Mutation not random????

[IndigoChild5559]

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.

Indeed I remember very well a study I read about 30 years ago that concluded that bacteria mutate favoring adaptaion, not randomly. But that was 30 years ago. I have simply been keeping my eyes open all these years for any further studies that say something similar.

 

[IndigoChild5559]

Lot's of things can interfere with replication, many; probably most, random.

And yet despite this way of looking at it, the study still concluded that mutation was not random. And if not random, what is directing the mutation?

 

[Valjean]

And yet despite this way of looking at it, the study still concluded that mutation was not random. And if not random, what is directing the mutation?

No, the mutations were random, but they were differentially distributed within the genome. Critical areas were more robustly shielded and repaired.

 

[IndigoChild5559]

No, the mutations were random, but they were differentially distributed within the genome. Critical areas were more robustly shielded and repaired.

I quoted the specific part that said the mutations were not random.

 

[metis]

"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

Some are and some aren't.

 

[Valjean]

I quoted the specific part that said the mutations were not random.

Read the article again, not the headline. The mutations are not randomly distributed, but they are random. There is no force causing specific mutations. There are structures shielding certain sections of the genome, which might give the appearance of non-randomness.

 

[sayak83]

Indeed I remember very well a study I read about 30 years ago that concluded that bacteria mutate favoring adaptaion, not randomly. But that was 30 years ago. I have simply been keeping my eyes open all these years for any further studies that say something similar.

Some critical regions are more protected by DNA repair mechanisms so that mutations happens less in those places. The mutations therefore are not randomly distributed in the genome. But the mutations themselves are undirected. This is like wearing a helmet in a motorbike accident to shield ones head against damage against a crash. The crash itself causes undirected force to act on you, but the damage caused in non randomly distributed, as there is less damage to the well protected head than other parts of the body.

That is the gist of the paper

 

[IndigoChild5559]

Read the article again, not the headline. The mutations are not randomly distributed, but they are random. There is no force causing specific mutations. There are structures shielding certain sections of the genome, which might give the appearance of non-randomness.

The quote was from the body of the text, not the headline.

 

[Yazata]

"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

I just skimmed the paper and haven't yet read it in detail. But my first impression is that it's saying that the most vital genes appear to undergo mutations at a slower rate than less vital genes. This isn't really news since it's long been known (scale of decades) that some portions of the genome are highly conserved in all comparable organisms while others vary a lot. The reason for this seems to be that dna repair and protective mechanisms have evolved to be most active with regards to the most vital and thus highly conserved genes. The authors of this paper investigate this and attribute these repair and protective mechanisms to natural selection, so it isn't an argument for ID or anything like that.

More work needed on my part to understand the paper better, but that's my impression at this point.

https://www.nature.com/articles/s41586-021-04269-6.pdf

Edit: I see that Sayak83 made the same point before me. So credit to him.

 

[night912]

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.

Yes, I agree with you on the part where you don't understand where there getting at. The indications of this is because what you're saying is not what the article is saying.

 

[cladking]

Yes, I agree with you on the part where you don't understand where there getting at. The indications of this is because what you're saying is not what the article is saying.

Obviously nature isn't going to tinker much with things like how cells function or how the fetus develops. Almost every mutation would prove fatal so individuals who have off spring with such mutations do not pass down as many genes. This gets right to the heart of the simple fact that all individuals are equally fit and that all change is sudden.

 

[TagliatelliMonster]

This gets right to the heart of the simple fact that all individuals are equally fit and that all change is sudden.

That doesn't follow at all and it's demonstrably wrong also.

 

[cladking]

That doesn't follow at all and it's demonstrably wrong also.

Really?!

The absence of mutations that would probably be fatal does coincide with all individuals being equally fit?

Most mutations aren't going to kill but simply make the individual more likely likely to thrive under less common conditions. If such uncommon condition exist or arise the individual sires lots of mutants whom are more likely to thrive than any other individual. This is consistent with the theory that all change in species just like all change in life is sudden and brought about by new niches, new mutations, or new behavior.

