Natural selection v Intelligent design

[Loudmouth]

I would except that but all I can find is your opinion which is mostly dismissing me. The last post saying that I dont understand what I am talking about without any clarification of what you mean is a good example of the way you treat my posts. I could go back and find the majority of posts saying something like this. Those that dont probably 90% will be your opinion without any support from an independent source. So am I suppose to except what you say is correct without any verification. Especially when you have been so dismissive of me. It seems that you are already deciding that I am wrong and that you are right. Like I said if someone can back up what they say with independent evidence and not just their say so then I will except that. I dont mind being wrong but please explain how and why I am.

How does horizontal genetic transfer put evolution in doubt?

 

[Loudmouth]

Evolution relies on the passing down of genetic info through mutations that will make a change in a copy of the genes. If a mutation is beneficial it will be kept on through natural selection. This has to happen many times to be able to gradually morph a change in an animals shape of functions. The main tenet of this process is that new genetic info is created by random mutations and natural selection passed vertically from parent to sibling. So that process of evolution has to be dominate enough to be the main driving force to do this above all else.

If all the other forces at play are as predominate or even more prominent then this will undermine evolution because evolution cannot be confidently attributed to all these changes. It means that we cant tell where that new genetic info came from because it could have come from genetic info from other living things horizontally. If all life in the beginning was micro and is said to have a great amount of HGT then life was already sharing genetic info before more complex animals came along. It means that more complex animals may well have already have a vast amount of genetic info within their genomes to tap into to make changes into many forms.

How is this a problem for evolution?

Also, of the differences between the human and chimp genomes, how many are due to HGT?

This will explain the sudden appearance of complex forms such as the Cambrian period because its easier to understand that a creature could change because they already had the info there to use.

No, it doesn't. It simply means that once they had the info they passed it on horizontally. It doesn't mean that it was there from the start.

It wasn't a case of a very slow random process. If all these other driving forces dont completely undermine evolution then at the very least they cast a lot of doubt as to Darwinian evolution being the only force. Thats means that some if not many of the assertions made with all their links of transitions through the tree of life are not confirmed by mutations and natural selection only. That will cast doubt on a large chunk of the theory.

This took 5 million years. Looks pretty gradual to me.

 

[Jobar]

But to deny that just such huge changes can happen means you have to deny so much else! The fossil record, and genetics, just for starters.

No it doesn't. It means you simply see a different interpretation of the same evidence.

We're each entitled to our own opinions and interpretations, certainly.

But discussions such as these are about how we come to those opinions and interpretations, how we justify them to ourselves, and to each other. Just stating that you have opinions and interpretations isn't defending them!

(I hasten to add that no one is in any way required to offer such a defense. But if you choose to participate in threads like these, well, isn't that the whole point?)

 

[stevevw]

How does horizontal genetic transfer put evolution in doubt?

Because if HGT is a major player in where creature get there genetic info from then that would mean random mutations wont be responsible for the changes as much as has been made out. If all of life in the beginning was micro organisms and they had a great capacity to share genetic info how do we know that complex life that evolved from this didn't already have a lot of genetic info available to tap into. Instead of mutating change they had vast amounts of genetic info already there that could turn on and off certain functions and abilities. This maybe related to the so called junk DNA.

But HGT is only one way creatures can gain new genetic info as I have already linked. Between all of these other driving forces which use to be put aside by evolution as minor players are now being seen as major players. Darwinian evolution maybe the minor player after all or not much of a player at all. The other driving forces such as HGT, symbiosis, epigenetics, endosymbiosis which are being discovered by alternative views of how creatures will develop and change from areas such as genomics, developmental biology, ecology and social sciences are all adding to this view. The view that creatures don't just change through adaptation as Darwinian evolution states by mutations and natural selection.

 

[Archaeopteryx]

How is this a problem for evolution?

Also, of the differences between the human and chimp genomes, how many are due to HGT?

In another thread, he appeared to suggest that the genes for echolocation were somehow transmitted between dolphins and bats via HGT rather than being a result of convergent evolution. I asked him for evidence of this. Still waiting.

