https://youtu.be/luxbHIF3MAU

It is over an hour long, but one of the many, many examples was the dinosaur explosion:

https://www.sciencedaily.com/releases/2018/04/180416105803.htm

Dinosaurs had originated much earlier, at the beginning of the Triassic Period, some 245 million years ago, but they remained very rare until the shock events in the Carnian 13 million years later.

***

First there were no dinosaur tracks, and then there were many. This marks the moment of their explosion, and the rock successions in the Dolomites are well dated. Comparison with rock successions in Argentina and Brazil, here the first extensive skeletons of dinosaurs occur, show the explosion happened at the same time there as well.

Lead author Dr Massimo Bernardi, Curator at MUSE and Research associate at Bristol's School of Earth Sciences, said: "We were excited to see that the footprints and skeletons told the same story. We had been studying the footprints in the Dolomites for some time, and it's amazing how clear cut the change from 'no dinosaurs' to 'all dinosaurs' was."

Comment: This is one prime example Bechly mentioned. Evolution runs in spirts, never slow and steady

https://phys.org/news/2021-02-virally-derived-transposons-domesticated-evolve.html

"About half of our genome is made up of transposable elements (TEs), also known as transposons. These 'jumping genes' are short stretches of DNA that have the unique ability to duplicate themselves and change their position within our code. While these philanderings play an essential role in the evolution of the species, if unchecked, transposons can wreak havoc on the genome.

"Although the transcription and proliferation of TEs is usually constrained by DNA methylation or other repressive chromatin amendments, TEs sometimes escape these countermeasures. For example, at certain periods of germ cell gametogenesis and early embryonic development, many epigenetic controls are wiped clean during scheduled system-wide reboots. Fortunately, cells have a backup mechanism known as the PIWI/piRNA pathway which can repress TEs. A recent paper in Nature Reviews Molecular Cell Biology investigates the many ways in which piRNAs can silence TEs, and defines new mechanisms by which they might also control gene expression.

"In the PIWI/piRNA pathway, RNA molecules about 25-32 nucleotides long associate with the Argonaute proteins from the PIWI clade to form piRISC complexes. These complexes target TEs post-transcriptionally, and also through the induction of epigenetic changes at the loci from which they are expressed. Piwi is an abbreviation of "P-element Induced WImpy testis," with the "P" meaning paternal.

***

"Two main classes of TEs can be defined. Class I TEs are called retrotransposons, which generally function via reverse transcription of the DNA into an RNA intermediate, hinting at their retroviral ancestry. Retrotransposons are commonly grouped into three main orders of decreasing size and complexity; the retrotransposons with long terminal repeats (LTRs), the LINES (which have reverse transcriptase but not LTRs), and the SINEs (which have neither). Class II TEs are the DNA transposons, which typically encode several sequence curiosities including a special transposase used for insertion and excision.

"Lest we give the impression that the transposon hazard is something we should be better off without, consider that transposons are solely responsible for most, or at least many, of the higher evolutionary refinements we enjoy today. Everything from live birth to expansion of the neocortex appears to have been driven by genome-wide insertion of TEs into the promoter regions of key regulatory genes. No other evolutionary process capable of radically altering the expression of so many genes in such a short time has been identified, let alone imagined. (my bold)

***

"The magic sauce hidden in these transposable elements is that they happen to be good at creating transcription factor binding sites."

Comment: The article contains many specific types of genetic activity conducted by these TE's. Is this God's supreme method for advancing evolution?

https://phys.org/news/2021-02-fossil-coelacanth-evolved-dozens-genes.html

"The capture of the first living Coelacanth, a mighty ocean predator, off the coast of South Africa caused quite a stir in 1938, 65 million years after its supposed extinction. It became known as a "living fossil" owing to its anatomy looking almost identical to the fossil record. But while the Coelacanth's body may have changed little, its genome tells another story.

"Toronto scientists have now revealed that the African Coelacanth, Latimeria chalumnae, gained 62 new genes through encounters with other species 10 million years ago.

***

"What's even more fascinating is how these genes came about. Their sequences suggest they arose from transposons, also known as "selfish genes". These are parasitic DNA elements whose sole purpose is to make more copies of themselves, which they sometimes achieve by moving between species.

