Guided evolution (split from Evolution not limited to life on earth?)

[Phi for All]

26 minutes ago, exchemist said:

Interesting.

My OED says, for meaning (1), "Confidence, reliance, trust (in the ability, goodness etc of a person ; in the efficacy or worth of a thing; or in the truth of a statement or doctrine). It does go on to say "in early use, only with reference to religious subjects; this is still the prevalent application and often colours the wider use".  So not exclusively to be used in religious contexts, though it often is.

There is nothing at all, in any of the meanings, to suggest that belief despite evidence to the contrary is in any way intrinsic to the meaning of the word. (In fact, its use in everyday speech makes it obvious that cannot be the case.)

So I think you have made that bit up.  😄

I observe quite a big difference between the way someone believes in things they can verify, and things they can't but still believe. To me, it's all belief, but faith, and we're talking about religious faith here, seems different than trust.  I don't think your OED definition hits the mark. It mashes together the concepts I'm trying to separate.

It's definitely not about "I have faith that PersonX is a good person", which I would put under a third category of belief, wishful thinking. It's something you hope is true, can't prove, but aren't as adamant about. 

And yes, it's made up. That's the way the language works when there's a need to differentiate. The way I'm asked to believe in science is different than the ways I was asked to believe in Christianity. 

And I'll admit that you have a completely different outlook in the UK on religion than my examples in the evangelical US. I have relatives that will tell you faith is the strongest form of belief BECAUSE it requires no evidence. They talk about how your faith must be unshakeable and steadfast, and how any doubt is wrong. They're proud that they don't question the things they're taught. Asking for evidence is almost sacrilegious.

So yes, making a distinction between faith and trust isn't a mainstream concept, but it's one that's helped me in reasoning my way in modern human life. 

[exchemist]

1 hour ago, Phi for All said:

I observe quite a big difference between the way someone believes in things they can verify, and things they can't but still believe. To me, it's all belief, but faith, and we're talking about religious faith here, seems different than trust.  I don't think your OED definition hits the mark. It mashes together the concepts I'm trying to separate.

It's definitely not about "I have faith that PersonX is a good person", which I would put under a third category of belief, wishful thinking. It's something you hope is true, can't prove, but aren't as adamant about. 

And yes, it's made up. That's the way the language works when there's a need to differentiate. The way I'm asked to believe in science is different than the ways I was asked to believe in Christianity. 

And I'll admit that you have a completely different outlook in the UK on religion than my examples in the evangelical US. I have relatives that will tell you faith is the strongest form of belief BECAUSE it requires no evidence. They talk about how your faith must be unshakeable and steadfast, and how any doubt is wrong. They're proud that they don't question the things they're taught. Asking for evidence is almost sacrilegious.

So yes, making a distinction between faith and trust isn't a mainstream concept, but it's one that's helped me in reasoning my way in modern human life. 

OK but you are talking about one (particularly crude) view of religious faith. The term is broader than that, at least on this side of the Atlantic, in speech and in the written word. One may speak of faith in an institution, or in a person, or in predictions, e.g.of the Met Office or a financial adviser. Admittedly such usages may be intended to draw a parallel with religious faith, but in a positive sense, whereas the sense of belief at variance with evidence would obviously have a negative connotation. But maybe in view of this exchange I should be careful not to use the term in discourse with Americans.  

  

[Phi for All]

14 minutes ago, exchemist said:

OK but you are talking about one (particularly crude) view of religious faith. The term is broader than that, at least on this side of the Atlantic, in speech and in the written word. One may speak of faith in an institution, or in a person, or in predictions, e.g.of the Met Office or a financial adviser. Admittedly such usages may be intended to draw a parallel with religious faith, but in a positive sense, whereas the sense of belief at variance with evidence would obviously have a negative connotation. But maybe in view of this exchange I should be careful not to use the term in discourse with Americans.  

I understand all that, I just see no particular efficacy in using the same term to describe what I see as completely different behavior. If history has taught me that someone is usually very capable at work assigned to them, I'll tell them I trust them with this new assignment, not that I have faith in them. I'm using past experience as a metric of my trust.

