Random Mutations and Biological Evolution

[Mark78L]

13 minutes ago, Genady said:

"Genes adapt"? Why not a random change?

"Mutation a direct response"? Why not a random change?

"Conscious adaptation"? Why not a random change?

Why not random change - because advancements in science are rarely made by agreeing with the status quo. And there is a case for mutations being a conscious occurrence in response to stimuli. Why not a conscious adaption?

Below is the conclusion drawn from the study I shared, which opens the possibility of mutations being a conscious adaption...why would we not consider it?

"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."

[swansont]

1 hour ago, Mark78L said:

This paper highlights the mutational bias generated by epigenetic stimuli associated with the plant Arabidopsis thaliana, which indicates that mutational evolution is not random, but a conscious response to improve survival on the part of the organism

A plant is making a conscious response?

[Mark78L]

6 minutes ago, swansont said:

A plant is making a conscious response?

You don't think that cells are operating on any conscious level?

[Bufofrog]

3 minutes ago, Mark78L said:

You don't think that cells are operating on any conscious level?

I don't.

[Genady]

51 minutes ago, Mark78L said:

... there is a case for mutations being a conscious occurrence in response to stimuli.

No, there is not.

[Mark78L]

To Bufofrog (I think I'm restricted due to this being my first day of responding for a long time)

If brain cells are not operating on any conscious level, then how does consciousness arise from them? Is consciousness not simply the ability to store information and recall that information? Are you saying cells do not store information and cannot recall said information?

14 minutes ago, Genady said:

No, there is not.

Yes there is... (I didn't realise this discussion malarchy could be so simple)....;)

[Genady]

29 minutes ago, Mark78L said:

Yes there is... 

That's all for now. When I see "a case for mutations being a conscious occurrence in response to stimuli", I will consider it.

[Mark78L]

4 minutes ago, Genady said:

That's all for now. When I see "a case for mutations being a conscious occurrence in response to stimuli", I will consider it.

What did you think of the Nature study I linked to at the beginning of the thread? That study provides the "case for mutations being a conscious occurrence in response to stimuli". You must have missed it.
 

[Genady]

2 minutes ago, Mark78L said:

What did you think of the Nature study I linked to at the beginning of the thread? That study provides the "case for mutations being a conscious occurrence in response to stimuli". You must have missed it.
 

There is no word "conscious" in that study.

[Mark78L]

1 minute ago, Genady said:

There is no word "conscious" in that study.

Why do you need the word 'conscious' to be present in order to draw that conclusion? The study found that evolutionary mutations weren't random and appeared to be focused. While the word conscious wasn't used, the implied interpretation is there. The progression of science and relevant discoveries require a detachment from "literal thinking". The results of the study challenge the random evolutionary model, what other explanation can there be for focused mutational changes that aren't random?

Surely any inquisitive mind would be open to this concept given the data here? Here's another quote from the study:
"Our discovery yields a new account of the forces driving patterns of natural variation, challenging a long-standing paradigm regarding the randomness of mutation and inspiring future directions for theoretical and practical research on mutation in biology and evolution."

[CharonY]

1 hour ago, Mark78L said:

You don't think that cells are operating on any conscious level?

There are mechanisms that alter mutation rate. But consciousness does not play into it. Though we do not understand the concept of consciousness, it is generally accepted that some level of complex structures are involved (e.g. brains) and certainly does not extend to the cellular level. 

Just now, Mark78L said:

"Our discovery yields a new account of the forces driving patterns of natural variation, challenging a long-standing paradigm regarding the randomness of mutation and inspiring future directions for theoretical and practical research on mutation in biology and evolution."

They are referring to observed mutation bias. I.e. that certain areas (which are critical to survival) seem to be more protected from mutations. The paradigm they refer to is that these areas would expect to mutate at the same rate as the rest of the genome, but if we look at subsequent generations, those mutants would not survive and we would see differences in mutation rate because of selection.

In this paper they argue that those areas are protected via epigenetic functions, where for example repair enzymes are directed preferentially to those critical regions. Again, at no level consciousness plays a role. You also have to read the full paper. You cannot just take a sentence and imagine what it might mean. 

 

[Genady]

11 minutes ago, Mark78L said:

Why do you need the word 'conscious' to be present in order to draw that conclusion? The study found that evolutionary mutations weren't random and appeared to be focused. While the word conscious wasn't used, the implied interpretation is there. The progression of science and relevant discoveries require a detachment from "literal thinking". The results of the study challenge the random evolutionary model, what other explanation can there be for focused mutational changes that aren't random?

