Who Owns Cooption?

If anyone can see my comments sorry for the duplicate postings, the longer ones did not show up until I cut them down in size WayneFrancis

Wayne "Bacteria are NOT “A” species. Bacteria are “A” Kingdom more specifically Bacteria are Monera." Alright, for your nitpicking pleasure let me rephrase. In the case of the bacteria that are eating TnT derivatives they are not only still bacteria they are the same species of bacteria. Technically they are a different strain of a single species. I think everyone but you got the point with fewer words. It has now been amply demonstrated that organisms as diverse as bacteria and baboons can exchange heritable genetic information through viral vectors. What does this do to evolutionary ideas that take genetic isolation between higher level taxonomic classifications as a given? You might want to ask Lynn Margulis about it. DaveScot

Gumpngreen - let me start off by saying I agree with you. With cave fish, and many other systems, we find that it isn't that the genetic code is changed to remove the feature but its the expression of the genes that reduce its development therefore it conserves energy. These genes don't only deal with the development of eyes. Most genes have multiple rolls within the organism so you would not expect those genes to disappear from the organism just because 1 feature is no longer needed. What does happen is they seem to express less during the critical development period of the feature that is no longer needed. The mechanisms that control this are still being investigated (ie "We just don't know yet"). Sadly we see plenty of examples of genes expressing to much or to little that in critical areas of development all the time. It is much harder to identify cases where genes may be expressing more or less then they normally would and producing an advantageous trait. Some times these instances of gene expression can be controlled by genetic factors but you are right often they seem to be controlled by environmental factors. WayneFrancis

Gumpngreen - let me start off by saying I agree with you. With cave fish, and many other systems, we find that it isn't that the genetic code is changed to remove the feature but its the expression of the genes that reduce its development therefore it conserves energy. These genes don't only deal with the development of eyes. Most genes have multiple rolls within the organism so you would not expect those genes to disappear from the organism just because 1 feature is no longer needed. What does happen is they seem to express less during the critical development period of the feature that is no longer needed. The mechanisms that control this are still being investigated (ie "We just don't know yet"). Sadly we see plenty of examples of genes expressing to much or to little that in critical areas of development all the time. It is much harder to identify cases where genes may be expressing more or less then they normally would and producing an advantageous trait. Some times these instances of gene expression can be controlled by genetic factors but you are right often they seem to be controlled by environmental factors. I could go into some detail about holoprosencephaly and how this can be effected by things like diabetes, rubella, certain drugs being taken, and many other conditions during early pregnancy can cause this condition to occur by interfering with the expression of genes in early development. But I'll focus on a easier to understand example. WayneFrancis