And I really needed a word to describe the kind of belief that the Abrahamic religions were requiring of me. Sacred ideas, inviolate texts, holiness everywhere, and things that didn't make sense but I was supposed to believe them anyway, That belief was supposed to be unshakeable, and these beliefs were the most important beliefs. So that's what I use the term faith for, belief that doesn't require evidence to support it. 

[exchemist]

3 minutes ago, Phi for All said:

I understand all that, I just see no particular efficacy in using the same term to describe what I see as completely different behavior. If history has taught me that someone is usually very capable at work assigned to them, I'll tell them I trust them with this new assignment, not that I have faith in them. I'm using past experience as a metric of my trust.

And I really needed a word to describe the kind of belief that the Abrahamic religions were requiring of me. Sacred ideas, inviolate texts, holiness everywhere, and things that didn't make sense but I was supposed to believe them anyway, That belief was supposed to be unshakeable, and these beliefs were the most important beliefs. So that's what I use the term faith for, belief that doesn't require evidence to support it. 

Yes I can see the logic of that, especially for someone with what sounds like a rather ghastly experience of religion in youth (I was more fortunate).  I am merely pointing out it is not a distinction you can necessarily expect others, in other English speaking countries, to understand automatically by these terms.

Faith is not a pejorative word over here. Its connotations are generally neutral to positive.  "Blind faith" would be pejorative, however, and I think that is what you are describing, actually.

[Phi for All]

Just now, exchemist said:

Yes I can see the logic of that, especially for someone with what sounds like a rather ghastly experience of religion in youth (I was more fortunate).  I am merely pointing out it is not a distinction you can necessarily expect others, in other English speaking countries, to understand automatically by these terms.

Faith is not a pejorative word over here. Its connotations are generally neutral to positive.  "Blind faith" would be pejorative, however, and I think that is what you are describing, actually.

I think you're right. When I'm talking about people believing strongly in something they can't support, I'm using faith to mean blind faith.

[Luc Turpin]

5 hours ago, CharonY said:

What you are talking about are generally not related to evolution as they occur only within the organism and are (generally) not transmitted to the next generation via the germline (there is evidence for some exceptions, though).

In broader terms, it is important to note that DNA itself is not doing anything. Simplified, their main role is a data repository that needs to be first transcribed into mRNA and then translated into proteins. The latter are doing all the work. Obviously our cells (and by extension our body) need to be able to address changes in the environment, each cell type has to fulfill different functions despite all having the same DNA. So what is happening is that transcription/translation is regulated via a wide range of internal and external cues resulting e.g. different protein compositions in different cell types or adaptive changes in response to some environmental signals.

However, this dynamic is within an organism and is not transmitted to the next generation (e.g. in a Lamarckian sense).

So, below indicated factors have marginal impact on evolution?

1-      Some epigenetic states transmitted intergenerationally; Heritable “epialleles” common in plants and subject to natural selection

2-      Epigenetic variation enhancing phenotypic plasticity and phenotypic variance, thus can modulate the effect of natural selection on sequence-based genetic variation.

3-      Phenotypic plasticity central to adaptability, epigenetic mechanisms generating plasticity and acclimation important to consider in evolutionary theory

4-      Some genes under selection to be ‘imprinted’ identifying the sex of the parent from which they were derived, leading to parent-of-origin-dependent gene expression and effects, which can generate hybrid disfunction and contribute to speciation.

5-      Epigenetic processes contributing directly to DNA sequence evolution, because they act as mutagens and modulate genome stability by keeping transposable elements in check

From this article

https://pubmed.ncbi.nlm.nih.gov/33866814/#:~:text=Epigenetics%20is%20the%20study%20of,the%20preservation%20of%20genome%20integrity

“Epigenetic effects are not only common, but can also underlie and influence many aspects of evolution. This is true for both epigenetic effects that are only expressed within a single generation, as well as for trans-generational epigenetic inheritance.”

https://www.nature.com/articles/s41437-018-0113-y

"Epigenetic marks, including DNA methylation and Histone modifications, can be triggered by environmental effects, and lead to permanent changes in gene expression, affecting the phenotype of an organism"

https://onlinelibrary.wiley.com/doi/10.1002/jez.b.22571

Please let me know what you think

[CharonY]

This is a bit of a discussion going on, and goes beyond textbook knowledge. I.e. the questions there are not clearly resolved. There are certainly proponents stating that we have overlooked their importance for too long, and there might be something to it. Others might argue that the importance might be overstated as existing models seem to deal with overall questions fairly well. It is not my field, so I am certainly not familiar with all the intricacies (and my knowledge is also somewhat dated) but my reading when things came out was that yes, there is likely an influence, but given all the other aspects that are already known to play a role, it looks more like an addition that one has to acknowledge only in certain models. 

