Why do animals and plants appear to be well adapted to their environments? Lamarck had an answer that appears to make sense. Environmental changes promote behavioral changes which promote corresponding structural adaptations in animals and plants that are transmitted to offspring. However, Lamarck's hypothesis contradicts the prevailing theory that natural selection acts on random genetic mutations. The post Darwin discovery of genes defeated Lamarck's theory while simultaneously demonstrating the validity of much of Darwin's theory. Yet there is still some wiggle room here for a superficially Lamarckian, non-random component within the prevailing, random mutation, framework.
Maybe natural selection acts on random mutations to produce outcomes that appear Lamarckian because environmental changes impact particular genes differently. Particular genes can be stimulated by an environmental change. Maybe the rate of mutation on stimulated genes increases relative to the rate in genes unaffected by the environmental change. Because random mutations in that gene are more likely to occur more quickly than would otherwise be the case, the likelihood of a rare beneficial mutation also increases. Natural selection then favors the rare beneficial mutation in the overall population.
When cells replicate their DNA, the replication by transcription mechanism sometimes stalls. Sometimes, when a stalled replication resumes, a gene sequence is deleted or extra copies of it are made. A combination of factors could make these copying errors more likely to occur for those particular genes that are actively responding to environmental stresses, so that those particular genes are more likely to show copy number variation.
I read that there is some evidence that "adaptive mutation" of this sort could be occurring in microorganisms. For example, there is more copy number variation of the copper-resistance gene CUP1 when it is stimulated by environmental copper. When CUP1 was modified by a team of researchers led by Jonathan Houseley, a specialist in molecular biology and genetics at the Babraham Institute in Cambridge, to react to a non-toxic sugar instead of to copper, an increase in copy number variation result was again seen after the modified CUP1 gene was stimulated by that environmental sugar.
There is substantial skepticism that adaptive mutation plays a significant role in evolution among biologists. More and better evidence for stimulated gene localized copy number variation, and a mechanism that translates stimulation of a gene into a higher mutation rate, will be required for this speculative hypothesis to be accepted. Efforts to prove or disprove adaptive mutation in microorganisms may accelerate as a result of the recent positive CUP1 gene results. If biologists one day determine that adaptive mutation is true, and probably had some role in humans being one branch on the primate tree, then will more people put aside their religious beliefs and accept that humans are ancestors of microorganisms?