An Unrecognized Fallacy?

[Luc Turpin]

17 hours ago, CharonY said:

I would suggest that you pull out a paper where you find such a situation and we can discuss it. The question to me is whose expectations the results are not matching.

 

Pick one!

Convergent Evolution

https://www.science.org/doi/10.1126/science.ado1663

Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations

https://www.cell.com/cell-genomics/fulltext/S2666-979X(24)00170-8

Meet the Microscopic Thieves Fighting Infections With Stolen Genes

https://scitechdaily.com/meet-the-microscopic-thieves-fighting-infections-with-stolen-genes/

Bizarre bacteria defy textbooks by writing new genes,

https://www.nature.com/articles/d41586-024-01477-8

Cooperative genes in smart systems: Toward an inclusive new synthesis in evolution,

https://www.sciencedirect.com/science/article/abs/pii/S007961072400035X

Ancient retroviruses played a key role in the evolution of vertebrate brains, suggest researchers 

https://phys.org/news/2024-02-ancient-retroviruses-played-key-role.html

The New Biology: A Battle between Mechanism and Organicism

https://www.hup.harvard.edu/books/9780674972247

Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory,

https://academic.oup.com/mbe/article/40/4/msad079/7100680?login=false

De novo genes with an lncRNA origin encode unique human brain developmental functionality,

https://www.nature.com/articles/s41559-022-01925-6

Sedimentary DNA can influence evolution: Establishing mineral facilitated horizontal gene transfer as a route to bacterial fitness,"

https://www.biorxiv.org/content/10.1101/2023.01.24.525235v1

DNA replication in early embryos differs from previous assumptions, study shows

https://phys.org/news/2024-08-dna-replication-early-embryos-differs.html#google_vignette

Bacteria encode hidden genes outside their genome; do we?

https://phys.org/news/2024-08-bacteria-encode-hidden-genes-genome.html

“Alien Biology” Uncovered: Bacteria’s Floating Genes Leave Scientists Baffled

https://scitechdaily.com/alien-biology-uncovered-bacterias-floating-genes-leave-scientists-baffled/

Why is There No Cure For Huntington’s

https://jonlieffmd.com/blog/why-is-there-no-cure-for-huntingtons

 

14 hours ago, swansont said:

The underlying issue is how you can lack knowledge and yet be utterly convinced that you’re correct. 

I am not utterly convinced that I am correct, just less certain that the prevailing theory is utterly correct.

Edited October 2 by Luc Turpin

[CharonY]

3 hours ago, Luc Turpin said:

Pick one!

Convergent Evolution

https://www.science.org/doi/10.1126/science.ado1663

Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations

https://www.cell.com/cell-genomics/fulltext/S2666-979X(24)00170-8

Meet the Microscopic Thieves Fighting Infections With Stolen Genes

https://scitechdaily.com/meet-the-microscopic-thieves-fighting-infections-with-stolen-genes/

Bizarre bacteria defy textbooks by writing new genes,

https://www.nature.com/articles/d41586-024-01477-8

Cooperative genes in smart systems: Toward an inclusive new synthesis in evolution,

https://www.sciencedirect.com/science/article/abs/pii/S007961072400035X

Ancient retroviruses played a key role in the evolution of vertebrate brains, suggest researchers 

https://phys.org/news/2024-02-ancient-retroviruses-played-key-role.html

The New Biology: A Battle between Mechanism and Organicism

https://www.hup.harvard.edu/books/9780674972247

Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory,

https://academic.oup.com/mbe/article/40/4/msad079/7100680?login=false

De novo genes with an lncRNA origin encode unique human brain developmental functionality,

https://www.nature.com/articles/s41559-022-01925-6

Sedimentary DNA can influence evolution: Establishing mineral facilitated horizontal gene transfer as a route to bacterial fitness,"

https://www.biorxiv.org/content/10.1101/2023.01.24.525235v1

DNA replication in early embryos differs from previous assumptions, study shows

https://phys.org/news/2024-08-dna-replication-early-embryos-differs.html#google_vignette

Bacteria encode hidden genes outside their genome; do we?

https://phys.org/news/2024-08-bacteria-encode-hidden-genes-genome.html

“Alien Biology” Uncovered: Bacteria’s Floating Genes Leave Scientists Baffled

https://scitechdaily.com/alien-biology-uncovered-bacterias-floating-genes-leave-scientists-baffled/

Why is There No Cure For Huntington’s

https://jonlieffmd.com/blog/why-is-there-no-cure-for-huntingtons

 

I am not utterly convinced that I am correct, just less certain that the prevailing theory is utterly correct.

