Mutation not random????

[IndigoChild5559]

"It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation."
https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

 

[Altfish]

"It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation."
https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

Interesting, let's see what peer review brings

 

[exchemist]

"It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation."
https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

The headline, and the quoted comments, do not seem to me to be supported by the description of the findings.

It seems to say certain crucial parts of the genome are preferentially protected from mutation. That does not mean that those mutations that do occur are non-random. All it says is that not all parts of the genome are equally susceptible to mutations.

We already know there are repair mechanisms for DNA that reduce the damage that could otherwise accumulate from mutations. What this seems to say is that there are regions where extra protection applies, that's all.

I'd like to see the actual Nature article on this, seeing as the comments attributed to the researchers here appear at variance with what they have actually found.

Aha, got it, here's the abstract:

Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.

The key phrase is that mutations are said not to be "random with respect to their consequences", i.e. occurring with equal probability right across the whole genome. But, as far as I can see, they are not saying there is anything non-random about those mutations that do occur.

But as this is not my speciality, I'd welcome comments from a biologist.

A very interesting article: thanks for posting.

 

[Dan From Smithville]

The original article is open access. Here is a link. https://www.nature.com/articles/s41586-021-04269-6.pdf

I just got it and haven't read the paper yet myself. Presumably, if it is correct, the constraint would be a trait subject to natural selection and evolution itself.

 

[sun rise]

I'm not a biologist either but that's not stopping me. What the article seems to be saying is that natural selection is operating on the genetic level to favor preserving key elements of the genome from typically deleterious mutation. In other words, Darwin's findings basically apply at the genetic level.

 

[cladking]

I'm not a biologist either but that's not stopping me. What the article seems to be saying is that natural selection is operating on the genetic level to favor preserving key elements of the genome from typically deleterious mutation. In other words, Darwin's findings basically apply at the genetic level.

I believe very similar results were found nearly 20 years ago. At least there were experiments showing mutations were linked to non-random environmental factors.

Darwin got just about everything wrong apparently. Simply stated species suddenly arise to fill every niche; every void. There is no gradual change caused by "survival of the fittest".

 

[epronovost]

I'll reinforce what was already mentioned and detailed by @exchemist. This article seems to play up the sensationalism of the discovery a bit too hard. While the discovery on mechanism to protect key section of the DNA of a plant from damaging mutation is indeed very interesting and might yield numerous application in medicine and agriculture, it's not really the paradigm shifts its being sold at in the article's title and the slight quote mining that was done.

 

[Native]

"It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation."
https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

Of course mutations are not random. Everything is under an eternal evolutionary journey as the RNA and DNA helical structure genom is governed by the influence of all kinds of electromagnetic frequencies all over in cosmos.

 

[Twilight Hue]

"It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation."
https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

It's a good thing. Imagine the chaos if everything lost its stability. Still, random mutation applies as a scientific fact.

 

[Dan From Smithville]

Of course mutations are not random. Everything is under an eternal evolutionary journey as the RNA and DNA helical structure genom is governed by the influence of all kinds of electromagnetic frequencies all over in cosmos.

What is a helical structure genom [sic]?

 

[TagliatelliMonster]

The headline, and the quoted comments, do not seem to me to be supported by the description of the findings.

It seems to say certain crucial parts of the genome are preferentially protected from mutation. That does not mean that those mutations that do occur are non-random. All it says is that not all parts of the genome are equally susceptible to mutations.

We already know there are repair mechanisms for DNA that reduce the damage that could otherwise accumulate from mutations. What this seems to say is that there are regions where extra protection applies, that's all.

I'd like to see the actual Nature article on this, seeing as the comments attributed to the researchers here appear at variance with what they have actually found.

Aha, got it, here's the abstract:

Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome—mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.

The key phrase is that mutations are said not to be "random with respect to their consequences", i.e. occurring with equal probability right across the whole genome. But, as far as I can see, they are not saying there is anything non-random about those mutations that do occur.

But as this is not my speciality, I'd welcome comments from a biologist.