Surely any inquisitive mind would be open to this concept given the data here? Here's another quote from the study:
"Our discovery yields a new account of the forces driving patterns of natural variation, challenging a long-standing paradigm regarding the randomness of mutation and inspiring future directions for theoretical and practical research on mutation in biology and evolution."

The word "stimuli" is not present either. Also, they don't talk about occurrence of mutations but rather about lack of them. Plus, they don't imply your interpretation but rather suggest biochemical, epigenetic mechanism protecting the sensitive areas of genome from random mutations.

[studiot]

18 minutes ago, CharonY said:

They are referring to observed mutation bias. I.e. that certain areas (which are critical to survival) seem to be more protected from mutations. The paradigm they refer to is that these areas would expect to mutate at the same rate as the rest of the genome, but if we look at subsequent generations, those mutants would not survive and we would see differences in mutation rate because of selection.

 

On 1/5/2021 at 6:15 AM, Arete said:

There are countless observations of natural selection in so called "higher organisms". Many feature as model organisms for natural selection - stickleback fish, toads, anoles, killifish, guppies, monkeyflowers, grasshoppers, Drosophila, jellyfish, lycophytes, to name a few. There are dozens of well known manipulative experiments that have comprehensively demonstrated natural selection in populations of relatively long lived, multicellular organisms, and thousands of population genetic studies on natural populations which do the same.

Natural selection in modern humans is also directly observed. The best example that immediately comes to mind is the Framingham Heart Study.

I think the concept that you're missing is that selection is dependent on population size. In small populations, genetic drift can overwhelm selection, leading to the loss of beneficial alleles and the fixation of deleterious ones. Conversely, the larger the population size, the lower the selection coefficient required to lead to fixation or extinction of a given mutation. https://www.nature.com/scitable/knowledge/library/natural-selection-genetic-drift-and-gene-flow-15186648/

 

I would like to thank both Arete and CharonY for several excellent posts apiece, extending my knowledge of the subject.

It is really good to hear someone who knows their subject.

 

25 minutes ago, Mark78L said:

challenging a long-standing paradigm regarding the randomness of mutation

My comment on the study.

Random might not be the best adjective for the mutation process.

Accidental might be better ?

[Mark78L]

30 minutes ago, CharonY said:

...but if we look at subsequent generations, those mutants would not survive and we would see differences in mutation rate because of selection.

You're conclusion is based on the assumption that random mutations have resulted in a selective bias where key genes are less prone to mutation, and that his explains the study's uncharacteristic results. This is pure speculation on your part. What is the factor that confers protection to specific genes and not others from random mutation?

Even your conclusion contradicts the status quo, that random mutations define evolution, because you are admitting that, actually, those mutations are not random across the genome, but are instead focused on particular genes that provide a benefit - which indicates a level of conscious input in accordance with external stiumli, and focused protection on the most important survival genes.

How can specific genes develop more robust protection compared with other genes around them? All nDNA genes are made from the same substrates, are subject to the same insults, and are repaired by the same mechanisms. How, for instance, can random free radical damage have a preference over which DNA genes are damaged and mutated?
 

44 minutes ago, CharonY said:

There are mechanisms that alter mutation rate. But consciousness does not play into it. Though we do not understand the concept of consciousness...

Contradictory to make such a bold statement as fact when in the same sentence you highlight the elephant in the room - "we do not understand the concept of consciousness"... and yet you're adamant that consciousness does not play a role, when you admit this concept is not understood.

31 minutes ago, studiot said:

My comment on the study.

Random might not be the best adjective for the mutation process.

Accidental might be better ?

Thanks, but doesn't accidental imply consciousness? If something occurs accidentally then it is in opposition to the intention of something (the mutation occurred against the will of the organism, by accident) Intention requires consciousness.

[CharonY]

15 minutes ago, Mark78L said:

Even your conclusion contradicts the status quo, that random mutations define evolution, because you are admitting that, actually, those mutations are not random across the genome, but are instead focused on particular genes that provide a benefit - which indicates a level of conscious input in accordance with external stiumli, and focused protection on the most important survival genes.

You have a number of misconceptions here. First, random mutations do not define evolution. As Arete pointed out, most mutations are neutral. Second, in the paper the beneficial or essential genes are actually protected from mutations.