 

[Archaeopteryx]

Because if HGT is a major player in where creature get there genetic info from then that would mean random mutations wont be responsible for the changes as much as has been made out. If all of life in the beginning was micro organisms and they had a great capacity to share genetic info how do we know that complex life that evolved from this didn't already have a lot of genetic info available to tap into. Instead of mutating change they had vast amounts of genetic info already there that could turn on and off certain functions and abilities. This maybe related to the so called junk DNA.

But HGT is only one way creatures can gain new genetic info as I have already linked. Between all of these other driving forces which use to be put aside by evolution as minor players are now being seen as major players. Darwinian evolution maybe the minor player after all or not much of a player at all. The other driving forces such as HGT, symbiosis, epigenetics, endosymbiosis which are being discovered by alternative views of how creatures will develop and change from areas such as genomics, developmental biology, ecology and social sciences are all adding to this view. The view that creatures don't just change through adaptation as Darwinian evolution states by mutations and natural selection.

You do understand that, even if correct, this would not put evolution into doubt? It would simply mean that there is an additional source of genetic variation?

 

[FrumiousBandersnatch]

Because if HGT is a major player in where creature get there genetic info from then that would mean random mutations wont be responsible for the changes as much as has been made out. If all of life in the beginning was micro organisms and they had a great capacity to share genetic info how do we know that complex life that evolved from this didn't already have a lot of genetic info available to tap into. Instead of mutating change they had vast amounts of genetic info already there that could turn on and off certain functions and abilities. This maybe related to the so called junk DNA.

Both mechanisms of change were involved. If you have heritable variation and selection pressure, evolution is inevitable. HGT is an additional means of sharing variation - it's the natural equivalent of GMO. It happens a lot among prokaryotes because they lack a nucleus to isolate their genetic code. HGT is what allows an antibiotic resistance trait evolved by one bacterial population to be transferred to others.

It happens much less in eukaryotes, but some viruses can cause genetic sequences to be inserted in the genome of even humans - large parts of the 'junk DNA' are viral code. These viral insertion events are individually relatively rare, but provide yet another way to track evolutionary lines - multiple shared viral sequences are a clear indication of common ancestry - i.e. macro-evolution. See Endogenous Retroviruses. For 4 other independent lines of molecular evidence for macro-evolution, see the rest of that page.

But HGT is only one way creatures can gain new genetic info as I have already linked. Between all of these other driving forces which use to be put aside by evolution as minor players are now being seen as major players. Darwinian evolution maybe the minor player after all or not much of a player at all. The other driving forces such as HGT, symbiosis, epigenetics, endosymbiosis which are being discovered by alternative views of how creatures will develop and change from areas such as genomics, developmental biology, ecology and social sciences are all adding to this view. The view that creatures don't just change through adaptation as Darwinian evolution states by mutations and natural selection.

Symbiosis and endosymbiosis are co-evolutionary adaptations; but yes, there are many ways for creatures to change that Darwin was not aware of. That's why people roll their eyes at complaints that Darwinian evolution doesn't account for all these new discoveries; we know - Darwinian evolution was subsumed by the 'Modern Evolutionary Synthesis' around 80 years ago, much as Newtonian mechanics was subsumed by Einstinian Relativity. Since then, the Modern Synthesis has itself continued to evolve as new discoveries are made.

Nevertheless, as I and others have already said several times, evolution by heritable variation and selection remains the key explanatory concept at all levels .

 

[stevevw]

You do understand that, even if correct, this would not put evolution into doubt? It would simply mean that there is an additional source of genetic variation?

Maybe so and time will tell I guess as these things have been discovered mainly since genomic evidence has come into the picture. Darwin didn't know a lot of this and couldn't have known when formulating his theory. So really he was only seeing things from an outside view through observational evidence which is really more superficial. But since the discovery of genetics more and more discoveries have contradicted what Darwin said. That's because it is looking into the inner mechanisms of change and how it can happen which is the only way we can truly know what is actually responsible for change.