If mutation were random there would be more death rather than more life. There would be an increased chance of a species becoming extinct rather than changing to a new niche.

 

[TagliatelliMonster]

Really?!

Yes. It's demonstrably wrong that all individuals are equally fit.

As for the part about "sudden change", that's relative and it depends what you mean by it.
Even if you mean it correctly, in the sense of things like punctuated equilibrium, then you're still incorrect, as even though mechanisms like PE are moments of bigger evolutionary shifts, slow gradual change is pretty much ongoing constantly.

And the "sudden" shifts in evolutionary pathways are only "sudden" in geological time. The changes themselves are still gradual. What actually shifts are selection pressures, allowing for more changes to be selected for, causing more "rapid" evolutionary change whereas in periods of environmental stability and species already having reached local optimums, selection will be more inclined to favor the status quo.


Consider it like this.... It's a bit simplistic, but the point is valid.

Every generation, there is a set of mutations that occurred. Every individual has a few dozen of them. Most do nothing, some might be beneficial, some might be harmful.
Let's say that in times of stability there's a chance of 0.001% of a mutation being beneficial (low, because selection favors the status quo - it's in balance and difficult to improve further)

Then some stuff occurs and the environment changes, making selection pressures shift. New niches open up. Now opportunities arise. Some food sources disappear, others appear. Some natural enemies migrate away / go extinct and some new ones appear.

Now, the chance of mutations being beneficial go up. Now, perhaps the chance is 0.1%.
This vastly enlarges the set of mutations that might be selected for. Meaning that changes more easily occur. Evolutionary change thus speeds up. But it's still gradual.

As the new reality gets established and species once again fill their niches and approach their local optimum, further "improvement" again becomes more difficult. The potential set of beneficial mutations thus goes down again. Evolution slows down with it.

The absence of mutations that would probably be fatal does coincide with all individuals being equally fit?

No.

Here's a simple present day example.
2 otherwise healthy kids catch covid.
1 dies from it, the other didn't even notice he was infected.

Which of these 2 was least fit?

 

[Valjean]

Obviously nature isn't going to tinker much with things like how cells function or how the fetus develops. Almost every mutation would prove fatal so individuals who have off spring with such mutations do not pass down as many genes. This gets right to the heart of the simple fact that all individuals are equally fit and that all change is sudden.

Why do we keep having to explain mutations, natural selection and evolution over and over again? Aren't people listening? Aren't they understanding?

All three of your assertions here are simply wrong.

 

[cladking]

Why do we keep having to explain mutations, natural selection and evolution over and over again? Aren't people listening? Aren't they understanding?

All three of your assertions here are simply wrong.

You are using improper terminology and a poor perspective to see a very highly complex reality and distill it to something that is exceedingly simple but entirely incorrect.

You are simply wedded to the idea that the fit survive and others perish or become dinner. So long as you maintain the idea that individuals which perish are by definition inferior, weak, slow, or less adapted than those which thrive then you will wind up exactly where you started; species change because only the fittest survive. You are engaging in circular reasoning on steroids.

If niches evolved then your oversimplification would have a little more accuracy. Indeed, if God's hand were driving the biosphere to some nirvana that would gradually be improved then the so called theory of evolution could be exactly accurate. But reality doesn't work this way. If God does exist He is not micromanaging all of reality and telling each individual what to do. Each individual has its own consciousness that tells it what to do and the environment/ biosphere undergoes only sudden and sometimes massive changes resulting is sudden and sometimes massive changes in species.

This is so simple it's surprising I have to keep explaining it. Darwin's "theory" is a remnant of another age which will never evolve but rather suddenly be seen in a new light showing it is wrong and always has been wrong. All individuals can thrive in its perfect environment: The lame, sick, and those born with defective genes notwithstanding.

 

[cladking]

And the "sudden" shifts in evolutionary pathways are only "sudden" in geological time. The changes themselves are still gradual. What actually shifts are selection pressures, allowing for more changes to be selected for, causing more "rapid" evolutionary change whereas in periods of environmental stability and species already having reached local optimums, selection will be more inclined to favor the status quo.