Gumpngreen - let me start off by saying I agree with you. With cave fish, and many other systems, we find that it isn't that the genetic code is changed to remove the feature but its the expression of the genes that reduce its development therefore it conserves energy. These genes don't only deal with the development of eyes. Most genes have multiple rolls within the organism so you would not expect those genes to disappear from the organism just because 1 feature is no longer needed. What does happen is they seem to express less during the critical development period of the feature that is no longer needed. The mechanisms that control this are still being investigated (ie "We just don't know yet"). Sadly we see plenty of examples of genes expressing to much or to little that in critical areas of development all the time. It is much harder to identify cases where genes may be expressing more or less then they normally would and producing an advantageous trait. Some times these instances of gene expression can be controlled by genetic factors but you are right often they seem to be controlled by environmental factors. I could go into some detail about holoprosencephaly and how this can be effected by things like diabetes, rubella, certain drugs being taken, and many other conditions during early pregnancy can cause this condition to occur by interfering with the expression of genes in early development. But I'll focus on a easier to understand example. Identical Twins are genetically identical, as close as you are going to get because even within a single person you are able to find different DNA because of random mutations. While they are genetically identical there are clearly many parts of development that are environmental. This is why even identical twins have different finger prints. These things are not strickly coded in the DNA. Another good example of gene expression causing apparently large amounts of change in species is Canis lupus. Canis lupus is the species of all wolves/dogs. Since 1993 they are recognized as a single species. The diversity we see in Canis lupus seems to be entirely gene expression but this gene expression is may be effected by the environment, as in holoprosencephaly, but that the change in gene expression seems to be genetically fixed. By this I mean that it can still change over time but that it is still a genetic trait that can be passed from parent to offspring. If a population subspecies of Canis lupus, lets say cocker spaniels, was released into the wild, by wild I mean an area completely absent of human society and the wastes that we produce, we would expect this population to slowly revert back to Gray wolves over many generations because the trait of being docile is not advantageous in the wild. Remember it has only been about 15,000 year or so that wolves have been in large contact with humans and started genetic changes that produced all the subspecies of dogs we see and those sub species, most scientist will agree are artificially selected and inbreed to obtain specific traits. All these traits are not “new genetic information” but instead caused by slight changes in genetic information that control the expression of particular genes. This is why we can select for certain traits. There is a lot of research going on in this area. We see the same type of changes in another genus. Vulpes (aka Foxes) , in the family Canidea. The same changes can be found. Populations of different species in vulpes can selectively breed to be more docile thus tend to do better around human populations. Besides becoming more docile, which means not only are they less likely to attack humans thus humans are less likely to retaliate and kill them, they get characteristic changes that we see between wolves and domesticated dogs. Ears tend to go floppy, tails tend to turn up, and coats start to take on a much more diverse set of pattern and colors. These are what I call secondary traits. We notice them more because they are very visual but they just happen to be traits that are controlled by the same genes that are responsible for aggression. Foxes and wolves around human societies then have the chance to fill a niche. First as a scavenger, around human societies, then eventually being adopted into the human society. Eventually will dogs and wolves be, once again, classified as separate species? I believe so. This is because genetically they will eventually become incompatible. This may take a few million years but its bound to happen just by the accumulation of normal, very well understood, “micro evolutionary events”. Will they still be “wolves” and “dogs”? Yes but you’ll see the classification of Canis Lupus go to the level of Genus and the populations that have been genetically isolated for long periods of time become species instead of sub species. We don’t expect to see a “on/off” point where they suddenly can’t interbreed but just a slow change in viability/fertility rates of offspring. We see that now within the genus of Equus where different species like Equus caballus (domestic horse) and Equus asinus (donkey) where the viability rate of hybrid offspring between these 2 species (mules) is fairly high but the fertility rate is extremely low. We look at Equus caballus and Equus quagga and we see the viability rate of their hybrid offspring (Zebroids) drastically lower then that of mules. There are actually 3 species of zebra and they are much more genetically different then donkeys and domestic horses. Their hybrid offspring are often not viable and depending on the hybrid the fertility rates can be rare to nonexistent. At the other end of the spectrum there is the Equus Przewalskii/ Equus caballus hybrid that not only has an extremely high viability rate but are almost always fertile. You may then ask “Why are they a separate species?” This is a valid question. At the time that they where classified there where enough differences between the two to make them two separate species. Genetically speaking they are different to horses too. They have 66 chromosomes while domestic horses have 64, FYI Donkeys have 62. Even with this chromosomal difference the offspring are still highly viable and fertile. Genetic studies show that Equus przewalskii and Equus caballus do not form a monophyletic clade. They are more akin to the relationship between sisters in the “tree of life” then one evolving from the other. Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus B. Wallner, G. Brem, M. Müller, R. Achmann Animal Genetics 2003 34:6 453 Thus they are still separate species just as many of the “big cats” are separate species even though they technically can interbreed with high viability/fertility rates. We can see while it has been about 15,000 years in the making we can do the same in just a handful to a dozen generations of selective breeding. Yes Dogs and Wolves are still really just wolves or more specifically they are just Canis lupus. This doesn’t mean we shouldn’t try to learn about the causes of the changes. All this said Scientist still don't know all the answers and most would say that when science knows all the answers there will be no need for scientists. So we are still learning. We are still finding out what causes different changes. It is turning out from genetic research that the big differences between chimps and humans isn’t some grand genetic change but actually just genes being expressed at slightly different times and amounts during development. It is studies into this area that will eventually tell us why we have bigger brains. Why we are more akin to bonoboos then chimps in our social interactions and many other things. Will it tell us why we have a broken vitamin C gene? Will that be a “secondary trait” to us becoming more intelligent? Could our increased intelligence be a “secondary trait” to the broken vitamin C gene? Who knows but if we don’t try to look for an answer we will never find one weather it is there or not. Thankfully when we do look for answers we do find them and our knowledge increases. I don’t, in any way, see this as a strike against “God”. What seems random and undirected to us would not be random and undirected to a “God” Is 55:8 For my thoughts are not your thoughts, neither are your ways my ways, saith the LORD WayneFrancis