This is just a paper dump and gets dangerously close to an attempt at a Gish gallop. As I said, the issues seems that you might not understand the background of the papers sufficiently and I am not going to start guessing where it might be based on a random assortment of papers. To avoid that, you should pick out one paper and explain why you think that the results contradict existing assumptions (rather than pointing out novelty, as per usual in research). I will also encourage you to only look at papers rather than pop-sci articles, which often grossly misunderstand the publications.

As the topic has gravitated towards evolution, I would suggest that you frame your question in that regard and state, exactly what you think the expectations of researchers are and how the results defied expectations (again, don't confuse it with regular novelty).

  

21 hours ago, Luc Turpin said:

I may very well be making rather bold statements, but it never ceases to amaze me that when I look at research on the topic, that results don't match with expectations.

[...]

Agree to share a paper with you. The expectations are oftentimes those of the researcher.

 

 

[TheVat]

4 hours ago, Luc Turpin said:

Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory

From the article intro:

 

Quote

Although gain of transcription and translation features guarantees de novo birth of a protein coding gene, it does not ensure that the gene would persist in the genome for many generations. The newly born gene can lose the features as easily as it gained them unless it has been fixed in the genome, for example via evolutionary selection. Specifically, if the protein synthesized by the de novo gene provides a fitness advantage to the host organism, it will undergo positive selection (Keeling et al. 2019). Simultaneously, the protein should have low toxicity and cost of synthesis, to survive negative selection....

Reading what you cite is helpful.  

Edited October 2 by TheVat
fix

[Luc Turpin]

1 hour ago, TheVat said:

From the article intro:

 

Reading what you cite is helpful.  

How about the rest of the references?

Yes, it loses the gained features, but even a temporary trajectory runs counter to the no direction of evolution.

 

 

 

Edited October 2 by Luc Turpin

[CharonY]

34 minutes ago, Luc Turpin said:

Yes, it loses the gained features, but even a temporary trajectory runs counter to the no direction of evolution.

Please explain what you mean with no direction of evolution and how it applies here.

[Luc Turpin]

2 hours ago, CharonY said:

This is just a paper dump and gets dangerously close to an attempt at a Gish gallop. As I said, the issues seems that you might not understand the background of the papers sufficiently and I am not going to start guessing where it might be based on a random assortment of papers. To avoid that, you should pick out one paper and explain why you think that the results contradict existing assumptions (rather than pointing out novelty, as per usual in research). I will also encourage you to only look at papers rather than pop-sci articles, which often grossly misunderstand the publications.

As the topic has gravitated towards evolution, I would suggest that you frame your question in that regard and state, exactly what you think the expectations of researchers are and how the results defied expectations (again, don't confuse it with regular novelty).

  

 

 

 

59 minutes ago, CharonY said:

Please explain what you mean with no direction of evolution and how it applies here.

 

Random mutations occur and those offering a survival advantage get passed on to future generations. My comprehension is that beyond that, there is no sense of direction in evolution. However, as stated in the tittle of the article (Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory) and for other studies showing evolutionary convergence (including the one posted here), there appears to be more direction than anticipated to evolution. This runs counter to the dictum that evolutionary events are random. 

 I could have also chosen one of the HGT articles. Evolution was all about VGT, then came HGT, which was a surprise in itself. However, it was considered a minor player in evolution in earlier days. But, again, recent research seems to suggest that it plays a very big role in evolution; again, a surprise. So, here we are with not only passing our genes to the next generation, but also someone else’s genes. 

Both of these (non-random and commonality rather than individuality) would be requirements for purpose, but not showing purpose in of itself.

Edited October 2 by Luc Turpin

[swansont]

40 minutes ago, Luc Turpin said:

Random mutations occur and those offering a survival advantage get passed on to future generations. My comprehension is that beyond that, there is no sense of direction in evolution. However, as stated in the tittle of the article (Neutral Models of De Novo Gene Emergence Suggest that Gene Evolution has a Preferred Trajectory) and for other studies showing evolutionary convergence (including the one posted here), there appears to be more direction that anticipated to evolution. This runs counter to the dictum that evolutionary events are random. 

 I could have also chosen one of the HGT articles. Evolution was all about VGT, then came HGT, which was a surprise in itself. However, it was considered a minor player in evolution in earlier days. But, again, recent research seems to suggest that it plays a very big role in evolution; again, a surprise. So, here we are with not only passing our genes to the next generation, but also someone else’s genes. 

Both of these (non-random and commonality rather than individuality) would be requirements for purpose, but not showing purpose in of itself.

You were asked to explain what you mean by no direction in evolution and how it applies here. You did not do so.

I’d also ask for you to tell us why you think “evolution” (as in evolution has no direction) and “gene evolution” refer to the same thing.

 

“This runs counter to the dictum that evolutionary events are random.”

This is not true. The dictum is that mutations are random. Selection is not. Thus, there is no dictum that evolutionary events are random.