That being said, I believe there is more lit out there specific regarding plants, but as I am not a plant person, I have no insights about their significance.

That all being said, if one wants to start about the basics of evolution, one should start with the basics before exploring more complicate advanced topics. Inevitably, starting off the other way round will lead to misunderstanding and confusion.

[iNow]

7 hours ago, exchemist said:

So I think you have made that bit up.

I’m grateful for the open exchange of ideas you shared with Phi and largely agree with you both.

I will just add that language itself also evolves, and here in my own posting behavior I become one of the selection mechanisms by which words and usages ultimately propagate.   ✌️

[StringJunky]

3 hours ago, iNow said:

I’m grateful for the open exchange of ideas you shared with Phi and largely agree with you both.

I will just add that language itself also evolves, and here in my own posting behavior I become one of the selection mechanisms by which words and usages ultimately propagate.   ✌️

iNow is a forcing in the evolution of letters.  Alluding to another contentious conversation elsewhere: forcings are inherently the designers of what happens to mutations.

[AIkonoklazt]

8 hours ago, exchemist said:

OK but you are talking about one (particularly crude) view of religious faith. The term is broader than that, at least on this side of the Atlantic, in speech and in the written word. One may speak of faith in an institution, or in a person, or in predictions, e.g.of the Met Office or a financial adviser. Admittedly such usages may be intended to draw a parallel with religious faith, but in a positive sense, whereas the sense of belief at variance with evidence would obviously have a negative connotation. But maybe in view of this exchange I should be careful not to use the term in discourse with Americans.  

  

I think the term "with Americans" in the end should really be "with people with certain kinds of experiences and interactions that are not conducive to that particular usage of the term" or simply "people who have largely negative associations with the term."

The meaning some people attach to the term "faith" is actually those attached to the term "religiosity."

9 hours ago, Phi for All said:

I have relatives that will tell you faith is the strongest form of belief BECAUSE it requires no evidence. They talk about how your faith must be unshakeable and steadfast, and how any doubt is wrong. They're proud that they don't question the things they're taught. Asking for evidence is almost sacrilegious.

Yikes (bolded for emphasis)
William James basically said that if you've experienced something, you have, and if you haven't, you just haven't https://krypton.mnsu.edu/~jp6372me/THE WILL TO BELIEVE .pdf In that sense, there's no sacrilege in asking questions simply in order to know something.

Getting into the technicality of the assumed passage regarding "doubting Thomas," what Thomas was doing wasn't doubting but something else entirely:
 

Quote

• Thomas refused the believe the testimony of many witnesses and reliable witnesses.
• Thomas made an extreme demand for evidence; evidence of not only sight but of touch, and to repeatedly touch the multiple wounds of Jesus.
• Thomas steadfastly refused to believe unless these conditions were met (I will not believe).

i. “Normally this is taken to indicate that Thomas was of a more skeptical turn of mind than the others, and, of course, he may have been. But another possibility should not be overlooked, namely that he was so shocked by the tragedy of the crucifixion that he did not find it easy to think of its consequences as being annulled.” (Morris)

ii. “Perhaps he had abandoned hope; — the strong evidence of his senses having finally convinced him that the pierced side and wounded hands betokened such a death that revivification was impossible.” (Alford)

iii. Adam Clarke called Thomas’ unbelief unreasonable, obstinate, prejudiced, presumptuous, and insolent. Still, it was good and significant that Thomas still wanted to be around those who believed.

iv. The unbelief of Thomas was strong, but honestly spoken. It was good that he refused to pretend to believe when he did not believe.