"I use “still are bacteria” to make it clear that in any event it remains a demonstration of adaption within species not origin of a new species." Bacteria are NOT "A" species. Bacteria are "A" Kingdom more specifically Bacteria are Monera. The Kingdoms are Monera - (aka Bacteria) Protoctista - (Protists) Fungi - (Mushrooms, Yeasts, Molds) Plantae - (Plants) Animalia - (Animals) So when you say something like The bacteria A evolved into bacteria B but is is still a bacteria you are saying the equivalent to Vendian biota evolved into all animals we see today but they are still just animals Sorry to point this out but you need to learn about the phylogenic classification system a bit more. You also have to understand that there is more diversity in species in the "bacteria kingdom" then there is in species within the "animal kingdom" WayneFrancis

Gumpngreen, Cool post. Thanks for sharing it. There's another article about this research on sciencedaily.com: http://www.sciencedaily.com/releases/2004/10/041021080317.htm It contains this bizarre factoid: "We know that loss of shh [sonic hedgehog gene] function in humans expands eye development, resulting in a single large eye in the middle of the forehead. Actually, the Cyclops in The Odyssey was probably not a product of Homer's imagination. Therefore, we reasoned that increased shh could do the opposite in cavefish, that is, function as an inhibitor of eye development." keiths

"I use “still are bacteria” to make it clear that in any event it remains a demonstration of adaption within species not origin of a new species." Bacteria are NOT "A" species. Bacteria are "A" Kingdom more specifically Bacteria are Monera. The Kingdoms are Monera - (aka Bacteria) Protoctista - (Protists) Fungi - (Mushrooms, Yeasts, Molds) Plantae - (Plants) Animalia - (Animals) So when you say something like The bacteria A evolved into bacteria B but is is still a bacteria you are saying the equivalent to Vendian biota evolved into all animals we see today but they are still just animals Sorry to point this out but you need to learn about the phylogenic classification system a bit more. You also have to understand that there is more diversity in species in the "bacteria kingdom" then there is in species within the "animal kingdom" Gumpngreen - let me start off by saying I agree with you. With cave fish, and many other systems, we find that it isn't that the genetic code is changed to remove the feature but its the expression of the genes that reduce its development therefore it conserves energy. These genes don't only deal with the development of eyes. Most genes have multiple rolls within the organism so you would not expect those genes to disappear from the organism just because 1 feature is no longer needed. What does happen is they seem to express less during the critical development period of the feature that is no longer needed. The mechanisms that control this are still being investigated (ie "We just don't know yet"). Sadly we see plenty of examples of genes expressing to much or to little that in critical areas of development all the time. It is much harder to identify cases where genes may be expressing more or less then they normally would and producing an advantageous trait. Some times these instances of gene expression can be controlled by genetic factors but you are right often they seem to be controlled by environmental factors. I could go into some detail about holoprosencephaly and how this can be effected by things like diabetes, rubella, certain drugs being taken, and many other conditions during early pregnancy can cause this condition to occur by interfering with the expression of genes in early development. But I'll focus on a easier to understand example. Identical Twins are genetically identical, as close as you are going to get because even within a single person you are able to find different DNA because of random mutations. While they are genetically identical there are clearly many parts of development that are environmental. This is why even identical twins have different finger prints. These things are not strickly coded in the DNA. Another good example of gene expression causing apparently large amounts of change in species is Canis lupus. Canis lupus is the species of all wolves/dogs. Since 1993 they are recognized as a single species. The diversity we see in Canis lupus seems to be entirely gene expression but this gene expression is may be effected by the environment, as in holoprosencephaly, but that the change in gene expression seems to be genetically fixed. By this I mean that it can still change over time but that it is still a genetic trait that can be passed from parent to offspring. If a population subspecies of Canis lupus, lets say cocker spaniels, was released into the wild, by wild I mean an area completely absent of human society and the wastes that we produce, we would expect this population to slowly revert back to Gray wolves over many generations because the trait of being docile is not advantageous in the wild. Remember it has only been about 15,000 year or so that wolves have been in large contact with humans and started genetic changes that produced all the subspecies of dogs we see and those sub species, most scientist will agree are artificially