Quote

How can specific genes develop more robust protection compared with other genes around them? All nDNA genes are made from the same substrates, are subject to the same insults, and are repaired by the same mechanisms. How, for instance, can random free radical damage have a preference over which DNA genes are damaged and mutated?

How about you read the paper you quoted? You can start with the header "Epigenome-mediated mutation bias" and go from there. There is some lit indicated there that you want to catch up on, too.

And I doubt anyone serious considers a cell making conscious decisions. If you define consciousness that way, it becomes remarkably meaningless. Or rather, you would imply that you as a whole organism do not experience things much different than the individual cells in your body which is rather a bold statement. Assuming I am actually communicating with you rather than you hair follicles.

[studiot]

1 hour ago, Mark78L said:

Thanks, but doesn't accidental imply consciousness? If something occurs accidentally then it is in opposition to the intention of something (the mutation occurred against the will of the organism, by accident) Intention requires consciousness.

This is (supposed to be) a scientific discussion.

And in scientific discussions we are supposed to state explicitly, not imply.

That is why I am searching for an unambiguous term.

Random has already been shown to be inappropriate.

It is also inappropriate because when used in a scientific manner it has an exact meaning that does not apply here without mathematical demonstration.

Perhaps you might like to choose another word or phrase ?

And no I did not mean accidental as the opposite of deliberate.

I meant 'by chance'.

Nor am I ruling out the possibility of deliberate mutation, but I do dispute that it follows that if the results of chance are not random then they must be deliberate.

 

[Genady]

1 hour ago, studiot said:

This is (supposed to be) a scientific discussion.

And in scientific discussions we are supposed to state explicitly, not imply.

That is why I am searching for an unambiguous term.

Random has already been shown to be inappropriate.

It is also inappropriate because when used in a scientific manner it has an exact meaning that does not apply here without mathematical demonstration.

Perhaps you might like to choose another word or phrase ?

And no I did not mean accidental as the opposite of deliberate.

I meant 'by chance'.

Nor am I ruling out the possibility of deliberate mutation, but I do dispute that it follows that if the results of chance are not random then they must be deliberate.

 

Do we need another term? The subject is mutation, and this is all we need, I think. What would be a purpose of an extra adjective? 

[CharonY]

1 hour ago, studiot said:

This is (supposed to be) a scientific discussion.

And in scientific discussions we are supposed to state explicitly, not imply.

That is why I am searching for an unambiguous term.

Random has already been shown to be inappropriate.

It is also inappropriate because when used in a scientific manner it has an exact meaning that does not apply here without mathematical demonstration.

Perhaps you might like to choose another word or phrase ?

And no I did not mean accidental as the opposite of deliberate.

I meant 'by chance'.

Nor am I ruling out the possibility of deliberate mutation, but I do dispute that it follows that if the results of chance are not random then they must be deliberate.

 

I think the mechanism itself can be called "mutation" without an adjective. E.g. if you just refer to a change in the genetic sequence. Whether you want to add something else, would depend on the context. If you refer to random mutation, you might refer to a model where the mutation rates are uniform (which would be a null-hypothesis situation). An alternative use of random mutation is not based on site-specificity (it has been long known that there are e.g. hot spots, i.e. areas with higher mutation rates, for example), but on outcomes. I.e. mutations are random with respect to whether the result is beneficial, detrimental or neutral to the host. I think this is where OP might be a bit confused about. 

[studiot]

1 hour ago, CharonY said:

I think the mechanism itself can be called "mutation" without an adjective. E.g. if you just refer to a change in the genetic sequence.

Agreed.

1 hour ago, CharonY said:

Whether you want to add something else, would depend on the context. If you refer to random mutation, you might refer to a model where the mutation rates are uniform (which would be a null-hypothesis situation). An alternative use of random mutation is not based on site-specificity (it has been long known that there are e.g. hot spots, i.e. areas with higher mutation rates, for example), but on outcomes. I.e. mutations are random with respect to whether the result is beneficial, detrimental or neutral to the host. I think this is where OP might be a bit confused about. 

Yes, but it may not be the OP who is confused about the meaning of random.

The notion of random is based on the proposition of equal probabilities for every possible outcome. This is mathematically equivalent to your null hypothesis comment.

My definition of a random is therefore

" A process is random when all possible outcomes have equal probabilities"

The question then becomes

How do we assess the process when the probabilities are not equal, perhaps for the reasons you have already mentioned or perhaps for other reasons ?