"The findings show the dramatic effect traveling transposon DNA can have on the creation of genes and provide a glimpse into some of the forces that shaped the genome of one of the most ancient and mysterious organisms.

"'Our findings provide a rather striking example of this phenomenon of transposons contributing to the host genome," says Tim Hughes, senior study author and a professor of molecular genetics....

"'We don't know what these 62 genes are doing, but many of them encode DNA binding proteins and probably have a role in gene regulation, where even subtle changes are important in evolution," says Hughes, who is Canada Research Chair in Decoding Gene Regulation and John W. Billes Chair of Medical Research at the Temerty Faculty of Medicine at U of T.

"Transposons are sometimes also called "jumping genes" because they switch location in the genome, thanks to a self-encoded enzyme that recognises and move its own DNA code via "cut and paste" mechanism. New copies can arise through serendipitous jumps during cell division when the whole genome is replicated.

***

"There are myriad examples of transposon-derived genes across species, but the Coelacanth stands out for the sheer scale of it.

"It was surprising to see coelacanths pop out among vertebrates as having a really large number of these transposon-derived genes because they have an undeserved reputation of being a living fossil," says graduate student Isaac Yellan who spearheaded the study.

"'The Coelacanth may have evolved a bit more slowly but it is certainly not a fossil," he says.

"After scanning all available genomes, Yellan was able to find related genes, but their distribution across species was patchy and not what you'd expect from common ancestry. In addition to the single CGGBP-like gene in all mammals, birds and reptiles, Yellan found copies in some, but not all, fish he looked at, as well as in lamprey, a primitive vertebrate, and a type of fungus. Worms, molluscs, and most insects had none. And then there were 62 in the Coelacanth, whose genome became available in 2013.

With common ancestry ruled out, it appears instead that the transposons came into various lineages at different times by being carried between species through what is known as horizontal gene transfer.

"Horizontal gene transfer fuzzies up the picture of where the transposons came from but we know from other species that it can occur via parasitism," says Yellan. "The most likely explanation is that they were introduced multiple times throughout evolutionary history."

"It remains unclear what the genes are doing but several lines of evidence point to a finely-tuned role in gene regulation. Computational modeling and test tube experiments established that the genes' products are proteins which bind unique sequence signatures on the DNA, suggests a role in gene expression, similar to the human counterpart. Furthermore, the genes are varyingly switched on across dozen or so Coelacanth organs for which data exist, suggesting finely-tuned roles that are tissue-specific."

Comment: Is gene horizontal transfer an organismal ability, or does God step in and make the changes? Since I think God speciates, I feel He steps in. Specifically, we observe the results of gene transfer, but do not know the underlying mechanism. The coelacanth didn't change its body form (phenotype) but other apparently necessary gene regulations.

dhw: I am not disputing the fact that there is gene loss! I am disputing the argument that gene loss CAUSES speciation, and this whole discussion began by my disputing the claim that evolutionary advances “always result from loss of genes”. All you have come up with is the fact that genes get lost during adaptation, and initially you disputed the concept of new genes. The fact that speciation must involve reorganization of genes is so obvious that it is barely worth stating.

DAVID: We can stop here. Basically we do not know how speciation works. Just theories, not Darwin's

dhw: You are happy to demolish Darwin’s theory of random mutations, but having championed Behe’s theory as if it were some kind of breakthrough, you would now prefer not to discuss it because I’ve questioned its premises. Yes, we can stop here. We can stop every discussion on every subject, because we don’t “know” the origin of life, if God exists, what are his nature, purposes, methods if he does exist, how to resolve the theodicy problem, how consciousness arose and functions, whether or not we have free will, whether cells are intelligent or not…etc. and how speciation happened. But I would like to think that both of us are constantly learning from these discussions, and if nothing else they are keeping our old brains ticking!

I'm with you. your thoughts about areas of discussion are right on. All I meant was the current subject is rather beaten to death for the moment, so let's find other aspects with whic h to challenge each other.