[CharonY]

3 hours ago, Luc Turpin said:

Random mutations occur and those offering a survival advantage get passed on to future generations. My comprehension is that beyond that, there is no sense of direction in evolution.

This is a flawed on multiple levels, but specifically we recognize shaping forces of evolution, including natural selection, sexual selection but also drift and gene flow. I think you are confusing what layperson think in terms of direction of evolution. Examples include things like evolution towards higher intelligence. These are wrong as evolution as a whole has not predisposition towards any given feature.

However, as Darwin recognized first, there are shaping forces, and within a given ecological/environmental context, there is a tendency toward higher fitness (which is not necessarily the same as survival). Likewise, evolutionary history creates boundaries to the evolutionary landscape. I.e. if your species has a given body plan, subsequent developments tend to be based on them rather than allowing radical changes, once a certain complexity threshold is reached. These are all well known things and only surprising if one is not aware of them.

HGT has origins in the bacterial realm and was mostly ignored by folks who worked on complex organisms. In fact, microbial evolution is very tricky as certain tools used for animals and plants did not work. There are no fossil records and you need to use molecular methods that were fairly new. The mechanism was known for longer of that, and the overall role of mobile genetic elements was only poorly understood, mostly because techniques likes sequencing were unaffordable. Now we do have a broader appreciation of it though it is still difficult to figure out how they as yet another of the many mechanisms of evolution. None of these change anything regarding the basic premises. Also, we will keep finding new molecular mechanisms we might eventually find that some have a more important impact in some species, no impact in others and so on. These are just regular discoveries within the confines of evolutionary theories, not contradicting them, just because folks did not know that they exist.

This argument seems to suggest a very limited view on evolution as we understand it. The new building blocks we find tend to help us understand evolution better and so far there has been no need for major revisions. Rather, we tend to add things, which is why we keep talking about synthesis,  rather than revision.

 

 

 

[Luc Turpin]

16 hours ago, swansont said:

You were asked to explain what you mean by no direction in evolution and how it applies here. You did not do so.

I did explain my position of no direction: "Random mutations occur and those offering a survival advantage get passed on to future generations. My comprehension is that beyond that, there is no sense of direction in evolution"

16 hours ago, swansont said:

“This runs counter to the dictum that evolutionary events are random.”

This is not true. The dictum is that mutations are random. Selection is not. Thus, there is no dictum that evolutionary events are random.

Selection being random or not does not change the fact that according to 'dictum", evolution has no aim, no purpose, no goal; which was the point that I was trying to make. We are either insignificant things that happen to be standing on a piece of rock that is hurtling to nowhere in the vast expanse of nothingness of the universe, or there is something going on. You cannot have a piece of the pie without the pie.

12 hours ago, CharonY said:

This is a flawed on multiple levels, but specifically we recognize shaping forces of evolution, including natural selection, sexual selection but also drift and gene flow. I think you are confusing what layperson think in terms of direction of evolution. Examples include things like evolution towards higher intelligence. These are wrong as evolution as a whole has not predisposition towards any given feature.

However, as Darwin recognized first, there are shaping forces, and within a given ecological/environmental context, there is a tendency toward higher fitness (which is not necessarily the same as survival). Likewise, evolutionary history creates boundaries to the evolutionary landscape. I.e. if your species has a given body plan, subsequent developments tend to be based on them rather than allowing radical changes, once a certain complexity threshold is reached. These are all well known things and only surprising if one is not aware of them.

HGT has origins in the bacterial realm and was mostly ignored by folks who worked on complex organisms. In fact, microbial evolution is very tricky as certain tools used for animals and plants did not work. There are no fossil records and you need to use molecular methods that were fairly new. The mechanism was known for longer of that, and the overall role of mobile genetic elements was only poorly understood, mostly because techniques likes sequencing were unaffordable. Now we do have a broader appreciation of it though it is still difficult to figure out how they as yet another of the many mechanisms of evolution. None of these change anything regarding the basic premises. Also, we will keep finding new molecular mechanisms we might eventually find that some have a more important impact in some species, no impact in others and so on. These are just regular discoveries within the confines of evolutionary theories, not contradicting them, just because folks did not know that they exist.

This argument seems to suggest a very limited view on evolution as we understand it. The new building blocks we find tend to help us understand evolution better and so far there has been no need for major revisions. Rather, we tend to add things, which is why we keep talking about synthesis,  rather than revision.

I reiterate, shaping forces (natural selection, sexual selection, drift and gene flow) do not change the fact that "dictum" states that annihilation is our ultimate faith. A non-random or random evolution does not change the outcome.

