“Range of effect of observed mutations”: I’m not sure what that means. Could you explain that differently? I can’t parse that phrase in the context of discussing neutral theory because the immediate effect of a neutral mutation is ‘no effect’. Biologists have studied what makes many mutations ‘neutral’ in selection.
But the reason why they are neutral, and don’t kentucky fry your genetic system when they occur, is that there is information in the cell that directs them to the right place.
OK. A decent starting place for understanding the mechanisms behind genetic mutations is this Wikipedia article. It’s not because they are directed toward insensitive areas. It’s more of a statistical thing: There are simply fewer possible mutations that persist with other than near-neutral impact (selection). The ones that truly ‘fry’ your genome tend not to propagate, and that certainly biases what you’ll find in nature (Aside: In surveys where scientists have inserted random mutations in saturation experiments, the distribution of neutral and negative mutations varies from species to species.)
Note: Gah, I can’t believe I forgot to reference Motoo Kimura in regard to neutral theory!
This is why education needs to change. Your viewpoint summarizes the best knowledge of the 1980s. A lot has happened since then. A great review is Caporale’s The Implicit Genome. Mutations are targeted in their incidence, not just their selection. This has been shown repeatedly, but fails to be noted in the textbooks because textbook theory is dominated by a giant echo of Darwin. It isn’t actually based on evidence. Evidence shows that organisms have a lot of control over their evolutionary destinations.
As an example, organisms contain multiple DNA polymerases. When an organism needs a mutation, it often switches DNA polymerases to one which induces mutations, and then amplifies the genes which are likely to need changes.
Additionally, though the link between these and function has not yet been firmly established, single-stranded DNA forms stem-loop structures with semi-palindromic sequences, which basically point to the areas of DNA which are replaceable.
Many organisms have pseudogenes for regular genes, which serve as templates for swapping out functionality. That is, the pseudogene is a permanent storage for alternate configurations of the regular gene.
None of this is told in biology classes, because anything where evolution doesn’t happen by accident starts to smell like design whether it is mentioned or not. It’s not that it is some obscure area of biology. This is standard biology. If I remember correctly, it was even Francisco Ayala wrote the review paper describing the ways in which pseudogenes are used as functional templates for gene modification.
However, despite it being normal biology, many people view the attempt to tell students about all this amazingness as some creationist conspiracy. Additionally, they give the dunce cap to any scientist who tries to incorporate these ideas into a different view of biology or even evolution.
That is true. But I am not “most biologists.” Most changes are neutral and that is the default hypothesis until disproven.
From reading this sentence, I’m not sure you know what neutral theory is. Can you explain it to us so we know we are on the same page?
So what are the other obvious hypotheses you’ve considered and ruled out? If you cannot even enumerate all the other hypotheses that make sense of this, why should biologists grant that this is a designed system?
Neutral theory is silent about design. Evolution does not explain design away, because common descent could be God’s design principle. However, this is not evidence for design.
I’m not sure you understand what neutral theory is from reading your statement. You’re gonna have to return to square one.
It seems that you do not know what neutral theory is @johnnyb. Can you explain it to us? We know exactly why this is. It is not a mystery.
This is a category error. Somatic hypermutation is off topic. Do you know how neutral theory answers these questions?
I think the more you ponder the God-Guidance of Evolution, the less anxious about that position you will become. I haven’t found that it causes any additional trouble to my Unitarian Universalist mind.
Okay. I’m sorry. I’d genuinely love to understand what you are saying.
Well you may be among less than 10 people in the world calling this evidence of ID, and I cannot understand the logic of your position. When you write about it, it seems like you do not know what neutral theory is.
So you can chalk this up to disagreement, but the reason it might be met with suspicion is the history of the ID movement on such matters, and the impenetrability of your point. Though I do want to understand. Go for. Try and explain.
I didn’t say that it is Darwinism, I said that it is an echo of it. The reason for this is that, when pressed, neutral theorists usually do resort to Darwinian mechanisms when the plausibility of developing the systems of neutral theory are shown to be inadequate for making themselves. I.e., when you point out that the reason neutral theory works is because of the predisposition of the cell to not mutate sensitive areas, the response is usually Darwinian (selection, man!).
That’s what differentiates Theory A and Theory B. Theory A is about observables, and leaves the causes of those observations to be explained by something else. For most biologists, they choose Darwinism as their something else. Theory B tries to say that all of evolution is like this, and that even the directionalization of mutation is created by random wanderings in mutation space.
I think Theory A is a better theory, but that ID is a better “background theory” for why Theory A works than Darwinism.
Could we be splitting hairs here? The fact that I exist is evidence of Intelligent Design. What @swamidass means is that it is not “special” evidence of Intelligent Design. It’s just your ordinary “isn’t the Universe grand? It must be the product of God!” type of statement.
I got my BS in Chemistry in the mid-1980s (strong emphasis on Phys Chem and Biochem), Ph.D. in Biochemistry and Mol Bio in the '90s and continue in biochemistry/enzymology today. I’ve followed the primary literature on mutational mechanisms since sophomore year in college. Understand that no part of the genome is immune from mutation. All biochemical replication, recombination and repair systems have inherent physical limits to fidelity. That’s simply a consequence of basic physics and chemistry and was recognized by chemists and enzymologists in both theoretical and experimental work in the '60s or '70s. Surveys and experiments covering mutation rates have been going on for decades. The basal rates of point mutations for many organisms (not viruses) typically run in the ballpark of 10E-9 to 10E-10 per base per replication. That mutation rates may increase above basal depending on the region of the genome and other activity was known before I started grad school. That some classes of mutations (e.g. transitions vs. tranversions & etc.) occur at different rates was also well established decades ago.
As @swamidass also wondered, I’m not sure what that has to do with neutral theory. Changes in mutation rates means that more variation will tend to arise in areas with increased rates of mutation. That includes positive, neutral and negative mutations. And, mutations will still hit all parts of the genome… Again, there is no part of the genome where all neutral mutations are specifically directed by the biochemical mechanisms of the cell.
I know you’re interested in the broad set of ideas related to the Extended Evolutionary Synthesis. But just be aware that much of the hypotheses are sketchy at best. Most scientists familiar with the subjects consider the hype very overinflated. IMO, it will likely regress to a meaningless buzzword in the future, connoting something very different than as it was originally conceived (see also: the term ‘epigenetics’). I’d suggest that if one outside of the scientific areas took the criticisms of current evolutionary research from the articles of a number of the more vocal EES proponents or popular press, one would come away with a very skewed and flawed misunderstanding of work in the field. I’m not going to rehash the subject here as others have done it before and better than I’d have time for. Arlin Stoltzfus (not of the EES groups), is probably a more reliable source for criticism of areas misunderstood related to mutations and evolutionary biology. Dan Graur is another professor who has written blogs & articles on the web that relate to mutation and evolution. Larry Moran’s ‘Sandwalk’ blog has a series of articles about “EES”. If you’d like links, I can post them, but Google should work faster.