v. Some find it interesting that Thomas made no mention of wounds in the feet of Jesus. “There is no mention in this Gospel, or in Matthew or Luke, of the piercing of the feet. That the feet of Jesus may have been nailed to the cross, rather than fastened with a rope, which was the common practice, is an inference from Luke 24:39.” (Tasker)

 

Edited January 10 by AIkonoklazt

[Luc Turpin]

8 hours ago, CharonY said:

This is a bit of a discussion going on, and goes beyond textbook knowledge. I.e. the questions there are not clearly resolved. There are certainly proponents stating that we have overlooked their importance for too long, and there might be something to it. Others might argue that the importance might be overstated as existing models seem to deal with overall questions fairly well. It is not my field, so I am certainly not familiar with all the intricacies (and my knowledge is also somewhat dated) but my reading when things came out was that yes, there is likely an influence, but given all the other aspects that are already known to play a role, it looks more like an addition that one has to acknowledge only in certain models. 

That being said, I believe there is more lit out there specific regarding plants, but as I am not a plant person, I have no insights about their significance.

That all being said, if one wants to start about the basics of evolution, one should start with the basics before exploring more complicate advanced topics. Inevitably, starting off the other way round will lead to misunderstanding and confusion.

I will then take a pause here and explore by myself the basics of evolution.

Thanks for the discussion and suggestion.

[Luc Turpin]

I am autodidact, so I guess it shows.

[Luc Turpin]

Evolution is about passing on genes to the next generation, and genes change by random mutations, with an intricate environmental interplay. However, do naturally occurring CRISPR and Fanzor gene-editing systems diminish randomness in evolution?  Do they, as built-in mechanisms with at least virus countering intentions, increase systematicity in evolution?

“CRISPR-Cas9 was adapted from a naturally occurring genome editing system that bacteria use as an immune defense. When infected with viruses, bacteria capture small pieces of the viruses' DNA and insert them into their own DNA in a particular pattern to create segments known as CRISPR arrays. The CRISPR arrays allow the bacteria to "remember" the viruses (or closely related ones). If the viruses attack again, the bacteria produce RNA segments from the CRISPR arrays that recognize and attach to specific regions of the viruses' DNA. The bacteria then use Cas9 or a similar enzyme to cut the DNA apart, which disables the virus.”

https://medlineplus.gov/genetics/understanding/genomicresearch/genomeediting/https://medlineplus.gov/genetics/understanding/genomicresearch/genomeediting/

 

“A diverse set of species, from snails to algae to amoebas, make programmable DNA-cutting enzymes called Fanzors—and a new study from scientists at MIT's McGovern Institute for Brain Research has identified thousands of them. Fanzors are RNA-guided enzymes that can be programmed to cut DNA at specific sites, much like the bacterial enzymes that power the widely used gene-editing system known as CRISPR. The newly recognized diversity of natural Fanzor enzymes, reported Sept. 27 in the journal Science Advances, gives scientists an extensive set of programmable enzymes that might be adapted into new tools for research or medicine.”

https://phys.org/news/2023-10-thousands-programmable-dna-cutters-algae-snails.html

[CharonY]

3 minutes ago, Luc Turpin said:

However, do naturally occurring CRISPR and Fanzor gene-editing systems diminish randomness in evolution?  Do they, as built-in mechanisms with at least virus countering intentions, increase systematicity in evolution?

I think you have to be careful when thinking about randomness in evolution. In fact, there are multiple levels to think about it. First, is the mechanisms which create diversity. They include mutations, recombination and associated mechanisms. They are mostly random for most intents and purposes, but looking deeply into it, there are certain chemical reactions resulting in certain mutations that are slightly more likely than others, for example. But the likelihood that they are happening at all, are mostly stochastic.

Then, you have the mechanisms affecting the inheritance of genetic material. Here, we clearly have random effects (e.g. drift) but also non-random mechanisms (e.g. selection).

Finally, we also have the overall view on evolution. The important bit here is that because of potential strong effects of selection, evolution is not an entirely random walk. However, the measure here is fitness (i.e. ability to transmit genetic material to the next generation, not fitness in the physiological or survival sense). But fitness is highly context-specific and depend on the organism and its ecological niche. So while not random, there is also no clear goal, either.