Some are saying that it is putting Darwinian evolution into doubt. All change are seen in terms of adaptation with Darwinian evolution. There are too many variables that can affect a creature and the environment but Darwinian evolution was trying to exclusively say that all change came from mutations and natural selection. There has always been a lot of unexplained things that Darwinian evolution could account for that didn't fit the evidence. So they were pushed to the sides as minor anomalies. But as time has gone by more and more of these hard to explain things have started to contradict what evolution says.

So now the things that were said to be minor glitches in the theory are starting to be the main driving forces for change because they fit the evidence better and explain many of the anomalies and contradictions. Its not all about adaptation but there are other forces that can shape living things and their environments. All the evidence for change is pointing to non adaptive processes and that's why these newer views are becoming more relevant because it can fit the evidence better. Creatures are subject to many things that actively work between themselves, other creatures and the environment. They are all able to interact with each other and may be able to transfer genetic info a lot more easily than thought between themselves and the environments they live in.

 

[stevevw]

Both mechanisms of change were involved. If you have heritable variation and selection pressure, evolution is inevitable. HGT is an additional means of sharing variation - it's the natural equivalent of GMO. It happens a lot among prokaryotes because they lack a nucleus to isolate their genetic code. HGT is what allows an antibiotic resistance trait evolved by one bacterial population to be transferred to others.

It happens much less in eukaryotes, but some viruses can cause genetic sequences to be inserted in the genome of even humans - large parts of the 'junk DNA' are viral code. These viral insertion events are individually relatively rare, but provide yet another way to track evolutionary lines - multiple shared viral sequences are a clear indication of common ancestry - i.e. macro-evolution. See Endogenous Retroviruses. For 4 other independent lines of molecular evidence for macro-evolution, see the rest of that page.

Symbiosis and endosymbiosis are co-evolutionary adaptations; but yes, there are many ways for creatures to change that Darwin was not aware of. That's why people roll their eyes at complaints that Darwinian evolution doesn't account for all these new discoveries; we know - Darwinian evolution was subsumed by the 'Modern Evolutionary Synthesis' around 80 years ago, much as Newtonian mechanics was subsumed by Einstinian Relativity. Since then, the Modern Synthesis has itself continued to evolve as new discoveries are made.

Nevertheless, as I and others have already said several times, evolution by heritable variation and selection remains the key explanatory concept at all levels .

Fair enough and thanks for the explanation. I will do some more research on this as it is fascinating. I am not a geneticist so I cannot confidently say I understand how it all works together and what role each influence can play. Whether evolution is still dominate enough to be the main driving force or whether people are interpreting other mechanisms for evolution or not I don't really know. Thats where I have to rely on people like yourself and others on links to learn from the experts.

But I do get this sense that there are some and it may be a growing trend that are questioning the ability of evolution to be responsible for change as much as they think. Its not just that there are other forces at play but that other things like the lack of clear evidence that random mutations can have such a strong positive influence for change. Its both the other driving forces for change and the lack of a strong selective force that I think are making people think twice about the capabilities of evolution. Sure it can make some changes but I think its the amount of change that is in question.

 

[stevevw]

How is this a problem for evolution?

Also, of the differences between the human and chimp genomes, how many are due to HGT?



No, it doesn't. It simply means that once they had the info they passed it on horizontally. It doesn't mean that it was there from the start.



This took 5 million years. Looks pretty gradual to me.

I'm always suspect of this picture. To me its half variations of apes and half variations of humans. The bottom row can accommodate the amount of variations of humans that have ever lived if you choose the best ones you find. There have been humans who have had the larger fuller skull at the right hand side and the skull at the far left as well. The others can be from variations of extinct apes of all shapes and sizes. Just like the skulls at Georgia where several varying shapes which were attributed to different species around the same time were the seen as variations of the same species. So can all these skulls when you consider that they are not only taking them from a period of the same time but from all time. Humans in the past were different to how we look today. There were some who were more robust but there were modern looking ones at the same time. Thats just the variations humans have.

 

[Archaeopteryx]

Maybe so and time will tell I guess as these things have been discovered mainly since genomic evidence has come into the picture. Darwin didn't know a lot of this and couldn't have known when formulating his theory.

