New study shows ‘non-random’ mutation

Photo: Arabidopsis thaliana, © Marie-Lan Nguyen / Wikimedia Commons / CC-BY 2.5.

A correspondent asked me about a recent article in the journal NatureMutation bias reflects natural selection in Arabidopsis thaliana, aka the commonly studied flowering herb, thalus cress. The abstract states: “Since the first half of the 20th century, the theory of evolution has been dominated by the idea that mutations occur randomly with respect to their consequences. Here we test this hypothesis with large investigations of de novo mutations in the plant Arabidopsis thaliana.” They show that “the mutation bias associated with the epigenome reduces the occurrence of deleterious mutations in Arabidopsischallenging the dominant paradigm that mutation is a directionless force in evolution.

Whether the mutation is “directionless” or “random” is a traditional axiom of evolutionary biology. My correspondent wanted to know what it means to consider that some mutations may be “non-random” after all. She supposed she was asking a “dumb question”.

Exactly the question to ask

In fact, it’s not a silly question at all – it’s exactly the right question to ask! In the context of this article, what “non-random” means is that mutations are less likely to occur in the DNA encoding genes – especially in what they call “essential genes”. This overturns two standard assumptions of modern evolutionary theory.

In evolutionary biology, mutations are generally thought to be “random” in two respects:

  1. Mutations occur with equal probability across the entire genome. There is therefore no part of the genome that is MORE or LESS susceptible to mutations than any other part of the genome. This is supposed to mean that the mutations are not directed or concentrated, but in a sense are randomly distributed across the genome.
  2. Mutations occur without regard to the needs of organisms, meaning they are random and not directed for or against what organisms need to survive.

the Nature the study found evidence against (1) and (2). In Arabidopsiscertain parts of the genome are LESS likely to mutate, and the parts of the genome that are less mutated tend to be the REALLY important parts of the genome that you wouldn’t want to mutate because in those sections the mutations would break the most probably genes that are very important to the organism.

A look at the specifics

Now let’s get into more details. In the genomes of most higher organisms, only a small percentage of DNA represents genes that code for proteins. the Nature study revealed that sections of the Arabidopsis The genome that codes for genes is LESS likely to mutate than “intergenic” regions – the sections of the genome between genes that don’t code for proteins. They found that “the frequency of mutations was 58% lower in the gene bodies than in the neighboring intergenic space.”

They further found that ‘essential genes’, such as the basic genes responsible for translation (e.g. converting information from DNA into proteins), had even LOWER mutation rates compared to d other genes that had more specialized functions.

Please also note this important point: the study was able to directly measure the mutations after they had occurred in the plant, but before the mutations could have been affected by natural selection, which could “knock out” some mutations. which have deleterious effects. The authors therefore believe they have provided a true and accurate measure of mutations as they occur in DNA.

Or to put it another way, mutations do not occur randomly in the sense that certain parts of the genome are less susceptible to mutations than other parts of the genome. Instead, mutations occur based on the needs of the organism. In other words, in some ways, life seems to be designed minimize mutations where they would damage basic body functions the most.

Implications for evolutionary biology

The implications for evolutionary biology are profound. If the mutations are not evenly distributed in the genome and are not random to the needs of the organism, then two basic tenets of the standard neo-Darwinian model are wrong. This could also cause problems for neo-Darwinism, as it suggests that mutation rates are lowest in areas where mutations would likely be needed to promote evolution – i.e., they are the lower in the genes.

If mutation rates are low in the DNA encoding the genes, it will take even longer for complex new traits to emerge by mutating functional genes. This exacerbates what Darwin skeptics call the “wait time” problem, where it takes too long for necessary mutations to occur – far longer than the time allowed by the fossil record.

The return of the waiting time problem

Proponents of intelligent design have already identified the latency problem as a fundamental mathematical obstacle to neo-Darwinian evolution. Our colleagues published an article in the Journal of Theoretical Biology Last year, “On the waiting time until coordinated mutations are fixed in regulatory sequenceswhich mathematically modeled the wait time to generate traits requiring N mutations to provide an advantage. The document found a serious challenge to neo-Darwinism:

[T]The fossil record is often interpreted as having long periods of stasis, interrupted by more abrupt changes and “explosive” origins. These changes include, for example, the evolution of life, photosynthesis, multicellularity and the “Avalon explosion”, animal body plans and the “Cambrian explosion”, complex eyes, jaws and vertebrate teeth, territorialization (e.g., in vascular plants, arthropods and tetrapods), insect metamorphosis, animal flight and feathers, reproductive systems including angiosperm flowers, amniote eggs and placenta in mammals, echolocation in whales and bats, and even the cognitive abilities of modern humans. Based on radiometric dating of time windows available in the fossil record, these genetic changes would have occurred very rapidly on a macroevolutionary timescale. In order to assess the chances of a neo-Darwinian process causing such major phenotypic changes, it is important to give rough but reasonable estimates of how long it would take a population to evolve for the multiple genetic changes required to occur. . [Internal citations omitted.]

According to the standards of the field, the study in Journal of Theoretical Biology adopted standard evolutionary assumptions that mutations are random – that is, they are equally likely across the entire genome and occur without regard to the needs of the organism. But the new study Nature suggests that both of these assumptions are wrong – and wrong in a way that makes it likely Stronger for neo-Darwinism to develop new traits.