DAVID: We can stop here. Basically we do not know how speciation works. Just theories, not Darwin's

You are happy to demolish Darwin’s theory of random mutations, but having championed Behe’s theory as if it were some kind of breakthrough, you would now prefer not to discuss it because I’ve questioned its premises. Yes, we can stop here. We can stop every discussion on every subject, because we don’t “know” the origin of life, if God exists, what are his nature, purposes, methods if he does exist, how to resolve the theodicy problem, how consciousness arose and functions, whether or not we have free will, whether cells are intelligent or not…etc. and how speciation happened. But I would like to think that both of us are constantly learning from these discussions, and if nothing else they are keeping our old brains ticking!

dhw: …no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

dhw: That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

DAVID: Note the red above. I answered your suggestion with agreement.

Your answer ranks gene loss alongside the other two factors in CAUSING speciation. I am proposing that gene loss is the RESULT of speciation – the genes are not needed and are therefore discarded.

dhw: Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

DAVID: I've seen no mention from him of new genes. Why do you ignore the article on chimps and us? It says there was gene loss and reorganization!!!

dhw: I am not disputing the fact that there is gene loss! I am disputing the argument that gene loss CAUSES speciation, and this whole discussion began by my disputing the claim that evolutionary advances “always result from loss of genes”. All you have come up with is the fact that genes get lost during adaptation, and initially you disputed the concept of new genes. The fact that speciation must involve reorganization of genes is so obvious that it is barely worth stating.

We can stop here. Basically we do not know how speciation works. Just theories, not Darwin's

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

dhw: That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

DAVID: Note the red above. I answered your suggestion with agreement.

Your answer ranks gene loss alongside the other two factors in CAUSING speciation. I am proposing that gene loss is the RESULT of speciation – the genes are not needed and are therefore discarded.

dhw: Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

DAVID: I've seen no mention from him of new genes. Why do you ignore the article on chimps and us? It says there was gene loss and reorganization!!!

I am not disputing the fact that there is gene loss! I am disputing the argument that gene loss CAUSES speciation, and this whole discussion began by my disputing the claim that evolutionary advances “always result from loss of genes”. All you have come up with is the fact that genes get lost during adaptation, and initially you disputed the concept of new genes. The fact that speciation must involve reorganization of genes is so obvious that it is barely worth stating.

DAVID: Your suggestion of the changes in genes is reasonable. Adding new genes which work in concert to create a new species, coordinating with loss of genes and changing some gene network expression is a complex design requirement.

dhw: Thank you. I am not denying the complexity.

DAVID: It also requires a concept of what it is that is wanted for the new species to be able to do. Only a designer can accomplish this. Your answer has no mechanism for coordination of all these steps except the nebulous concept that cells are innately intelligent, source of that intelligence unknown.

dhw: I keep agreeing that the source is unknown, but God is one possibility. What is “wanted” is an awareness of the conditions in which the organism finds itself (as opposed to your own theory, which requires a crystal ball to anticipate future conditions) and the intelligence to find ways of coping with them (adaptation) or exploiting them (innovation) – though it’s sometimes difficult to draw a line between the two processes. The concept of cellular intelligence is no more nebulous than the concept of an unknown intelligent being providing the first cells with a programme for every single development in the history of evolution that he does not directly dabble.

At least I can accept a designer is required.

dhw: …no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

dhw: That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

Note the red above. I answered your suggestion with agreement.

DAVID: The absolute requirement of new genes is pure unproven assumption of Darwinism.

dhw: I’m pleased to hear this, as I was under the impression from your earlier posts that the very concept of new genes was doubtful. (That was the first reason you gave for rejecting my proposal.) If we have biologists favouring new genes as essential to speciation, it would be silly to reject the possibility. And now that you have acknowledged the existence of new genes, please tell us what they might be used for if not for some kind of innovation. And your comment still does not answer my question, now bolded.

I have answered:

DAVID: The possible proof of this is the small human gene tiny size compared to other organisms. Analysis of chimp gene relationships found (described previously here) the gene bases are 98% similar to human, but really 79% different in organization. Also our chromosome number is different. There are studies that describe human gene losses compared to chimps in the process of speciation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298176/

dhw: Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

I've seen no mention from him of new genes. Why do you ignore the article on chimps and us? It says there was gene loss and reorganization!!!

dhw: Your designer would have created the mechanism in the first place, but even if he dabbled, the process of inventing, restructuring and discarding cells would have been the same. So why do you think speciation cannot possibly have been caused (whether dabbled or not) by a combination of new genes with old genes taking on new functions, while other old genes are discarded because they are no longer of any use?