And I will reiterate while coming back to the main topic of the thread that so many changes to the theory of evolution were required to reconcile it with evidence that the theory is unrecognizable from what it was. One change at a time does not seem much change, but all of the changes put together modifies the whole landscape dynamic of evolution. HGT, symbiosis, cladogenesis and punctuated equilibrium, epigenetic effects, plasmid sharing in bacteria, non-reductive aspects of macroevolution, population genetics, adaptive dynamics etc., where all unexpected, and in need of reconcilable requirements. So, I correct myself; the theory does not need to change as it already has done so throught change from a thousand changes. I do not know who should be doing this, but a discussion as to the implications of systhesis of theory on the human condition and our place in the universe is required to be undertaken as our current view of these seem to be outdated and based on a disproven belief system.

 

 

Edited October 3 by Luc Turpin

[swansont]

1 hour ago, Luc Turpin said:

I did explain my position of no direction: "Random mutations occur and those offering a survival advantage get passed on to future generations. My comprehension is that beyond that, there is no sense of direction in evolution"

Saying there is no sense of direction in evolution is merely repeating the question, not explaining what you mean. But, as you say later, there is no end goal in mind; evolution does not anticipate needing features. The feedback of selection depends only on the current environment. i.e. you do not evolve a feature now because it will be useful some number of generations down the line 

 

1 hour ago, Luc Turpin said:

Selection being random or not does not change the fact that according to 'dictum", evolution has no aim, no purpose, no goal; which was the point that I was trying to make. 

And what that means is that the changes from evolution depend on the current environment. Selection is for a trait that's useful right now. But that selection is not random - more individuals survive if they have that trait.

 

 

1 hour ago, Luc Turpin said:

I reiterate, shaping forces (natural selection, sexual selection, drift and gene flow) do not change the fact that "dictum" states that annihilation is our ultimate faith.  

I have no idea what that's supposed to mean.

 

1 hour ago, Luc Turpin said:

And I will reiterate while coming back to the main topic of the thread that so many changes to the theory of evolution were required to reconcile it with evidence that the theory is unrecognizable from what it was.

Do we no longer have descent with modification? Because that's the main idea of Darwin. Your description is like seeing a tree in the winter and then in the summer, and saying it's not a tree because now it has leaves on it, and the branches are longer. Most of us recognize the tree. You don't but that sounds like a "you" problem.

 

 

[Luc Turpin]

3 minutes ago, swansont said:

Saying there is no sense of direction in evolution is merely repeating the question, not explaining what you mean. But, as you say later, there is no end goal in mind; evolution does not anticipate needing features. The feedback of selection depends only on the current environment. i.e. you do not evolve a feature now because it will be useful some number of generations down the line 

And what that means is that the changes from evolution depend on the current environment. Selection is for a trait that's useful right now. But that selection is not random - more individuals survive if they have that trait.

 

Agree with both, but with the following caveat; what happens when the genetic program is already in the organism, before the environment pushes for a certain need? There is evidence for it. The program is there before the need. What about that? Unexpected again.

6 minutes ago, swansont said:

I have no idea what that's supposed to mean.

Trying to say in a different way that evolution has no goal or aim.

8 minutes ago, swansont said:

Do we no longer have descent with modification? Because that's the main idea of Darwin. Your description is like seeing a tree in the winter and then in the summer, and saying it's not a tree because now it has leaves on it, and the branches are longer. Most of us recognize the tree. You don't but that sounds like a "you" problem.

 

 

Yes to the question, but how these modifications are acquired is a whole lot more complicated that the opening statement which was one random mutation at a time. The tree was not supposed to change from winter to summer; accepting that it does is a step forward. My contention remains though that the tree is also being transformed to something else by evidence. It is much-much more complicated than what was anticipated. It is as if life was trying to find any which way possible for it to survive; a very controversial and unproven contention. Or maybe it is just that so much time has elapsed between the beginning and now, that nature had time to go through so many scenarios and stumbled upon those that worked. Survival was an accident, not an intent. Only those that survive are able to tell the tale. It looks like a miracle, but it's not; it's only probability.

[Luc Turpin]

Some say the latter scenario is probable; others say it is not; at least for matters related to abiogenesis.

"Biologists currently estimate that the smallest life form as we know it would have needed about 256 genes. (See Proceedings of the National Academy of Sciences Volume 93, Number 19, pp. 10268-10273 at http://journals.at-home.com/get_doc/1854083/8551). A gene is typically 1000 or more base pairs long, and there is some space in between, so 256 genes would amount to about 300,000 bases of DNA. The deoxyribose in the DNA ``backbone'' determines the direction in which it will spiral. Since organic molecules can be generated in both forms, the chance of obtaining all one form or another in 300,000 bases is one in two to the 300,000 power. This is about one in 10 to the 90,000 power. It seems to be necessary for life that all of these bases spiral in the same direction. Now, if we imagine many, many DNA molecules being formed in the early history of the earth, we might have say 10 ¹⁰⁰ molecules altogether (which is really much too high). But even this would make the probability of getting one DNA molecule right about one in 10 to the 89,900 power, still essentially zero. And we are not even considering what proteins the DNA generates, or how the rest of the cell structure would get put together! So the real probability would be fantastically small."