Exactly. Darwin couldn't have known. But you do understand that evolutionary biology has advanced considerably since Darwin first penned the Origin? We are in no way obligated to defend a 19th century version of the theory.

So really he was only seeing things from an outside view through observational evidence which is really more superficial.

There was nothing "superficial" about what Darwin did. He was meticulous in his approach, immersed in years of study before publishing his seminal work.

But since the discovery of genetics more and more discoveries have contradicted what Darwin said. That's because it is looking into the inner mechanisms of change and how it can happen which is the only way we can truly know what is actually responsible for change.

And? So what? As you yourself acknowledged, there were many things that Darwin couldn't have foreseen, which have since been integrated into the theory. You seem to be under the impression that evolutionary biology has remained static since the 19th century.

Some are saying that it is putting Darwinian evolution into doubt. All change are seen in terms of adaptation with Darwinian evolution. There are too many variables that can affect a creature and the environment but Darwinian evolution was trying to exclusively say that all change came from mutations and natural selection. There has always been a lot of unexplained things that Darwinian evolution could account for that didn't fit the evidence. So they were pushed to the sides as minor anomalies. But as time has gone by more and more of these hard to explain things have started to contradict what evolution says.

It bears repeating: You do understand that, even if correct, this would not put evolution into doubt? It would simply mean that there is an additional source of genetic variation? Read your own sources.

 

[stevevw]

Exactly. Darwin couldn't have known. But you do understand that evolutionary biology has advanced considerably since Darwin first penned the Origin? We are in no way obligated to defend a 19th century version of the theory.

Yes I agree but the basic idea is still much the same in that mutations and natural selection are the driving forces for gradual change over long periods of time. That all creatures stem back to a common ancestor and from that common ancestor all living things gradually branched out through natural selection. Hence we have Darwin's tree of life still fairly similar and still one of the main tenets of evolution.

There was nothing "superficial" about what Darwin did. He was meticulous in his approach, immersed in years of study before publishing his seminal work.

I mean superficial in that he was looking to the outside of a creature and not the genetics that were the actual blue prints for their body plans.

And? So what? As you yourself acknowledged, there were many things that Darwin couldn't have foreseen, which have since been integrated into the theory. You seem to be under the impression that evolutionary biology has remained static since the 19th century.

No I realize that new discoveries are taken into consideration. But its the role they are given that is in question. Whereas some want to assign these new discoveries to the side lines as minor problems that need to be explained. Others are saying they are actually the main driving forces for evolution and evolution by mutations and natural selection should take a more minor role. It seems the evidence is a better fit for these new ways of seeing how creatures change. They take into account all the anomalies that evolution found hard to explain.

It bears repeating: You do understand that, even if correct, this would not put evolution into doubt? It would simply mean that there is an additional source of genetic variation? Read your own sources.

Like I said it depends on what role you decide to give these additional sources. From what you say it seems like others you believe that these additional sources are minor players. Some are saying they are the major driving forces and evolution is the minor player.

 

[FrumiousBandersnatch]

.. Whether evolution is still dominate enough to be the main driving force or whether people are interpreting other mechanisms for evolution or not I don't really know.

How could any of the other mechanisms effect long-term change without underlying heritable variation and selection?

Its not just that there are other forces at play but that other things like the lack of clear evidence that random mutations can have such a strong positive influence for change.

You don't think random mutations are responsible for the difference between wild plants and farmed varieties, the varieties of dogs and horses? We've only had artificial genetic engineering for 45 years. There are also tens of thousands of lab studies demonstrating the 'strong positive influence for change' of random mutations. Hundreds of special strains of animals, from fruit flies to rabbits, have been bred for research, all from the deliberate selection of those with the desired random mutations.

Its ... the lack of a strong selective force that I think are making people think twice about the capabilities of evolution.

Perhaps there are people who don't understand how selection pressure works. Strong selection pressures involve mass death and potential extinction. In what sense do you think a selection pressure could be stronger?