Some huge shifts in an environment can have very little effect on specific species. If there's something to chase down and eat after everything else changes then foxes, for example, might undergo little change. Generally though massive changes probably affect every species over time. The new prey for the foxes might be a little smarter, maneuverable, or faster than the old prey and there will be an imperceptible change that we can't see because it affects consciousness rather than the way the bone fossilize. There is nothing complex about this. Individuals evolve to adapt to their environment more than species ever do. Even when a species suddenly changes the off spring and parents have far more in common than a moose and squirrel.

As the new reality gets established and species once again fill their niches and approach their local optimum, further "improvement" again becomes more difficult. The potential set of beneficial mutations thus goes down again. Evolution slows down with it.

If this were true there would be more individuals dying during these periods. Not only is this illogical since high stress should mean less wastage in nature but there's no evidence for it. There are always missing links where species change rather than an abundance of fossils. Yes, obviously these changes occur over a brief period which would tend to limit the number of preserved fossils. ie- fossilization is more a function of time than individual bodies.

 

[cladking]

Yes, obviously these changes occur over a brief period which would tend to limit the number of preserved fossils. ie- fossilization is more a function of time than individual bodies.

All else being equal fossilization is cyclical and peaks during the times that species are changing. But we don't see this do we? We see few fossils in the boundaries. We see sudden changes is species just as we see sudden changes in all life and all consciousness because all change not caused by nature is due to consciousness.

 

[Valjean]

You are using improper terminology and a poor perspective to see a very highly complex reality and distill it to something that is exceedingly simple but entirely incorrect.

If anything is simplistic it's the religious view, not biology. Can't get much simpler than magic poofing.

You are simply wedded to the idea that the fit survive and others perish or become dinner. So long as you maintain the idea that individuals which perish are by definition inferior, weak, slow, or less adapted than those which thrive then you will wind up exactly where you started; species change because only the fittest survive. You are engaging in circular reasoning on steroids.

Where did you get that ideaI never proposed it. "Fit" doesn't mean faster, stronger or superior. It just means better adapted to a particular niche.

If niches evolved then your oversimplification would have a little more accuracy. Indeed, if God's hand were driving the biosphere to some nirvana that would gradually be improved then the so called theory of evolution could be exactly accurate. But reality doesn't work this way. If God does exist He is not micromanaging all of reality and telling each individual what to do. Each individual has its own consciousness that tells it what to do and the environment/ biosphere undergoes only sudden and sometimes massive changes resulting is sudden and sometimes massive changes in species.

Niches don't evolve in the biological sense, and I'm not sure what "oversimplification" you're talking about.
What evidence do you have for this god, or his micromanagement of natural history?

This is so simple it's surprising I have to keep explaining it. Darwin's "theory" is a remnant of another age which will never evolve but rather suddenly be seen in a new light showing it is wrong and always has been wrong. All individuals can thrive in its perfect environment: The lame, sick, and those born with defective genes notwithstanding.

No. Natural selection is real, and is massively evidenced.
What "new light" are you talking about? How is natural selection wrong?
What "perfect environment" are you talking about, and how can a single environment be universally salubrious?

 

[cladking]

If anything is simplistic it's the religious view, not biology. Can't get much simpler than magic poofing.
Where did you get that ideaI never proposed it. "Fit" doesn't mean faster, stronger or superior. It just means better adapted to a particular niche.
Niches don't evolve in the biological sense, and I'm not sure what "oversimplification" you're talking about.
What evidence do you have for this god, or his micromanagement of natural history?
No. Natural selection is real, and is massively evidenced.
What "new light" are you talking about? How is natural selection wrong?
What "perfect environment" are you talking about, and how can a single environment be universally salubrious?

I can't respond to this because everywhere I said "not" or "no" you read something else.

But just to be clear "fit" by any name does not exist. All individuals are equally adaptive or fit. Some thrive in different environments than others but they are no less fit, adaptable, or less likely to be naturally selected. This is simply a confusion caused by looking at something so complex using reductionistic means.