"Biologists are hypothesizing some RNA-based life form that might have had a smaller genome and might have given rise to a cell with about 256 genes. Until this is demonstrated, one would have to say that the problem of abiogenesis is very severe indeed for the theory of evolution."

This is about life coming out of matter; not life persisting through the ages.

[swansont]

1 hour ago, Luc Turpin said:

Agree with both, but with the following caveat; what happens when the genetic program is already in the organism, before the environment pushes for a certain need? There is evidence for it. The program is there before the need. What about that? Unexpected again. 

Variation of traits is not unexpected.

“the genetic program is already in the organism” is too vague of a statement. You need to give specifics.

 

 

27 minutes ago, Luc Turpin said:

Some say the latter scenario is probable; others say it is not; at least for matters related to abiogenesis.

"Biologists currently estimate that the smallest life form as we know it would have needed about 256 genes. (See Proceedings of the National Academy of Sciences Volume 93, Number 19, pp. 10268-10273 at http://journals.at-home.com/get_doc/1854083/8551). A gene is typically 1000 or more base pairs long, and there is some space in between, so 256 genes would amount to about 300,000 bases of DNA. The deoxyribose in the DNA ``backbone'' determines the direction in which it will spiral. Since organic molecules can be generated in both forms, the chance of obtaining all one form or another in 300,000 bases is one in two to the 300,000 power. This is about one in 10 to the 90,000 power. It seems to be necessary for life that all of these bases spiral in the same direction. Now, if we imagine many, many DNA molecules being formed in the early history of the earth, we might have say 10 ¹⁰⁰ molecules altogether (which is really much too high). But even this would make the probability of getting one DNA molecule right about one in 10 to the 89,900 power, still essentially zero. And we are not even considering what proteins the DNA generates, or how the rest of the cell structure would get put together! So the real probability would be fantastically small."

"Biologists are hypothesizing some RNA-based life form that might have had a smaller genome and might have given rise to a cell with about 256 genes. Until this is demonstrated, one would have to say that the problem of abiogenesis is very severe indeed for the theory of evolution."

This is about life coming out of matter; not life persisting through the ages.

This is in quotes and yet you don’t give the source. It’s also an example of what I said about parroting creationist material.

[CharonY]

3 hours ago, Luc Turpin said:

I reiterate, shaping forces (natural selection, sexual selection, drift and gene flow) do not change the fact that "dictum" states that annihilation is our ultimate faith. A non-random or random evolution does not change the outcome.

This statement makes no sense. 

 

3 hours ago, Luc Turpin said:

And I will reiterate while coming back to the main topic of the thread that so many changes to the theory of evolution were required to reconcile it with evidence that the theory is unrecognizable from what it was.

Except researchers clearly recognize it, they just understand that there is more to it. Newtonian physics have a lot of things added, but many principles are still there. You also seem to suggest that if we find more mechanisms with better tools than we had before, it automatically alters the framework. IOW, it seems to me that you think that a theory is a rigid framework that has to be followed to the letter without modifications. That is not how science or research works. You have been presented with additions that alters how we think about the mechanisms of evolution but we still recognize natural selection as a major shaping force.  But as we do so we are still operating on the basic assumptions of evolution and it seems you have a hard time seeing it. However:

2 hours ago, Luc Turpin said:

Agree with both, but with the following caveat; what happens when the genetic program is already in the organism, before the environment pushes for a certain need? There is evidence for it. The program is there before the need. What about that? Unexpected again.

So this sentence shows a clear misunderstanding what evolution is (not only how it works). This sentence conflates the levels of organism (on which molecular mechanisms work) with population-wide changes in the gene pool (on which evolution works). If one is not able to clearly separate those two, it makes it clear that one need to read up far more to get to the point to be able to form valid criticisms on the underlying science, or saying why things are unexpected. I asked to to provide research examples that demonstrate how unexpected results arise from our current understanding of evolution and you keep giving examples how you are surprised about it. HGT doesn't change the game, it changes the timelines and the breadth of gene flow (which we understand). Bacterial evolution (and for others with clonal reproduction) always follow different patterns than other organism, as their reproduction follows different rules. Nothing to be surprised about once folks figured out the genetics of it. 

Just to make it clear, when we talk about evolution shaping things, we are not talking about creating new molecular mechanisms or traits, which seems to be your primary confusion. Rather, we talk about how the frequency of these traits change over time due the range of shaping forces, including natural selection (the major force that pushes frequencies into a specific direction).  I am not sure what you mean with genetic program (again, the use of language strongly suggests that you should read a few textbooks before reading papers). But if you are talking about the genetic basis of traits, then it is prerequisite that they are already in the population before they are needed. Otherwise selection has nothing to work on. Again, I think at this point it is safe to say that the fundamentals are missing and have not really changed since the start of these threads and before those are clarified any attempts on deeper discussions will just be deflected by an armor of ignorance.