Who is 'thinking twice about the capabilities of evolution' because of 'the lack of a strong selective force'?

 

[Archaeopteryx]

Yes I agree but the basic idea is still much the same in that mutations and natural selection are the driving forces for gradual change over long periods of time. That all creatures stem back to a common ancestor and from that common ancestor all living things gradually branched out through natural selection. Hence we have Darwin's tree of life still fairly similar and still one of the main tenets of evolution.

Read your own sources, steve, particularly the article by Koonin.

No I realize that new discoveries are taken into consideration. But its the role they are given that is in question. Whereas some want to assign these new discoveries to the side lines as minor problems that need to be explained. Others are saying they are actually the main driving forces for evolution and evolution by mutations and natural selection should take a more minor role. It seems the evidence is a better fit for these new ways of seeing how creatures change. They take into account all the anomalies that evolution found hard to explain.

Like I said it depends on what role you decide to give these additional sources. From what you say it seems like others you believe that these additional sources are minor players. Some are saying they are the major driving forces and evolution is the minor player.

That's not the way your own source sees it! I even quoted the source for you:

Table 1 outlines the status of the central tenets of classical evolutionary biology in the age of evolutionary genomics and systems biology. All the classical concepts have undergone transformation, turning into much more complex, pluralistic characterizations of the evolutionary process (15). Depicting the change in the widest strokes possible, Darwin's paramount insight on the interplay between chance and order (introduced by natural selection) survived, even if in a new, much more complex and nuanced form, with specific contributions of different types of random processes and distinct types of selection revealed.

In other words, these discoveries have improved our understanding of evolution; they haven't upended it.

 

[pshun2404]

We're each entitled to our own opinions and interpretations, certainly.

But discussions such as these are about how we come to those opinions and interpretations, how we justify them to ourselves, and to each other. Just stating that you have opinions and interpretations isn't defending them!

(I hasten to add that no one is in any way required to offer such a defense. But if you choose to participate in threads like these, well, isn't that the whole point?)

You must not be a reader. I have offered many reasons for my position. Many backed by scientists in their own fields and even with support for my opinions from some EBs...interpretation of evidence is sometimes clouded by subjective preconceived conclusions. I have given sound examples where this has been done.

I have shown that in many cases (not the majority) that studies have been skewed, fudged, and in addition, evidence obtained that calls into question the conclusion INTENDED by the researcher has even been disregarded or discarded (NCBI, NIH, and other scientific organizations have confirmed this and I have provided references).

Now those these are not the majority, for every one caught 4 or 5 slip through unnoticed and add to the "shaping" of opinion, but they are not correct and dome not true. Information derived does not always mean what you are told it means, and there are other possibilities (also has been demonstrated and supported).

To outright reject possible explanations just because it ( or the researcher) does not agree with the current consensus (consider the Clovis theory examples and more) is the kind of foolishness that if held by others in other times would have left us in a Newtonian Mechanics Universe, with slavery in America, and very possibly women would still not vote. One must always be open to thinking outside the box. The true scientific spirit remains open to other possibilities (we see this in the Physical sciences all the time).

Now I have no desire to re-invent the wheel that I have been forced to re-invent a few times already but if there is something specific you are pointing to please feel free to express it. What specifically in that post do you have a problem with?

Paul

 

[FrumiousBandersnatch]

I'm always suspect of this picture. To me its half variations of apes and half variations of humans. The bottom row can accommodate the amount of variations of humans that have ever lived if you choose the best ones you find. There have been humans who have had the larger fuller skull at the right hand side and the skull at the far left as well. The others can be from variations of extinct apes of all shapes and sizes. Just like the skulls at Georgia where several varying shapes which were attributed to different species around the same time were the seen as variations of the same species. So can all these skulls when you consider that they are not only taking them from a period of the same time but from all time. Humans in the past were different to how we look today. There were some who were more robust but there were modern looking ones at the same time. Thats just the variations humans have.