Going back, things happening at the First (lowest) level, do not have systematic impacts as such, they are one of many traits that affect the impact the system in terms of e.g. how fast new traits might appear, but they work in conjunction with myriads of other factors affecting traits. Selection, on the other hand, works on a higher level and takes the combination of traits, in a given ecological situation and there impacts the gene pool systematically, if you want to call it that.

[Luc Turpin]

6 minutes ago, CharonY said:

I think you have to be careful when thinking about randomness in evolution. In fact, there are multiple levels to think about it. First, is the mechanisms which create diversity. They include mutations, recombination and associated mechanisms. They are mostly random for most intents and purposes, but looking deeply into it, there are certain chemical reactions resulting in certain mutations that are slightly more likely than others, for example. But the likelihood that they are happening at all, are mostly stochastic.

Then, you have the mechanisms affecting the inheritance of genetic material. Here, we clearly have random effects (e.g. drift) but also non-random mechanisms (e.g. selection).

Finally, we also have the overall view on evolution. The important bit here is that because of potential strong effects of selection, evolution is not an entirely random walk. However, the measure here is fitness (i.e. ability to transmit genetic material to the next generation, not fitness in the physiological or survival sense). But fitness is highly context-specific and depend on the organism and its ecological niche. So while not random, there is also no clear goal, either.

Going back, things happening at the First (lowest) level, do not have systematic impacts as such, they are one of many traits that affect the impact the system in terms of e.g. how fast new traits might appear, but they work in conjunction with myriads of other factors affecting traits. Selection, on the other hand, works on a higher level and takes the combination of traits, in a given ecological situation and there impacts the gene pool systematically, if you want to call it that.

Then, what does CRISPR and Fanzors gene-editing mechanisms do to the theory of evolution? Does it changes anything to our currrent understanding of how it works?

[Bufofrog]

1 minute ago, Luc Turpin said:

Then, what does CRISPR and Fanzors gene-editing mechanisms do to the theory of evolution? Does it changes anything to our currrent understanding of how it works?

I would say no.  CRISPR has nothing to do with evolution.

[Luc Turpin]

I was asking, because epigenetics was a gene transcription mechanism while CRISPR and Fanzors are gene editing mechanisms

7 minutes ago, Bufofrog said:

I would say no.  CRISPR has nothing to do with evolution.

Why would it not be if it is a gene editing mechanism and genes are passed on to future generations?

[CharonY]

17 minutes ago, Bufofrog said:

I would say no.  CRISPR has nothing to do with evolution.

Pretty much that. At least in the given context of understanding the basics of evolution. It is interesting for the specific question of the evolution of arms race among cells and viruses. There are a lot of them around, including the very long-known restriction enzyme systems, which bacteria use to degrade foreign DNA or the range of weapons that bacteria use against each other. It all makes sense from the viewpoint of a selfish gene (though that itself is a simplified narrative, of course).

 

10 minutes ago, Luc Turpin said:

Why would it not be if it is a gene editing mechanism and genes are passed on to future generations?

It doesn't change the overall system. It is just one of many existing traits (or virtually all traits) that exist. You could say the same for virtually anything in a cell from polymerases to ribosomes. CRISPR is nothing extraordinary in that regard. You see a lot of it around in press, because it is useful for biotechnological applications but so are polymerases and restriction enzymes. They are just much more established and therefore less showy.

[Luc Turpin]

Need to absorb all of this! Thanks!

[Bufofrog]

21 minutes ago, Luc Turpin said:

Why would it not be if it is a gene editing mechanism and genes are passed on to future generations?

At that point it would become part of evolution, but CRISPR itself is not part of evolution IMO.

[zapatos]

If evolution of flowers can in part be attributed to the behavior of certain organisms (such as bees) it would seem that the change of flowers (or other living things) by humans (via CRISPR) could also be called Evolution. Certainly humans are every bit as natural as bees are.

[Luc Turpin]

9 minutes ago, zapatos said:

If evolution of flowers can in part be attributed to the behavior of certain organisms (such as bees) it would seem that the change of flowers (or other living things) by humans (via CRISPR) could also be called Evolution. Certainly humans are every bit as natural as bees are.