[Luc Turpin]

2 hours ago, swansont said:

Variation of traits is not unexpected.

“the genetic program is already in the organism” is too vague of a statement. You need to give specifics.

May I provide an example?

An ancient gene stolen from bacteria set the stage for human sight"

The eye is so complex that even Charles Darwin was at a loss to explain how it could have arisen. Now, it turns out that the evolution of the vertebrate eye got an unexpected boost—from bacteria, which contributed a key gene involved in the retina’s response to light. The work, reported today in the Proceedings of the National Academy of Sciences, drives home the evolutionary importance of genes borrowed from other species.

https://www.science.org/content/article/ancient-gene-stolen-bacteria-set-stage-human-sight

2 hours ago, swansont said:

This is in quotes and yet you don’t give the source. It’s also an example of what I said about parroting creationist material.

Notwithstanding the lack of reference and parroting, does the calculation makes sense or not?

2 hours ago, CharonY said:

This statement makes no sense. 

Again, trying to say in a different way that evolution has no goal or aim.

2 hours ago, CharonY said:

Except researchers clearly recognize it, they just understand that there is more to it. Newtonian physics have a lot of things added, but many principles are still there. You also seem to suggest that if we find more mechanisms with better tools than we had before, it automatically alters the framework. IOW, it seems to me that you think that a theory is a rigid framework that has to be followed to the letter without modifications. That is not how science or research works. You have been presented with additions that alters how we think about the mechanisms of evolution but we still recognize natural selection as a major shaping force.  But as we do so we are still operating on the basic assumptions of evolution and it seems you have a hard time seeing it. However:

Absolutely not, I do not see a theory as a rigid framework.

Our disagreement is about if all of the changes have "changed" the "core" value of evolution. You say it has not and I say it has done so. From individuality struggling for survival through vertical gene transfer to a commonal approach where genes are shared through horizontal gene transfer. Sacrificing oneself for the betterment of the collective as some plants do is far away removed from red in tooth and claw. Can we really still consider genetics as being driven by selfish genes?

2 hours ago, CharonY said:

So this sentence shows a clear misunderstanding what evolution is (not only how it works). This sentence conflates the levels of organism (on which molecular mechanisms work) with population-wide changes in the gene pool (on which evolution works). If one is not able to clearly separate those two, it makes it clear that one need to read up far more to get to the point to be able to form valid criticisms on the underlying science, or saying why things are unexpected. I asked to to provide research examples that demonstrate how unexpected results arise from our current understanding of evolution and you keep giving examples how you are surprised about it. HGT doesn't change the game, it changes the timelines and the breadth of gene flow (which we understand). Bacterial evolution (and for others with clonal reproduction) always follow different patterns than other organism, as their reproduction follows different rules. Nothing to be surprised about once folks figured out the genetics of it. 

Just to make it clear, when we talk about evolution shaping things, we are not talking about creating new molecular mechanisms or traits, which seems to be your primary confusion. Rather, we talk about how the frequency of these traits change over time due the range of shaping forces, including natural selection (the major force that pushes frequencies into a specific direction).  I am not sure what you mean with genetic program (again, the use of language strongly suggests that you should read a few textbooks before reading papers). But if you are talking about the genetic basis of traits, then it is prerequisite that they are already in the population before they are needed. Otherwise selection has nothing to work on. Again, I think at this point it is safe to say that the fundamentals are missing and have not really changed since the start of these threads and before those are clarified any attempts on deeper discussions will just be deflected by an armor of ignorance.

Thank you for your words of wisdom; especially the last gem.

Why say that I am ignorant......every one already knows this!

While looking at leaves, you might have forgotten how the forest looks like, and I looking at the forest may very well not know how leaves look, but I am still looking at the forest.

I guess this ends it.

[CharonY]

1 hour ago, Luc Turpin said:

From individuality struggling for survival through vertical gene transfer to a commonal approach where genes are shared through horizontal gene transfer. Sacrificing oneself for the betterment of the collective as some plants do is far away removed from red in tooth and claw. Can we really still consider genetics as being driven by selfish genes?

Sorry but these are just buzzwords lined after each other with no attempts to even describe how they relate to evolutionary theories. If that was the first time you did that, I would simply ask for clarification, but we are many pages into the discussion and I find it rather exhausting at this point. The most charitable interpretation is that you still do not understand the fundamentals of evolution and are unfortunately not able to able to integrate what posters are trying to tell you.