For instance the outcome of a horse race is not random, even though every runner has a chance of winning, because the chances (probabilities) will not be equal.

[CharonY]

9 minutes ago, studiot said:

The notion of random is based on the proposition of equal probabilities for every possible outcome. This is mathematically equivalent to your null hypothesis comment.

I think I see your point. I think one would be very clear about the specific context to make sure which distinction one wants to make. Typically, the "random" is used as the opposite to "directed" mutations, where as a response to an environmental effect, genes are mutated towards a specific phenotype (such as in a Lamarckian model). However, if we discuss specific targets (say likelihood of one locus vs another) the "random" aspect might only be useful as a mentioned null.

[studiot]

15 minutes ago, CharonY said:

I think I see your point. I think one would be very clear about the specific context to make sure which distinction one wants to make. Typically, the "random" is used as the opposite to "directed" mutations, where as a response to an environmental effect, genes are mutated towards a specific phenotype (such as in a Lamarckian model). However, if we discuss specific targets (say likelihood of one locus vs another) the "random" aspect might only be useful as a mentioned null.

My point is that in the scientific section of a scientific website we should be scientifically accurate and correct (unlike the UK Prime Minister) common usage is not good enough for a basic scientific term with a very specific meaning.

If the probabilities are not equal then it does not mean the process does not have a stochastic model.
It means that something else is going on, ie that some additional factor is involved.
That something else could be deliberation by outside intelligent agency or internal intelligent agency, but not necessarily.

For instance calouses will develop on the hands and finger tips of archers and musicians.
Or suppose you tested a die that was 'born with' two fives, but no six due to a manufacturing error.
Your test, measuring the probabilities, would soon reveal both the extra 5 and the missing 6.
I know these are not genetic modifications, but they clearly indicate the fact that other, non intelligent, agencies could influence the process.

Edited February 1, 2022 by studiot

[CharonY]

Just now, studiot said:

My point is that in the scientific section of a scientific website we should be scientifically accurate and correct (unlike the UK Prime Minister) common usage is not good enough for a basic scientific term with a very specific meaning.

If the probabilities are not equal then it does not mean the process does not have a stochastic model.
It means that something else is going on.
That something else could be deliberation by outside intelligent agency or internal intelligent agency, but not necessarily.

For instance calouses will develop on the hands and finger tips of archers and musicians.
I know these are not genetic modifications, but they clearly indicate the fact that other, non intelligent, agencies could influence the process.

No I get that, but it is also important to note that depending on context there are different levels of accuracy that one might want to apply. I suppose saying that mutations are non-directional rather than random would be more accurate (and now that I think about it, I would probably prefer it). At the same time though, the question is whether talking to laypersons it is necessary or even helpful to provide all the caveats and details. If we get to the point when talking about mechanisms or the concept of hot-spots, epigenetic regulation and so on, then certainly. But if someone just wants a short answer it might be overkill. Just changing "random" to another adjective is likely to be inaccurate, depending on context and how precise we want to be. In other words, I think that in common conversation we have to figure out how accurate we want or can be while still being understood.

[studiot]

15 minutes ago, CharonY said:

At the same time though, the question is whether talking to laypersons it is necessary or even helpful to provide all the caveats and details

I wasn't the one quoting allegedly learned papers.

I was originally responding  to and commenting on such papers.

[joigus]

I agree with @studiot that "random" by itself doesn't mean anything much anything. People's height is "random". Yet, nobody's 14 metres high. Or 3 cm. There's such a thing as probability distributions. Randomness is not synonymous of equal probabilities. The fact that most people are in the same ballpark quantity of height doesn't mean cells "decide" anything, of course. So the argument that some probability distributions seem mighty selective doesn't mean anything as to "conscious decisions." But I'm not saying anything that @CharonY, or most members here, don't know. Just to add my voice to the astonishment of such silly arguments re-appearing here.

And if the person who re-ignited the argument thinks otherwise, they should present the evidence.

 

Edited February 2, 2022 by joigus

[CharonY]

49 minutes ago, studiot said:

I wasn't the one quoting allegedly learned papers.

I was originally responding  to and commenting on such papers.

Ah sorry, I think I went off a tangent and kind of forgot your original comment and its context. I apologize for that.

If you are referring to the quote from the paper regarding randomness I would agree that they were overselling it a bit using that terminology. It is a way to make the manuscript "sexier" I guess.