other words, a single point mutation. Allen says,
I promised a list of the real sources of variation that provide the raw material for evolutionary change. It’s taken me a while, but here it is. This list includes “random mutation,’ of course, but also 46 other sources of variation in either the genotypes or phenotypes of living organisms. Note that the list is not necessarily exhaustive, nor are any of the entries in the list necessarily limited to the level of structure or function under which they are listed. On the contrary, this is clearly a list of the minimum sources of variation between individuals in populations. A comprehensive list would almost certainly include hundreds (and possibly thousands) of more detailed processes. Also, the list includes processes that change either genotypes or phenotypes or both, but does not include processes that are combinations of other processes in the list, again implying that a comprehensive listing would be much longer and more detailed.
Here’s his list of forty-six other ways to produce genetic change.
Commenter -DG adds,
Not so much an addition as perhaps a minor correction with the deletions. Not all deletions necessarily result in a frameshift, although of course this would be the most common for deletions of any multiple not of three. But it is certainly possible for 3 (or some multiple of 3) nucleotides to be inserted or deleted at the same time resulting in insertion/deletions of the protein primary sequence. This seems to be especially prevalent in loop regions of the protein three-dimensional structure and may be one of the mechanisms by which new protein domains occasionally arise.
Commenter SPARC adds,
You may add exon shuffling. It belongs to the gene structure section (insertions/deletions) but in most cases the reading frame isn’t changed. I would further add exonization of transposable elements usage of alternate promoters, alternative splicing, multiple polyA signals and trinucleotide repeat expansions.
Commenter Art says,
It would be very nice if you could fold a whole ‘nother universe of genetic and regulatory mechanisms into your list. For the sake of completeness, and because the ID movement (typified by Behe’s recent dismissal of these core mechanisms) cannot deal with the concept.
I speak, of course, of the regulation of gene expression at the level of RNA and protein breakdown. Not only are they central to life (it’s doubtful that multicellular life could exist without the negative regulatory mechanisms afforded by these processes), they are inherently “accessible” to evolutionary modification. This is because, in the ID vernacular, they involve low information modes of recognition and action.
Keywords for a revised list: microRNA, siRNA, exosome, ubiquitin, cullin, E3 ligase, proteasome, SUMO.
Commenter -DG replies,
Great additions SPARC, since I work on protein evolution I really should have remembered to add exon shuffling. Along the same lines of alternative splicing we also have RNA editing. It isn’t carried out in many known systems but its an interesting system as well.