A very interesting article: thanks for posting.

I can only agree to this.
Read it as well. Noticed right away how the headline seems primarily click bait or sensationalism as the contents don't agree to that misleading title at all.

 

[Yerda]

Darwin got just about everything wrong apparently.

Getting things wrong in a productive manner is about 90% of the battle in science.

Simply stated species suddenly arise to fill every niche; every void.

The cognitive niche filled by humans wasn't filled for billions of years. That seems quite gradual to me.

 

[cladking]

Getting things wrong in a productive manner is about 90% of the battle in science.

The idea that the fit survive and the weak die is very highly destructive to the human race. All individuals are equally fit and merely suited to different environments.

I believe the concept has damaged science as well because it has become a lightning rod for disagreement and the assumed conclusion (that most change in species is gradual) is simply wrong.

The cognitive niche filled by humans wasn't filled for billions of years. That seems quite gradual to me.

There's no reason to believe a "cognitive niche" ever existed or that humans are filling one. There's no evidence humans are more "intelligent" than other animals because we can't define "intelligence" or even "consciousness". There is only very widespread anecdotal evidence that humans are more intelligent and then there is mostly ignored anecdotal evidence that we are not. It is only science that has made us so powerful but then we ignore the power of beavers, bees, and termites that control their environments. Evidence suggests more and more that it's not cognition that lies at the heart of human intelligence but rather complex language. Perhaps complex language is less useful in the hands of animals since they lack opposable thumbs and the printing press.

There's very little doubt that there are quite a few species filling a "cognitive gap" but apparently, each individual has to start at nearly square one because the language is insufficiently complex to pass down learning that isn't "innate" to the species.

 

[Yerda]

The idea that the fit survive and the weak die is very highly destructive to the human race. All individuals are equally fit and merely suited to different environments.

Darwin did a bit more than use a phrase. He provided the foundation for the entire field of evolutionary biology. Also I don't think he considered species or individuals strong or weak but just more or less likely to reproduce given a particular environment.

In any case, it's possible to be wrong about almost everything and still contribute a great deal to science.

I believe the concept has damaged science as well because it has become a lightning rod for disagreement and the assumed conclusion (that most change in species is gradual) is simply wrong.

What?

There's no reason to believe a "cognitive niche" ever existed or that humans are filling one. There's no evidence humans are more "intelligent" than other animals because we can't define "intelligence" or even "consciousness". There is only very widespread anecdotal evidence that humans are more intelligent and then there is mostly ignored anecdotal evidence that we are not. It is only science that has made us so powerful but then we ignore the power of beavers, bees, and termites that control their environments. Evidence suggests more and more that it's not cognition that lies at the heart of human intelligence but rather complex language. Perhaps complex language is less useful in the hands of animals since they lack opposable thumbs and the printing press.

There's very little doubt that there are quite a few species filling a "cognitive gap" but apparently, each individual has to start at nearly square one because the language is insufficiently complex to pass down learning that isn't "innate" to the species.

Ok, I guess it depends on how you choose to measure intelligence. From my perspective it looks like billions of humans are able to live as humans because we think and reason and plan and so on - in ways that other animals don't.

For instance, your job could be writing literary criticism or developing web apps. We can agree that this is a niche that no other animals fill, yes?

I'm not so concerned with absolute measures of intelligence here. I don't need to be smarter than a beaver - just better at writing code. This is a cognitive activity.

You see what I'm getting at?

 

[IndigoChild5559]

Of course mutations are not random. Everything is under an eternal evolutionary journey as the RNA and DNA helical structure genom is governed by the influence of all kinds of electromagnetic frequencies all over in cosmos.

The thing is, if mutation is not random, then we have no idea what drives mutation. It is obviously not just DNA begin hit with particles or something, because that would produce random mutations. So what do you think might be driving these adaptive mutations?

 

[cladking]

Darwin did a bit more than use a phrase. He provided the foundation for the entire field of evolutionary biology. Also I don't think he considered species or individuals strong or weak but just more or less likely to reproduce given a particular environment.