DAVID: Your suggestion of the changes in genes is reasonable. Adding new genes which work in concert to create a new species, coordinating with loss of genes and changing some gene network expression is a complex design requirement.

Thank you. I am not denying the complexity.

DAVID: It also requires a concept of what it is that is wanted for the new species to be able to do. Only a designer can accomplish this. Your answer has no mechanism for coordination of all these steps except the nebulous concept that cells are innately intelligent, source of that intelligence unknown.

I keep agreeing that the source is unknown, but God is one possibility. What is “wanted” is an awareness of the conditions in which the organism finds itself (as opposed to your own theory, which requires a crystal ball to anticipate future conditions) and the intelligence to find ways of coping with them (adaptation) or exploiting them (innovation) – though it’s sometimes difficult to draw a line between the two processes. The concept of cellular intelligence is no more nebulous than the concept of an unknown intelligent being providing the first cells with a programme for every single development in the history of evolution that he does not directly dabble.

DAVID: As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart.

dhw: …no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation.

That is not an answer. Why is it not feasible that there will be genes which a new species will not require and will therefore jettison?

DAVID: The absolute requirement of new genes is pure unproven assumption of Darwinism.

I’m pleased to hear this, as I was under the impression from your earlier posts that the very concept of new genes was doubtful. (That was the first reason you gave for rejecting my proposal.) If we have biologists favouring new genes as essential to speciation, it would be silly to reject the possibility. And now that you have acknowledged the existence of new genes,please tell us what they might be used for if not for some kind of innovation. And your comment still does not answer my question, now bolded.

DAVID: The possible proof of this is the small human gene tiny size compared to other organisms. Analysis of chimp gene relationships found (described previously here) the gene bases are 98% similar to human, but really 79% different in organization. Also our chromosome number is different. There are studies that describe human gene losses compared to chimps in the process of speciation:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298176/

Do these studies claim that evolutionary innovation is caused by loss of genes? And do they discount the possibility that evolutionary innovation is caused by new genes and new functions for old genes, while useless old genes are jettisoned? And do you happen to know if Behe has examined the incidence of new genes in new species?

dhw: We have long since agreed that Darwin was wrong to say that there are no jumps in Nature. Shapiro’s theory is that intelligent cells do the engineering, and it takes into account the research of others into cellular intelligence. I have offered you a proposal concerning the role of new genes, old genes and discarded genes in speciation, and although like all the other theories, it is not proven, I still don’t know why you object to it.

DAVID: You know full well I think a designer is required for all advance in evolution at the speciation level.

dhw: That is not an answer! Your designer would have created the mechanism in the first place, but even if he dabbled, the process of inventing, restructuring and discarding cells would have been the same. So why do you think speciation cannot possibly have been caused (whether dabbled or not) by a combination of new genes with old genes taking on new functions, while other old genes are discarded because they are no longer of any use?

Your suggestion of the changes in genes is reasonable. Adding new genes which work in concert to create a new species, coordinating with loss of genes and changing some gene network expression is a complex design requirement. It also requires a concept of what it is that is wanted for the new species to be able to do. Only a designer can accomplish this. Your answer has no mechanism for coordination of all these steps except the nebulous concept that cells are innately intelligent, source of that intelligence unknown.

DAVID: As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart.

dhw: I made that point myself earlier in this discussion. It makes no difference to the feasibility of my proposal, and no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

Answered: Gene loss, gene network modifications, changes in gene expressions altogether are reasonably capable of of speciation. The absolute requirement of new genes is pure unproven assumption of Darwinism. The possible proof of this is the small human gene tiny size compared to other organisms. Analysis of chimp gene relationships found (described previously here) the gene bases are 98% similar to human, but really 79% different in organization. Also our chromosome number is different. There are studies that describe human gene losses compared to chimps in the process of speciation:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4298176/

DAVID: You know full well I think a designer is required for all advance in evolution at the speciation level.