So it might seem to your inexpert eye, judging from low-resolution photographs of a small subset of the available evidence (which includes locations, dates, artefacts, behavioural signs, etc). There have been finds classified as new subspecies that were arguably variations of already known ones, but most have been resolved either by wider sampling & comparison or genetic means. How do you square your view with the genetic evidence that is consistent with the relationships previously established being broadly correct (there have been some minor adjustments)?

 

[stevevw]

So it might seem to your inexpert eye, judging from low-resolution photographs of a small subset of the available evidence (which includes locations, dates, artefacts, behavioural signs, etc). There have been finds classified as new subspecies that were arguably variations of already known ones, but most have been resolved either by wider sampling & comparison or genetic means. How do you square your view with the genetic evidence that is consistent with the relationships previously established being broadly correct (there have been some minor adjustments)?

We would expect to see similarities in the genetics of similar looking creatures. I am always dubious of the observational evidence as it is open for interpretation. Like I said there have been many incidences where fossils have been said to be one thing only to be found out later that they were wrong. Similar looking fossils found in the wrong place are then made into new species because they couldn't have been the same creature in that particular time zone. Even though they virtually look the same. The thing about the line of ape skulls is that they can find a perfect line of transitions for this but never for much else. If there were so many transitions for all life then there would be millions everywhere.

The genetics may be similar for showing apes to humans but when it comes to many of the other links claimed it breaks down. The tree of life has many contradictions. There are cases of animals that are closely related through their genetics that don't look like they have morphed from each other as well. So because of all this it makes you wonder if the picture isn't being selectively picked to build it that way. But I come back to the best evidence and that's the test done to actually verify random mutations being able to create new functions and complexity. And from what I understand they don't show any evidence that mutations can do this. If anything its the opposite and they cause more harm than any good. Even if a very rare mutation that incurred some benefit could happen it has to keep on happening. And in between that happening there would be many sick creatures that didn't make the grade all over the place.

Test have shown to just make two steps with point mutations in complex organism by first inactivating a binding cite that controls how a gene is expressed and then create a new binding cite in its place. This would convert gene regulation from one type to another but it doesn't actually change the gene. So this is a very small change in the overall scheme of changing one creature into another. They have found that even for these small changes with random mutations it would take 100 million years in humans. Considering the history of primates is around 55 million years there a big anomaly. So when you look into the actually detail of how the step by step process can work in the inner workings or the engine room for change with the genetics Darwinian evolution has a hard time explaining some of these problems.

 

[stevevw]

Read your own sources, steve, particularly the article by Koonin.

What do you mean Koonin speaks about the very things I have been saying. He goes through the different discoveries from Darwin to the modern day discoveries through genetics. The different views which bring into question evolution through adaptation. How HGt can be seen as something that undermines Darwin evolution.

That's not the way your own source sees it! I even quoted the source for you:

In other words, these discoveries have improved our understanding of evolution; they haven't upended it.

Koonin is going through the many different views. He may believe in evolution himself but he is trying to lay out things how they are in which some of the evidence disputes evolution. Here is some of his quotes and his conclusions.

I have included some comments which I have put in blue so they are separated from Koonins comments.

The observations of extensive, ubiquitous and occurring via multiple routes HGT outlined above lead to a fundamental generalization: the genomes of all life forms are collections of genes with diverse evolutionary histories. The corollary of this generalization is that the TOL concept must be substantially revised or abandoned because a single tree topology or even congruent topologies of trees for several highly conserved genes cannot possibly represent the history of all or even the majority of the genes (146–149). Thus, an adequate representation of life's history is a network of genetic exchanges rather than a single tree, and accordingly, the ‘strong’ TOL hypothesis, namely, the existence of a ‘species tree’ for the entire history of cellular life, is falsified by the results of comparative genomics.

Indeed, in mammalian genomes, sequences derived from mobile elements, primarily, retrotransposons (SINEs and LINEs) appear to constitute, at least, 40% of the genomic DNA.
Thats an awfully large chunk of mammals DNA

The central role of mobile elements in genome evolution further undermines the TOL concept, although phylogenetic trees of individual hallmark genes can be highly informative for the reconstruction of the evolution of the selfish elements themselves.