But honestly, it really looks like a typical gish gallop at this point as instead of trying to figure out the misconceptions when pointed out, you keep bringing up other snippets (and in this case, nonsense) without even trying to link them together. In recent posts you bring up HGT and take incidence of HGT as a hit on evolutionary theories without ever explaining why. As you do keep weaving and bringing up additional topics without even trying to integrate that into your understanding. I always found that asking questions but not thinking about the answers to be an utter waste of time of everyone involved. 

 

[Luc Turpin]

I do not believe in cosmic ancestry, but would still want an opinion about this

https://www.panspermia.org/threetests.htm

[swansont]

2 hours ago, Luc Turpin said:

May I provide an example?

An ancient gene stolen from bacteria set the stage for human sight"

The eye is so complex that even Charles Darwin was at a loss to explain how it could have arisen. Now, it turns out that the evolution of the vertebrate eye got an unexpected boost—from bacteria, which contributed a key gene involved in the retina’s response to light. The work, reported today in the Proceedings of the National Academy of Sciences, drives home the evolutionary importance of genes borrowed from other species.

https://www.science.org/content/article/ancient-gene-stolen-bacteria-set-stage-human-sight

How is this an example of a trait that evolved without being selected for?

Genetic variation exists

2 hours ago, Luc Turpin said:

 

Notwithstanding the lack of reference and parroting, does the calculation makes sense or not?

No, it does not, and if you understood evolution to any degree you would know why, 

and

You don’t get to ignore the request for a citation

2 hours ago, Luc Turpin said:

 

Absolutely not, I do not see a theory as a rigid framework.

This is inconsistent with other statements you’ve made.

 

2 hours ago, Luc Turpin said:

Our disagreement is about if all of the changes have "changed" the "core" value of evolution. You say it has not and I say it has done so.

What of Darwin’s basic concepts have been discarded? 

variation exists?
traits are inherited?
natural selection happens?
common ancestry?
 

 

 

[Luc Turpin]

13 hours ago, swansont said:

How is this an example of a trait that evolved without being selected for?

Genetic variation exists

The piece of gene came from another life form. It acquired the right sequence to be part of a genetic program for which its utility was required only in the future.

That is puzzling to me and to others less ignorant than I.

13 hours ago, swansont said:

No, it does not, and if you understood evolution to any degree you would know why, 

and

You don’t get to ignore the request for a citation

As requested https://www.cs.unc.edu/~plaisted/ce/abiogenesis.html

And this one explains why it is not so https://www.talkorigins.org/faqs/abioprob/abioprob.html

And this one says, well it's complicated https://www.talkorigins.org/faqs/abioprob/abioprob.html

Got my answer without the agravation.

13 hours ago, swansont said:

This is inconsistent with other statements you’ve made.

You always see me as "black" or "white", and as the enemy of science for which I am not. What I am mostly asking in all of my posts and threads is "are you sure about it'?

13 hours ago, swansont said:

What of Darwin’s basic concepts have been discarded? 

variation exists?
traits are inherited?
natural selection happens?
common ancestry?

None have been discarded, but how they "operate" or "function" is very different from what was originally anticipated. For example, traits being present in the next generation instead of the long time-scale normally anticipated for a trait to act upon a life form. This is one example of many that might indicate that there is more to the story than what was originally anticipated from evolution. Symbiosis was not part of the original deal and contradicted the original notion of evolution that it was all about competition. Epigenetics was also not part of the deal and contradicted the original notion of evolution that it was mostly about genes and not the environment.

14 hours ago, CharonY said:

Sorry but these are just buzzwords lined after each other with no attempts to even describe how they relate to evolutionary theories. If that was the first time you did that, I would simply ask for clarification, but we are many pages into the discussion and I find it rather exhausting at this point. The most charitable interpretation is that you still do not understand the fundamentals of evolution and are unfortunately not able to able to integrate what posters are trying to tell you.

But honestly, it really looks like a typical gish gallop at this point as instead of trying to figure out the misconceptions when pointed out, you keep bringing up other snippets (and in this case, nonsense) without even trying to link them together. In recent posts you bring up HGT and take incidence of HGT as a hit on evolutionary theories without ever explaining why. As you do keep weaving and bringing up additional topics without even trying to integrate that into your understanding. I always found that asking questions but not thinking about the answers to be an utter waste of time of everyone involved. 

 

I am tryng my damned best to be as coherent as possible, and agree that I am not all the time. I am also aware that what I am presenting is controversial and will elicit a strong reaction. At the very least, can we agree that the theory of evolution has undergone major significant changes since its early inception? 

It's old and not a scientific paper, but a good article for describing how far we came from and, I contend, how far we still have to go.

https://www.theguardian.com/science/2010/mar/19/evolution-darwin-natural-selection-genes-wrong

[swansont]

23 minutes ago, Luc Turpin said:

As requested https://www.cs.unc.edu/~plaisted/ce/abiogenesis.html

The home page is “A Creation Perspective”

Quote

 

And this one explains why it is not so https://www.talkorigins.org/faqs/abioprob/abioprob.html

And this one says, well it's complicated https://www.talkorigins.org/faqs/abioprob/abioprob.html

Got my answer without the agravation.

