Should mutations still be considered random or directed?

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Ayala (2007) explains that when scientists use the term “random” to describe mutations, they refer to the unintentional nature of the process; mutations do not “attempt” to supply what the organism “needs” within a given moment or place. Instead, environmental factors only influence the rate, but not the course of mutation.

Merlin (2010) provided a defense of the Modern Synthesis pertaining to the chance nature of genetic mutations by providing empirical support for this view and refuting arguments advocating directed mutations. He states that a genetic mutation is a matter of “evolutionary chance” if and only if it is not “directed,” i.e., if and only if it does not fulfill at least one of the two following conditions to be a “directed” mutation:

  1. it is more probable in an environment where it is beneficial than in another environment where it is deleterious or neutral, 2) it is clearly more probable in an environment where it is beneficial than other deleterious or neutral mutations (in the same environment) Merlin (2010).

Evolutionary Chance Mutation: A Defense of the Modern Synthesis’ Consensus View (umich.edu)

Thus, this raises the question, should mutations truly be considered a random process or a directed one? Based on previous studies and the literature, I aim to describe how current literature show show how random mutations is an outdated and wrong perspective on how mutations operate. But, I am not arguing that there is an intelligent designer guiding it this time. Instead, I am arguing that the information imbedded in DNA/RNA is what guides it.

For instance, Numerous studies have revealed that many of these non-coding regions play an important role in the accurate functioning of the DNA in regards to neutral mutations, such as psuedogenes and other examples.

Toddler: An Embryonic Signal That Promotes Cell Movement via Apelin Receptors (nih.gov)

(http://www.lncrnablog.com/)

The vast majority of mutations in regions that do encode proteins but are deleterious appears to be fine-tuned to lower the risk of harmful genetic changes. Moreover, mutations are guided by both the physical properties of the genetic code and the need to preserve critical protein function

Evidence of non-random mutation rates suggests an evolutionary risk management strategy | Nature

Evolution: are the monkeys’ typewriters rigged? | Royal Society Open Science (royalsocietypublishing.org)

The harmful mutations that do arise are regulated in a way that ensures the death of individuals so that resources are available for the young among prey and predators because too many predators or prey can cause a collapse of the ecosystem.

Predators indirectly control vector-borne disease: linking predator-prey and host-pathogen models - PubMed (nih.gov)

Now, what I expect from everyone is to explain to me why mutations should still not be viewed as directed despite what current literature suggests…

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That sentence was word salad. What does “accurate functioning of the DNA in regards to neutral mutations” even mean?

You have this backwards. The mutations occur at random. It’s the genetic code that’s finetuned, if anything, so that many mutations are silent and many of the non-silent ones cause a shift to a very similar amino acid.

There is nothing to suggest that they’re regulated.

Simple: you grossly misunderstand the current literature, and it suggests no such thing.

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Yes, they should be considered random.

I’m not sure why, but some people are confused by “random”. But replacing that with “directed” would be far more confusing (and would actually be wrong).

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What makes you say that?

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What definition of random are you operating under when you say this?

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Random with regard to the needs of the organism, and probably random with regard to codon position or site within a gene. Obviously there’s considerable transition bias and CpG bias, but a random distribution doesn’t have to be uniform.

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People might argue about what we mean by “random”. However, the meaning of “directed” is clear and unambiguous, and mutations do not fit that meaning.

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I actually agree. I think adaptive mutations would be a better label for what I am trying to argue in regards to current literature. For instance, the purpose would not solely be genetically engineering new function in an environment, which is what directed mutations entail. Instead, it would be to edit and limit the amount of errors the cell makes in maintaining existing function.

Moreover, the argument for function within non-coding DNA does not depend only on whether the organism would survive or not survive but can still be useful in regards to reproduction or fitting into a different environment.

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Would you expect the mutation rate to be lower in all functional elements then?

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Again, I think you have to be careful with that wording.

What we see is that adaptive mutations are more likely be what results from natural selection. But, if we are not looking at the results of selection, then mutations do not look adaptive.

I’m guessing that you are looking for something different from that.

If we look at the processes that produce mutations, those tend to be adaptive. So there are less mutations at locations where they are more likely to cause damage. But to say that the mutation producing processes are adaptive is very different from saying that individual mutations are adaptive (which they mostly aren’t).

When you use the expression “adaptive mutations” that will be taken as implying that individual mutations are adaptive. And that’s a mistake.

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You mean that adaptive mutations are what sometimes result from random mutation. Some mutations turn out to be adaptive, and those mutations are preserved by selection. It’s not the mutation that results from selection, it’s the fixation of that allele. If we look at differences between species, we overestimate the rate of adaptive mutations, because fixed alleles are enriched in adaptive ones and depleted in deleterious ones, relative to the actual mutation spectrum.

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My definition of adaptive mutations involves mutations directly or indirectly benefiting the organism’s ability to survive, reproduce, or fit into different or the same environment. I provided studies supporting this defintion but you did not respond to my examples.

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Well, I don’t think we would have any expectation on the mutation rate because it is all relative to the environment each organism occupies.

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That’s just another name for advantageous mutations. Nothing to do with what you’re trying to show, that mutations are biased toward advantage.

How is the mutation rate affected by environment?

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I’m not suggesting you should be able to predict the precise rate in any given element of any given organism, I’m asking whether or not you expect the general trend within an organism to be higher mutation rate in non-functional sequences, and a lower mutation rate in functional sequences.

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Are you saying the studies I provided don’t show advantageous mutations?

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I am not sure why this matters. For example, exposure to harmful chemicals may increase the mutation rate, but it will not cause more mutations that make the organism resistant to those chemicals. In this respect, mutations are considered random whether a specific mutation happens or not is unrelated to how useful that mutation would be.

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It’s not enough to show advantageous mutations. You have to show that the distribution of mutations is biased toward advantage. Advantageous mutations happen even if mutation is random.

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You’re suggesting that the genome is somehow fine-tuned to avoid harmful mutations, so I’m asking whether or not you therefore expect to see a lower mutation rate in functional sequences compared to non-functional sequences. I’m not talking about exposure to exogenous mutagens, just the normal generation of mutations, and I’m not talking about whether or not a given mutation might be deleterious or beneficial.

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Let’s apply that to the game of craps. Adaptive rolls are what happens when people win.

Would you conclude that a roll of the dice is not random because there are rolls where people win?

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