Thus, the more common path of evolution of duplicated genes might not be neofunctionalization postulated by Ohno but rather subfunctionalization whereby new para-logs retain distinct subsets of the original functions of the ancestral gene whereas the rest of the functions deferentially deteriorate.

At the level of general concepts of evolutionary biology with which I am primarily concerned here, genomic studies on gene duplication lead to, at least, two substantial generalizations. First, the demonstration of the primary evolutionary significance of duplication's including duplication's of large genome regions and whole genomes is a virtual death knell for Darwinian gradualism.

evolution clearly tends to generate new functional devices by tinkering with the old ones after making a backup copy rather than create novelty from scratch.
He is acknowledging here that evolution uses existing genes to make changes rather than create new genetic material.

On the whole, the theoretical and empirical studies on the evolution of genomic complexity suggest that there is no trend for complexification in the history of life and that, when complexity does substantially increase, this occurs not as an adaptation but as a consequence of weak purifying selection, in itself, paradoxical as this might sound, a telltale sign of evolutionary failure. It appears that these findings are sufficient to put to rest the notion of evolutionary ‘progress’, a suggestion that was made previously on more general grounds.
So it seems he is saying that the evidence from genetics isn't moving towards more complexity for which we would expect from evolution and strong natural selection of more complex info. IE simple life to more complex life. When complexity does occur it is the result of weak selection which seems to be something that would come from selection of existing genetics.

The rate of evolution of protein-coding genes might depend more on constraints related to the prevention of deleterious effects of misfolding than on constraints associated with the specific protein function.
This is what some are saying that evidence shows that mutations are primarily harmful and deleterious. So if there anything going on with mutations its trying to get rid of them and avoid their consequences rather then them being the source of positive create change in fitter and more complex creatures.

The apparent universality of these and other central characteristics of genome evolution suggests that relatively simple, non-selective models might be sufficient to form the framework of a general evolutionary theory with respect to which purifying selection would provide boundary conditions (constraints) whereas positive, Darwinian selection (adaptation) would manifest itself as a quantitatively modest, even if functionally crucial modulator of the evolutionary process.
So here it is saying that the main source of evolution may be from non selective sources which are those already mentioned like HGT and existing genetics. Darwinian selection through Adaptation seems to be modest and plays a minor role as I have said before.

Comparative genomics revealed a striking diversity of evolutionary processes that was unimaginable in the pre-genomic era. In addition to point mutations that can be equated with Darwin's ‘infinitesimal changes’, genome evolution involves major contributions from gene and whole genome duplication's, large deletions including loss of genes or groups of genes, horizontal transfer of genes and entire genomic regions, various types of genome rearrangements, and interaction between genomes of cellular life forms and diverse selfish genetic elements

Evolutionary genomics effectively demolished the straightforward concept of the TOL by revealing the dynamic, reticulated character of evolution where HGT, genome fusion, and interaction between genomes of cellular life forms and diverse selfish genetic elements take the central stage.

So the TOL becomes a network, or perhaps, most appropriately, the Forest of Life that consists of trees, bushes, thickets of lianas, and of course, numerous dead trunks and branches. Whether the TOL can be salvaged as central trend in the evolution of multiple conserved genes or this concept should be squarely abandoned for the Forest of Life image remains an open question.

This is what Koonin says just after the quote you linked earlier which you left out.
By contrast, the insistence on adaptation being the primary mode of evolution that is apparent in the Origin, but especially in the Modern Synthesis, became deeply suspicious if not outright obsolete, making room for a new worldview that gives much more prominence to non-adaptive processes.
So he is adding some contrast as well to saying that the insistence of making the Darwinian model of evolution from adaptation through mutations and natural selection as the main source of evolution has become suspect if not obsolete in the light of these new discoveries of alternative driving forces for change.

Here's another little snippet you left out soon afterwards.
However, I believe that the evidence amassed by evolutionary genomics is sufficient to necessitate the change of the central null hypothesis of genome evolution from adaptationist to neutral, with the burden of proof shifted to the adepts of pervasive adaptation.