That is not an answer! Your designer would have created the mechanism in the first place, but even if he dabbled, the process of inventing, restructuring and discarding cells would have been the same. So why do you think speciation cannot possibly have been caused (whether dabbled or not) by a combination of new genes with old genes taking on new functions, while other old genes are discarded because they are no longer of any use?

DAVID: As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart.

I made that point myself earlier in this discussion. It makes no difference to the feasibility of my proposal, and no matter how we define speciation, it would still leave wide open the question of how loss of genes can create anything new. Why do you think it is not feasible that the loss of genes RESULTS from speciation, as above?

DAVID: Well, we have clarified Behe's theory and it is highly suggestive of gene loss playing a major role in speciation since adaptation is mainly from gene degradation.

The examples you have given show that there is gene loss which can be explained by the fact that certain genes are no longer needed when conditions change. Existing genes will take on new functions. This is a far cry from gene loss playing a constructive role even in adaptation. Out of interest, I would like to know if Behe also found new genes in his examples, though I suspect that adaptation itself would not require them, whereas major innovations would. You did not answer my question: what else do you think new genes would be required for if not for innovation?

DAVID: However adaptation does not lead to speciation in the fossil record. Speciation creates gaps. Darwin's gradualism is not proven. Shapiro's theory is another approach, bootstrapping by editing DNA. This is all we have and in comparison I like Behe's approach better since it encompasses a review of genetic evidence. Shapiro is an extrapolation from free-living bacteria. And all Lenski has shown in his E. coli studies is some mutational adaptations in the same species.

dhw: We have long since agreed that Darwin was wrong to say that there are no jumps in Nature. Shapiro’s theory is that intelligent cells do the engineering, and it takes into account the research of others into cellular intelligence. I have offered you a proposal concerning the role of new genes, old genes and discarded genes in speciation, and although like all the other theories, it is not proven, I still don’t know why you object to it.

You know full well I think a designer is required for all advance in evolution at the speciation level. As we study it, it should require a careful definition of species. We have noted the differences in bears by fur color as not really species set apart..

The examples you have given show that there is gene loss which can be explained by the fact that certain genes are no longer needed when conditions change. Existing genes will take on new functions. This is a far cry from gene loss playing a constructive role even in adaptation. Out of interest, I would like to know if Behe also found new genes in his examples, though I suspect that adaptation itself would not require them, whereas major innovations would. You did not answer my question: what else do you think new genes would be required for if not for innovation?

DAVID: However adaptation does not lead to speciation in the fossil record. Speciation creates gaps. Darwin's gradualism is not proven. Shapiro's theory is another approach, bootstrapping by editing DNA. This is all we have and in comparison I like Behe's approach better since it encompasses a review of genetic evidence. Shapiro is an extrapolation from free-living bacteria. And all Lenski has shown in his E. coli studies is some mutational adaptations in the same species.

We have long since agreed that Darwin was wrong to say that there are no jumps in Nature. Shapiro’s theory is that intelligent cells do the engineering, and it takes into account the research of others into cellular intelligence. I have offered you a proposal concerning the role of new genes, old genes and discarded genes in speciation, and although like all the other theories, it is not proven, I still don’t know why you object to it.

DAVID: Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

dhw: Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

DAVID: Relax from your old teachings and beliefs. The bold is specifically not proven. Much is shown to be accomplished by reduplication, alterations in expressions, and setting up of new genome-wide networks among existing genes.

dhw: What old teachings and beliefs? Initially you were sceptical about the very existence of new genes! I didn’t say it was proven – it is my suggestion, but what else do you think new genes would be required for if not for innovation? The rest of what you say is covered by new functions for old genes.

DAVID: The polar bear difference is somewhat more than fur color but I'll buy adaption along with you. The mammoth is very different in appearance, but again it is an elephant with a woolly hide and giant tusks. Phenotype used for classification is useless. DNA study is the true guide to evolution. We both know this. Behe, with his emphasis on DNA, is pursuing a valid approach to cracking open the issue of speciation.

dhw: That may be so, but his theory as you have presented it quite patently does not even begin to prove that speciation is caused by loss of genes, or that "advances always result from loss of genes", which was the claim that started this discussion.