38 minutes ago, Bufofrog said:

At that point it would become part of evolution, but CRISPR itself is not part of evolution IMO.

But CRISPR, Fanzors, polymerases and restriction enzymes are initially natural, not man-made mechanisms. If I am correct, it is after discovering these mechanisms in nature that they were then replicated by man and put to use.

Therefore, if CRISPR, Fanzors and, I think, polymerases and restriction enzymes edit genes by natural means (not the human kind), which are then passed on to future generations; how could they then not affect evolution?

 

1 hour ago, CharonY said:

 

It doesn't change the overall system. It is just one of many existing traits (or virtually all traits) that exist. You could say the same for virtually anything in a cell from polymerases to ribosomes. CRISPR is nothing extraordinary in that regard. You see a lot of it around in press, because it is useful for biotechnological applications but so are polymerases and restriction enzymes. They are just much more established and therefore less showy.

Can you please expand as I still do not understand why something that edit's genes is not affecting evolution.

[CharonY]

41 minutes ago, Luc Turpin said:

But CRISPR, Fanzors, polymerases and restriction enzymes are initially natural, not man-made mechanisms. If I am correct, it is after discovering these mechanisms in nature that they were then replicated by man and put to use.

Therefore, if CRISPR, Fanzors and, I think, polymerases and restriction enzymes edit genes by natural means (not the human kind), which are then passed on to future generations; how could they then not affect evolution?

 

Can you please expand as I still do not understand why something that edit's genes is not affecting evolution.

First, it does not edit genes as such. It can be exploited for such purposes (in biology, we have a long history of using cellular enzymes for genetic work), however in nature it basically just recognizes foreign (viral) genetic material and just degrades it.

Second, there are other enzymes, such as recombinases that can integrate foreign DNA into its genome, as well as other mechanisms that prevent it (e.g. restriction enzymes). But even our usual DNA replication system that tries to copy without errors, does, in fact eventually introduce errors, which creates mutations. In other words, there are a lot of things that can alter DNA (internally and externally)

Here, you have to go back to the hierarchies that I a referred to earlier. On the mechanistic levels a lot of thing manipulate genetic material. Either by making errors or allowing errors and so on. Their impact on evolution is not zero, but rather it affects the overall genetic landscape in terms of e.g. expected mutation rate, potential role of horizontal gene transfer and so on. However, when it comes to the mechanisms of evolution, e.g. selection, the same rules apply as for any other traits that a cell or organism might have.

So if you have cell that is very promiscuous with gathering foreign DNA (e.g. it does not have restriction enzymes and has a highly active transformation system), it could get lucky and get DNA from the enviroment that is highly useful and it will be positively selected. Conversely, it might get a lot of useless DNA which just cost energy to replicate and then its fitness will go down.

I.e. you should not think too much in terms of yes/no but rather on which level and how much. If something impacts genetic material itself, it can affect certain overall parameters (again, mutation rate being the most obvious ones), but beyond that, it does not have a particularly different role. Depending on environment, these might be very important. For example, in an environment with a lot of viruses/phages, having CRISPR as protection might be very important. In other environments, it may be much less so.

1 hour ago, Bufofrog said:

At that point it would become part of evolution, but CRISPR itself is not part of evolution IMO.

I think we have to be a bit more precise. Luckily, I think we have moved away from the idea of guided evolution to a large extent. But now that we have arrived at a somewhat better place, I think absolutes are not really helpful. CRISPR is an enzyme complex as any other and proteins obviously do have functions, leading to traits, which might then be under selection.

So thinking that CRISPR somehow changes the course of evolution single-handedly is clearly not what is happening (if we ignore artificial breeding for the moment). Because at that point we might as well argue how dead we all would be without, say, ribosomes which I think is not terribly helpful (though there is a reason why they so conserved).

[sethoflagos]

20 minutes ago, CharonY said:

Here, you have to go back to the hierarchies that I a referred to earlier. On the mechanistic levels a lot of thing manipulate genetic material. Either by making errors or allowing errors and so on. Their impact on evolution is not zero, but rather it affects the overall genetic landscape in terms of e.g. expected mutation rate, potential role of horizontal gene transfer and so on. However, when it comes to the mechanisms of evolution, e.g. selection, the same rules apply as for any other traits that a cell or organism might have.