selected and inbreed to obtain specific traits. All these traits are not “new genetic information” but instead caused by slight changes in genetic information that control the expression of particular genes. This is why we can select for certain traits. There is a lot of research going on in this area. We see the same type of changes in another genus. Vulpes (aka Foxes) , in the family Canidea. The same changes can be found. Populations of different species in vulpes can selectively breed to be more docile thus tend to do better around human populations. Besides becoming more docile, which means not only are they less likely to attack humans thus humans are less likely to retaliate and kill them, they get characteristic changes that we see between wolves and domesticated dogs. Ears tend to go floppy, tails tend to turn up, and coats start to take on a much more diverse set of pattern and colors. These are what I call secondary traits. We notice them more because they are very visual but they just happen to be traits that are controlled by the same genes that are responsible for aggression. Foxes and wolves around human societies then have the chance to fill a niche. First as a scavenger, around human societies, then eventually being adopted into the human society. Eventually will dogs and wolves be, once again, classified as separate species? I believe so. This is because genetically they will eventually become incompatible. This may take a few million years but its bound to happen just by the accumulation of normal, very well understood, “micro evolutionary events”. Will they still be “wolves” and “dogs”? Yes but you’ll see the classification of Canis Lupus go to the level of Genus and the populations that have been genetically isolated for long periods of time become species instead of sub species. We don’t expect to see a “on/off” point where they suddenly can’t interbreed but just a slow change in viability/fertility rates of offspring. We see that now within the genus of Equus where different species like Equus caballus (domestic horse) and Equus asinus (donkey) where the viability rate of hybrid offspring between these 2 species (mules) is fairly high but the fertility rate is extremely low. We look at Equus caballus and Equus quagga and we see the viability rate of their hybrid offspring (Zebroids) drastically lower then that of mules. There are actually 3 species of zebra and they are much more genetically different then donkeys and domestic horses. Their hybrid offspring are often not viable and depending on the hybrid the fertility rates can be rare to nonexistent. At the other end of the spectrum there is the Equus Przewalskii/ Equus caballus hybrid that not only has an extremely high viability rate but are almost always fertile. You may then ask “Why are they a separate species?” This is a valid question. At the time that they where classified there where enough differences between the two to make them two separate species. Genetically speaking they are different to horses too. They have 66 chromosomes while domestic horses have 64, FYI Donkeys have 62. Even with this chromosomal difference the offspring are still highly viable and fertile. Genetic studies show that Equus przewalskii and Equus caballus do not form a monophyletic clade. They are more akin to the relationship between sisters in the “tree of life” then one evolving from the other. Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus B. Wallner, G. Brem, M. Müller, R. Achmann Animal Genetics 2003 34:6 453 Thus they are still separate species just as many of the “big cats” are separate species even though they technically can interbreed with high viability/fertility rates. We can see while it has been about 15,000 years in the making we can do the same in just a handful to a dozen generations of selective breeding. Yes Dogs and Wolves are still really just wolves or more specifically they are just Canis lupus. This doesn’t mean we shouldn’t try to learn about the causes of the changes. All this said Scientist still don't know all the answers and most would say that when science knows all the answers there will be no need for scientists. So we are still learning. We are still finding out what causes different changes. It is turning out from genetic research that the big differences between chimps and humans isn’t some grand genetic change but actually just genes being expressed at slightly different times and amounts during development. It is studies into this area that will eventually tell us why we have bigger brains. Why we are more akin to bonoboos then chimps in our social interactions and many other things. Will it tell us why we have a broken vitamin C gene? Will that be a “secondary trait” to us becoming more intelligent? Could our increased intelligence be a “secondary trait” to the broken vitamin C gene? Who knows but if we don’t try to look for an answer we will never find one weather it is there or not. Thankfully when we do look for answers we do find them and our knowledge increases. I don’t, in any way, see this as a strike against “God”. What seems random and undirected to us would not be random and undirected to a “God” Is 55:8 For my thoughts are not your thoughts, neither are your ways my ways, saith the LORD WayneFrancis