Darwin was important to science but I believe he led the understanding of change in species and its causes in the WRONG direction.

In any case, it's possible to be wrong about almost everything and still contribute a great deal to science.

Very true. But this makes him no less wrong.

What?

People are so busy defending Darwin that they don't see the errors. They believe there is a disagreement between those who reject science and those who support it so they gather round and choose sides. This perception is simply wrong on a few different levels.

From my perspective it looks like billions of humans are able to live as humans because we think and reason and plan and so on - in ways that other animals don't.

Again, I maintain that our success has nothing to do with "intelligence" which doesn't even exist as we define it. It has to do with complex language and the ability for everyone to stand on the shoulders of giants. Without complex language we'd each be babes in the woods and prey for any large predator.

I'm not so concerned with absolute measures of intelligence here. I don't need to be smarter than a beaver - just better at writing code. This is a cognitive activity.

You see what I'm getting at?

Yes, certainly. But it doesn't mean "intelligence" exists or that if it did you'd have more of it than every beaver.

There is no condition we call "intelligence". Rather all consciousness can do things that are "clever". This is an event rather than a condition. One can be a doctor and go for days without experiencing "cleverness'".

Human cleverness and animal cleverness have different causes but the results are the same.

 

[Valjean]

The thing is, if mutation is not random, then we have no idea what drives mutation. It is obviously not just DNA begin hit with particles or something, because that would produce random mutations. So what do you think might be driving these adaptive mutations?

No, that's not what the study indicates. It's just a discovery that some sections of the genome are better protected from mutation than others.
DNA replication is finely tuned, but not foolproof. Mistakes happen. DNA also has mechanisms for repair. The discovery that some essential sequences are more robust, while interesting, upends nothing. Mutation remains exactly what it's understood to be.

The thing is, if mutation is not random, then we have no idea what drives mutation. It is obviously not just DNA begin hit with particles or something, because that would produce random mutations. So what do you think might be driving these adaptive mutations?

Lot's of things can interfere with replication, many; probably most, random. The fact that some sections of code are more resistant to these insults does not contradict evolutionary theory.

 

[LegionOnomaMoi]

"It turns out that mutation is very non-random and it's non-random in a way that benefits the plant. It's a totally new way of thinking about mutation."
https://phys.org/news/2022-01-evolutionary-theory-dna-mutations-random.html

Even were the sensationalist account of the actual paper an accurate characterization, it would hardly be new. Indeed, the late, great biologist Robert Rosen noted in the prolegomena to one of his monographs that, at least at some level, the assumption of essential randomness is at odds with other crucial assumptions most biologists make:
"On the one hand, biologists have convinced themselves that the processes of life do not violate any known physical principles; thus they call themselves “mechanists” rather than “vitalists”. Further, biologists believe that life is somehow the inevitable necessary consequence of underlying physical (inanimate) processes; this is one of the wellsprings of reductionism. But on the other hand, modern biologists are also, most fervently, evolutionists; they believe wholeheartedly that everything about organisms is shaped by essentially historical, accidental factors, which are inherently unpredictable and to which no universal principles can apply. That is, they believe that everything important about life is not necessary but contingent. The unperceived ironies and contradictions in these beliefs are encapsulated in the recent boast by a molecular biologist: “Molecular biologists do not believe in equations.” What is relinquished so glibly here is nothing less than any shred of logical necessity in biology, and with it, any capacity to understand.” (pp. 13-14; italics in original)
Rosen, R. (1991). Life Itself: A Comprehensive Inquiry into the Nature, Origin, and Fabrication of Life (Complexity in Ecological Systems Series). Columbia University Press.

 

[Yerda]

Darwin was important to science but I believe he led the understanding of change in species and its causes in the WRONG direction.

I see.

Out of curiosity have you ever read about extended evolutionary synthesis?

Very true. But this makes him no less wrong.

Ok. He did better than I would have done in his time.

Again, I maintain that our success has nothing to do with "intelligence" which doesn't even exist as we define it. It has to do with complex language and the ability for everyone to stand on the shoulders of giants. Without complex language we'd each be babes in the woods and prey for any large predator.