Just to emphasise this crucial point, consider the major introgression of 'alien' DNA the ancestors of some of us experienced in the not too distant past. Yet the vast majority of our genome has been swept clean of neanderthal alleles (the so-called neanderthal deserts). This example is far from the picture of small random mutations slowly accumulating over time. And yet the end result is just what Darwin would have predicted. We retained useful alleles, particularly those helpful to climate adaptation and immune responses, and lost those those that didn't sit well with the core sapiens 'team' of genes. It undoubtedly influenced the speed of evolution, but the fundamental principle of evolution by natural selection remained unchallenged.

 

As we're in the Speculations section, I might add that I'm inclined to the view that evolution by natural selection is an inevitable process driven by differential efficiencies in the utilisation of energy flow through a system. The detailed mechanics of genetics then becomes more of a consequential effect than a prime.cause.

[Luc Turpin]

 

1 hour ago, CharonY said:

First, it does not edit genes as such. It can be exploited for such purposes (in biology, we have a long history of using cellular enzymes for genetic work), however in nature it basically just recognizes foreign (viral) genetic material and just degrades it.

Second, there are other enzymes, such as recombinases that can integrate foreign DNA into its genome, as well as other mechanisms that prevent it (e.g. restriction enzymes). But even our usual DNA replication system that tries to copy without errors, does, in fact eventually introduce errors, which creates mutations. In other words, there are a lot of things that can alter DNA (internally and externally)

Here, you have to go back to the hierarchies that I a referred to earlier. On the mechanistic levels a lot of thing manipulate genetic material. Either by making errors or allowing errors and so on. Their impact on evolution is not zero, but rather it affects the overall genetic landscape in terms of e.g. expected mutation rate, potential role of horizontal gene transfer and so on. However, when it comes to the mechanisms of evolution, e.g. selection, the same rules apply as for any other traits that a cell or organism might have.

So if you have cell that is very promiscuous with gathering foreign DNA (e.g. it does not have restriction enzymes and has a highly active transformation system), it could get lucky and get DNA from the enviroment that is highly useful and it will be positively selected. Conversely, it might get a lot of useless DNA which just cost energy to replicate and then its fitness will go down.

I.e. you should not think too much in terms of yes/no but rather on which level and how much. If something impacts genetic material itself, it can affect certain overall parameters (again, mutation rate being the most obvious ones), but beyond that, it does not have a particularly different role. Depending on environment, these might be very important. For example, in an environment with a lot of viruses/phages, having CRISPR as protection might be very important. In other environments, it may be much less so.

I think we have to be a bit more precise. Luckily, I think we have moved away from the idea of guided evolution to a large extent. But now that we have arrived at a somewhat better place, I think absolutes are not really helpful. CRISPR is an enzyme complex as any other and proteins obviously do have functions, leading to traits, which might then be under selection.

So thinking that CRISPR somehow changes the course of evolution single-handedly is clearly not what is happening (if we ignore artificial breeding for the moment). Because at that point we might as well argue how dead we all would be without, say, ribosomes which I think is not terribly helpful (though there is a reason why they so conserved).

Very good overall explanation

I am still having difficulty with how so much complexity is able to be mostly driven by mechanistic processes. It seems as if machines would break down even before being able to play the survival of fittest game.

1 hour ago, CharonY said:

 

I think we have to be a bit more precise. Luckily, I think we have moved away from the idea of guided evolution to a large extent. But now that we have arrived at a somewhat better place, I think absolutes are not really helpful. CRISPR is an enzyme complex as any other and proteins obviously do have functions, leading to traits, which might then be under selection.

 

In French, we would say, "le retour du balancier". (the return of the pendulum if this exists in English).

51 minutes ago, sethoflagos said:

As we're in the Speculations section, I might add that I'm inclined to the view that evolution by natural selection is an inevitable process driven by differential efficiencies in the utilisation of energy flow through a system. The detailed mechanics of genetics then becomes more of a consequential effect than a prime.cause.

I have questions to ask on this, but they might not belong in this thread, so I will let it go.