 

As you should have. When you copy-paste a question like that, it takes almost no effort. Yet you expected someone to put forth the effort to debunk it, yet again. That’s not engaging in good faith.

23 minutes ago, Luc Turpin said:

The piece of gene came from another life form. It acquired the right sequence to be part of a genetic program for which its utility was required only in the future.

Variation exists. Neutral mutations exist, too, which might become useful when the environment changes. Nothing should be surprising about it. It’s also possible that it becomes a negative, and is selected against. 

23 minutes ago, Luc Turpin said:

You always see me as "black" or "white", and as the enemy of science for which I am not. What I am mostly asking in all of my posts and threads is "are you sure about it'?

It’s a matter of contradicting yourself, which gives the appearance of trolling. And when your sources are of dubious quality, or don’t actually say what you imply they do, this becomes indistinguishable from the Gish gallop.

[Luc Turpin]

8 minutes ago, swansont said:

The home page is “A Creation Perspective”

And what about the two others?

9 minutes ago, swansont said:

As you should have. When you copy-paste a question like that, it takes almost no effort. Yet you expected someone to put forth the effort to debunk it, yet again. That’s not engaging in good faith.

I read all of them and gave captions to each of them. 

The point being made was that there are two sides and a middle ground to the debate. And one needs information from all sides before making a determination of who is right and who is wrong. What is bad faith about that? 

37 minutes ago, swansont said:

Variation exists. Neutral mutations exist, too, which might become useful when the environment changes. Nothing should be surprising about it. It’s also possible that it becomes a negative, and is selected against. 

Better said that I can, here is the main question that sets this appart from the unsurprising: "How would independently evolving genes, exons, or other lengthy DNA strands gradually acquire the correct sequences needed to serve as components of a genetic program whose function will only be performed when all the needed strands are installed — in a species different from the one(s) in which the strands were written? - Brig Klyce

43 minutes ago, swansont said:

 It’s a matter of contradicting yourself, which gives the appearance of trolling. And when your sources are of dubious quality, or don’t actually say what you imply they do, this becomes indistinguishable from the Gish gallop.

Contradicting myself or me being insufficiently clear or mischaracterization of my saying? I will work on being clearer in my thinking to avoid giving the impression of contradicting myself.

I will take a break here as I feel that I have gotten into trouble without realizing that I was in trouble until now.

[swansont]

3 hours ago, Luc Turpin said:

And what about the two others?

The two that pointed out that the idea was crap? What about them.

3 hours ago, Luc Turpin said:

I read all of them and gave captions to each of them. 

You obviously don’t understand them. It’s not clear you make an effort to. You also don’t assess the credibility of thecsource.

3 hours ago, Luc Turpin said:

The point being made was that there are two sides and a middle ground to the debate. And one needs information from all sides before making a determination of who is right and who is wrong. What is bad faith about that? 

Because this isn’t a two-sides, equal-consideration situation. Science is based on empirical evidence, and the merit of ideas is related to the depth and breadth of evidence there is to support them. Creationist ideas have been thoroughly debunked. There is no merit in them.

As Stephen Gould wrote “I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.”

And the “just asking questions” tone is known as sea-lioning, which is a bad-faith tactic.

https://en.m.wikipedia.org/wiki/Sealioning

 

[Luc Turpin]

4 hours ago, Luc Turpin said:

As requested https://www.cs.unc.edu/~plaisted/ce/abiogenesis.html

And this one explains why it is not so https://www.talkorigins.org/faqs/abioprob/abioprob.html

And this one says, well it's complicated https://www.scientificamerican.com/article/new-equation-tallies-odds-of-life-beginning1/

 

I provided the wrong address in my original post for the third reference; 

1 hour ago, swansont said:

You obviously don’t understand them. It’s not clear you make an effort to. You also don’t assess the credibility of thecsource.

You did not notice the mistake? Addresses two and three pointing to the same document? Were they read before making claims?

[swansont]

10 minutes ago, Luc Turpin said:

You did not notice the mistake? Addresses two and three pointing to the same document? Were they read before making claims?

I read the first talk.origins one. Or rather, I re-read it. I’m quite familiar with the points, since I used to be involved with the discussions back in the USENET days. The summary is good, since it gathers refutations from multiple creationist arguments, and rebuts multiple misconceptions.

Didn’t see a need to read more from t.o.

The SciAm one is paywalled

 

[Luc Turpin]

35 minutes ago, swansont said:

The SciAm one is paywalled

I was able to access SciaAm one without going through a paywall. It was readily accessible. 

Don't know why it was different for you!