Well, we have clarified Behe's theory and it is highly suggestive of gene loss playing a major role in speciation since adaptation is mainly from gene degradation. However adaptation does not lead to speciation in the fossil record. Speciation creates gaps. Darwin's gradualism is not proven. Shapiro's theory is another approach, bootstrapping by editing DNA. This is all we have and in comparison I like Behe's approach better since it encompasses a review of genetic evidence. Shapiro is an extrapolation from free-living bacteria. And all Lenski has shown in his E. coli studies is some mutational adaptations in the same species.

dhw: Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

DAVID: Relax from your old teachings and beliefs. The bold is specifically not proven. Much is shown to be accomplished by reduplication, alterations in expressions, and setting up of new genome-wide networks among existing genes.

What old teachings and beliefs? Initially you were sceptical about the very existence of new genes! I didn’t say it was proven – it is my suggestion, but what else do you think new genes would be required for if not for innovation? The rest of what you say is covered by new functions for old genes.

DAVID: The polar bear difference is somewhat more than fur color but I'll buy adaption along with you. The mammoth is very different in appearance, but again it is an elephant with a woolly hide and giant tusks. Phenotype used for classification is useless. DNA study is the true guide to evolution. We both know this. Behe, with his emphasis on DNA, is pursuing a valid approach to cracking open the issue of speciation.

That may be so, but his theory as you have presented it quite patently does not even begin to prove that speciation is caused by loss of genes, or that "advances always result from loss of genes", which was the claim that started this discussion.

dhw: This whole discussion began with my disputing the claim that “advances always result from loss of genes”. I only know Behe’s theory from what you tell me, so I don’t know if his examples are minor variations or totally new species. I remember you picking on the example of the polar bear lacking two genes found in the grizzly and the brown bear. I wouldn’t call this an advance. They are all bears, but they live in different conditions, and had to adapt accordingly. The obvious inference is that genes which operate in a warm climate won’t be of any use in a cold climate. I can’t see the logic in the argument that losing useless genes will create a new fur coat. But I can only discuss the points you reproduce here. Since we do in fact call these different bears different species, perhaps we shouldn’t be using the word “speciation” at all and should stick to the term used in the latest article: “major evolutionary transitions”, which I would equate with innovation and which, you will remember, occur when “vast numbers of existing genes are jettisoned and replaced by entirely different ones”. But I would also expect loss of genes as a RESULT of minor transitions and not as the cause.

DAVID: Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

dhw: Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

Relax from your old teachings and beliefs. The bold is specifically not proven. Much is shown to be accomplished by reduplication, alterations in expressions, and setting up of new genome-wide networks among existing genes.

The polar bear difference is somewhat more than fur color but I'll buy adaption along with you. The mammoth is very different in appearance, but again it is an elephant with a woolly hide and giant tusks. Phenotype used for classification is useless. DNA study is the true guide to evolution. We both know this. Behe, with his emphasis on DNA, is pursuing a valid approach to cracking open the issue of speciation.

DAVID: Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

Thank you for this revealing summary. It's a far cry from “advances always result from loss of genes”, and indeed it is pretty clear that the examples don’t even deal with advances! A polar bear can hardly be called an advance on a grizzly bear! It is perfectly logical that adaptation should RESULT in loss of genes since genes necessary for one environment may be of no use in another. I would suggest that adaptations will primarily involve new functions for existing genes, though some new ones may be necessary, but major innovations will certainly require new genes.

dhw: I would like to make a slight change to my proposal, in direct opposition to the theory I have been objecting to: Speciation is caused by the acquisition of new genes AND new functions for old genes, and is ACCOMPANIED by loss of unwanted genes etc.
If you now accept my revised proposal, I think we can close this thread.

DAVID: I do not agree fully with the bold above. Loss of genes appears to be one of causes of speciation along with a restructuring of expression of genes and may include new genes added. But based on Behe, some speciation changes are just deletion.

dhw: A restructuring of expression of genes is what I call new functions for old genes. This whole discussion began with my disputing the claim that “advances always result from loss of genes”. I only know Behe’s theory from what you tell me, so I don’t know if his examples are minor variations or totally new species. I remember you picking on the example of the polar bear lacking two genes found in the grizzly and the brown bear. I wouldn’t call this an advance. They are all bears, but they live in different conditions, and had to adapt accordingly. The obvious inference is that genes which operate in a warm climate won’t be of any use in a cold climate. I can’t see the logic in the argument that losing useless genes will create a new fur coat. But I can only discuss the points you reproduce here. Since we do in fact call these different bears different species, perhaps we shouldn’t be using the word “speciation” at all and should stick to the term used in the latest article: “major evolutionary transitions”, which I would equate with innovation and which, you will remember, occur when “vast numbers of existing genes are jettisoned and replaced by entirely different ones”. But I would also expect loss of genes as a RESULT of minor transitions and not as the cause.