Yes, certainly. But it doesn't mean "intelligence" exists or that if it did you'd have more of it than every beaver.

There is no condition we call "intelligence". Rather all consciousness can do things that are "clever". This is an event rather than a condition. One can be a doctor and go for days without experiencing "cleverness'".

Human cleverness and animal cleverness have different causes but the results are the same.

Ok. I'm given to thinking that intelligence is a meaningful idea and that measures of intelligence are getting at something real but that's just my view from here.

My gut says at some level it comes down to processing information in novel and useful ways. I believe that humans are capable of processing information in ways that are world changing and other animals aren't. We can read the world and rewrite it much more easily as a result - or something like that. (If I'm totally honest I expect that life and maybe the world itself is an information process but lets not get into those weeds).

 

[cladking]

Out of curiosity have you ever read about extended evolutionary synthesis?

I'm not sure I fully understand what they are getting at but it's closer to the mark than the so called theory of evolution. Change in species and individuals is almost always sudden and almost all large changes in species has always occurred suddenly. Survival of the fittest can't change one animal into another or make a species fit into A niche. Simply stated niches rarely if ever change gradually. They change suddenly and every individual and species will adapt suddenly or become extinct. Certainly if any environment would exist for countless millions of years then the species within it would gradually adapt to the changing conditions. But it is unrealistic to believe that any niche would last indefinitely.

Ok. He did better than I would have done in his time.

Me too! I would probably have supported him but I probably couldn't have made all the connections required to invent the theory.

Ok. I'm given to thinking that intelligence is a meaningful idea and that measures of intelligence are getting at something real but that's just my view from here.

"Intelligence" is a perception caused by the way we think. The condition we call "intelligence" is simply the experience of consciousness in the one dimension of thought caused by our language. We have a "train of thought" because we use the analog programming of language to think. No other species "thinks" and neither did humans before "babel".

Obviously there are mental differences between humans that transcend individual beliefs which define each modern human by defining his thought and his every action. Some people experience cleverness much more often than others and we each have mental processes at which we excel or at which we largely fail. "Idiot savants" excel at a few things and "polymaths" at very many. A few excel on very few things and some on very many. There are numerous extremes of many types but a great deal of it comes down to experience and genetics. But thinking faster or more slowly is a characteristic that most closely resembles what we call "intelligence" but is more related to things like awareness, alertness, and habits of thought rather than "intelligence".

It is highly improbable that animals understand any abstractions or experience thought. Ancient Language doesn't even have a word for "thought" and contains no abstractions. It was likely a mutation connecting our speech center to higher brain functions that launched the human "race". In other species this mutation would have proved to be of little utility but with human social behavior, social hunting, and opposable thumb it was of great utility.

One of the chief problems with "intelligence" is that it is ascribed as the source of individual and species success. It is believed by most to underlie the workings of science but none of this is true. humans are and always have been a product of complex language that allows each individual in each generation to pick up where the last left off. "Intelligence" is irrelevant to science and only experiment drives it. The belief in intelligence is closely correlated to the maintenance of the status quo: "People more intelligent than I built what exists so it must be preserved". The source of ideas is simply irrelevant to the progress of the human race. It doesn't matter who designs or carries out an experiment and it doesn't matter what Peers think because "Peers" can't have a single idea, only individuals create ideas and invent hypothesis or experiment.

My gut says at some level it comes down to processing information in novel and useful ways.

I hardly disagree. But I see little correlation between "thinking outside the box" and "cleverness". There is some but just listen to children and you'll see some very clever and different thinking.

I believe that humans are capable of processing information in ways that are world changing and other animals aren't.

Some beaver invented dams and some termite invented air conditioned cities. Probably these were small and large improvements over time but I doubt they required "intelligence" so much as insight (cleverness).

(If I'm totally honest I expect that life and maybe the world itself is an information process but lets not get into those weeds).

Indeed! First we need to understand what we see before we start looking at what we can't.