This is not meant to claim that many genomic characters (such as individual genes, amino-acid residues or nucleotides) are not conserved during evolution owing to their functional importance but to suggest that even this ‘sacred’, central tenet of evolutionary biology—‘what is conserved is functionally relevant’—is not an absolute, and the non-adaptive alternative is to be taken seriously. Together with the realization that genome contraction is at least as common in evolution as genome expansion, and the increase of genomic complexity is not a central evolutionary trend, the concept of non-adaptive genome evolution implies that the idea of evolutionary progress can be safely put to rest.
So here it is saying that the genome can contract as much as it can expand. So the opposite of evolution can happen as well. The trend is not towards genetic complexity as evolution likes to use as a central tenet of the theory. So non adaptive driving forces as mentioned can put to rest the idea that evolution states about it being a gradual progression towards more complex creatures.

The simplicity of these universal regularities suggests that they are shaped by equally simple, fundamental evolutionary processes, rather than by selection for specific functions. In some cases, explicit models of such processes have already been developed and shown to fit the data. These models either do not include selection at all or give selection a new interpretation.

The unexpected corollary of this model is that the primary driving force of purifying selection might not be the maintenance of a biological function but rather prevention of non-specific deleterious effects of a misfolded protein.
So it seems the main driving force is about preventing and getting rid of those nasty mutations rather than building more complex and better equipped creatures for survival. Survival is about avoidance not a gain of any ability. As the evidence shows mutations are mostly harmful and a cost to living things which is the opposite of evolution.
That will do me for tonight as my head is hurting. Good night and I will speak to you tomorrow. All the best Steve.

 

[Jobar]

You must not be a reader.

Oh, I've read quite a bit over the years. For instance, I've read a lot from Of Pandas and People. I've read the Wedge Document. And I've read large sections of Judge Jones' opinion from the Kitzmiller vs. Dover trial; I trust you're familiar with that? Surely you ought to be; if not, you really, really need to watch this.

In short, I suspect I've read a quite considerable amount more on this subject than you have.

 

[stevevw]

Oh, I've read quite a bit over the years. For instance, I've read a lot from Of Pandas and People. I've read the Wedge Document. And I've read large sections of Judge Jones' opinion from the Kitzmiller vs. Dover trial; I trust you're familiar with that? Surely you ought to be; if not, you really, really need to watch this.

In short, I suspect I've read a quite considerable amount more on this subject than you have.

Perhaps you have. The ID on trial was a fair time ago and a lot has changed since then with new discoveries. IE at the trial Judge Jones said there was no peer reviewed papers on ID. He was given a brief which showed the evidence for peer reviewed papers on ID which he seemed to not acknowledge. Since the trial there have bee many. I haven't seen the video but I will watch it later. I have seen some comment on it and disputes about the outcome. There were other things that the Judge either ignored or didn't take into consideration such as saying that ID is the same as creationism which is false and was established at the trial but ignored. For a break down of the trial and where it went wrong this book that is written by scientists and lawyers from the Discovery institute seems to cover all this.

Traipsing into Evolution is a book-length critique of federal Judge John E. Jones's decision in the Kitzmiller v. Dover case. In this concise yet comprehensive response, Discovery Institute scholars and attorneys show how Judge Jones's Kitzmiller decision was based upon faulty reasoning, non-existent evidence, and a serious misrepresentation of the scientific theory of intelligent design.
http://www.evolutionnews.org/2007/11/3_myths_about_the_dover_intell004483.html

INTELLIGENT DESIGN WILL SURVIVE KITZMILLER V. DOVER*
Unfortunately, Judge Jones appears to have confused the question of whether he finds ID personally convincing with the question of whether ID is a scientific theory. Because he was not convinced by the scientific arguments made by ID proponents, Judge Jones ruled that ID must not be science in principle. But it was not Judge Jones's place to determine the ultimate truth or falsity of ID's scientific arguments...
http://www.discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1372

You have to remember that the judicial system isn't the best way to settle this as we have seen how the justice system can be perverted and give the wrong outcomes. I would like to think it can be settled by the science if anything.