Behe is a pioneer in theory just like Shapiro. He does use the polar bear as a prime example of species change. You are correct. it is really a massive adaptation to specific environment. He also discusses the mammoth and its DNA differences from elephants, in which it is found between 500-800 genes were degraded. His book is filled with such examples of adaptation by gene degradation. His prime thought early in the book to quote is: "Darwin's mechanism works chiefly by squandering genetic information for short-term gain." By this he means adaptation which aids survival "by damaging or breaking genes." (pages 37-38) By no means does he says he is positive full speciation in evolution is the cause of speciation, but he feels he is offering strong evidence in a 342 page book filled with adaptive examples. All dog varieties are due to damaged/degraded genes, but following your thought they are still really mostly wolves, as shepherd/wolves exist. Susan and I have been to a local breeding/rescue ranch out of curiosity..

DAVID: I do not agree fully with the bold above. Loss of genes appears to be one of causes of speciation along with a restructuring of expression of genes and may include new genes added. But based on Behe, some speciation changes are just deletion.

A restructuring of expression of genes is what I call new functions for old genes. This whole discussion began with my disputing the claim that “advances always result from loss of genes”. I only know Behe’s theory from what you tell me, so I don’t know if his examples are minor variations or totally new species. I remember you picking on the example of the polar bear lacking two genes found in the grizzly and the brown bear. I wouldn’t call this an advance. They are all bears, but they live in different conditions, and had to adapt accordingly. The obvious inference is that genes which operate in a warm climate won’t be of any use in a cold climate. I can’t see the logic in the argument that losing useless genes will create a new fur coat. But I can only discuss the points you reproduce here. Since we do in fact call these different bears different species, perhaps we shouldn’t be using the word “speciation” at all and should stick to the term used in the latest article: “major evolutionary transitions”, which I would equate with innovation and which, you will remember, occur when “vast numbers of existing genes are jettisoned and replaced by entirely different ones”. But I would also expect loss of genes as a RESULT of minor transitions and not as the cause.

dhw: In the light of all this, why is my theory not feasible?

DAVID: Because the evidence presented does not support it for new genes. Where I agree is: new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation.

dhw: The evidence presented emphasizes the existence of new genes, and the fact that they replace old genes. I agree that the remaining genes will be restructured. All this is an exact repeat of my proposal that speciation is caused by the “acquisition of new genes (or new functions for old genes) and loss of unwanted genes. Natural selection merely decides which genes are necessary and which are not.” However, I must stress that I am not arguing with Behe – I can only discuss the points you raise. Now please tell me why my proposal is not feasible.

dhw: I would like to make a slight change to my proposal, in direct opposition to the theory I have been objecting to: Speciation is caused by the acquisition of new genes AND new functions for old genes, and is ACCOMPANIED by loss of unwanted genes etc.

DAVID: Yes, we both agree new genes appear, but the evidence is still on the side that speciation involves loss of genes. To repeat: "new functions of old genes by reorganization of gene expression and redeveloped gene wide network associations may well be the cause of speciation." Your proposal covers the same ground. Our difference is I think God is doing the coding.

dhw: I don’t know why you feel it is necessary to repeat everything I have said in my original proposal, but thank you for withdrawing your objection to new genes, dropping your insistence that loss of genes CAUSES speciation, and agreeing with me that old genes take on new functions. The argument has been about the cause of speciation, and I am perfectly happy, as I always have been, to acknowledge the possibility that there is a God who did the coding. If you now accept my revised proposal, I think we can close this thread.

I do not agree fully with the bold above. Loss of genes appears to be one of causes of speciation along with a restructuring of expression of genes and may include new genes added. But based on Behe, some speciation changes are just deletion.