DaveScot says "I use “still are bacteria” to make it clear that in any event it remains a demonstration of adaption within species not origin of a new species." Bacteria are NOT "A" species. Bacteria are "A" Kingdom more specifically Bacteria are Monera. The Kingdoms are Monera - (aka Bacteria) Protoctista - (Protists) Fungi - (Mushrooms, Yeasts, Molds) Plantae - (Plants) Animalia - (Animals) So when you say something like The bacteria A evolved into bacteria B but is is still a bacteria you are saying the equivalent to Vendian biota evolved into all animals we see today but they are still just animals Sorry to point this out but you need to learn about the phylogenic classification system a bit more. You also have to understand that there is more diversity in species in the "bacteria kingdom" then there is in species within the "animal kingdom" Gumpngreen - let me start off by saying I agree with you. With cave fish, and many other systems, we find that it isn't that the genetic code is changed to remove the feature but its the expression of the genes that reduce its development therefore it conserves energy. These genes don't only deal with the development of eyes. Most genes have multiple rolls within the organism so you would not expect those genes to disappear from the organism just because 1 feature is no longer needed. What does happen is they seem to express less during the critical development period of the feature that is no longer needed. The mechanisms that control this are still being investigated (ie "We just don't know yet"). Sadly we see plenty of examples of genes expressing to much or to little that in critical areas of development all the time. It is much harder to identify cases where genes may be expressing more or less then they normally would and producing an advantageous trait. Some times these instances of gene expression can be controlled by genetic factors but you are right often they seem to be controlled by environmental factors. I could go into some detail about holoprosencephaly and how this can be effected by things like diabetes, rubella, certain drugs being taken, and many other conditions during early pregnancy can cause this condition to occur by interfering with the expression of genes in early development. But I'll focus on a easier to understand example. Identical Twins are genetically identical, as close as you are going to get because even within a single person you are able to find different DNA because of random mutations. While they are genetically identical there are clearly many parts of development that are environmental. This is why even identical twins have different finger prints. These things are not strickly coded in the DNA. Another good example of gene expression causing apparently large amounts of change in species is Canis lupus. Canis lupus is the species of all wolves/dogs. Since 1993 they are recognized as a single species. The diversity we see in Canis lupus seems to be entirely gene expression but this gene expression is may be effected by the environment, as in holoprosencephaly, but that the change in gene expression seems to be genetically fixed. By this I mean that it can still change over time but that it is still a genetic trait that can be passed from parent to offspring. If a population subspecies of Canis lupus, lets say cocker spaniels, was released into the wild, by wild I mean an area completely absent of human society and the wastes that we produce, we would expect this population to slowly revert back to Gray wolves over many generations because the trait of being docile is not advantageous in the wild. Remember it has only been about 15,000 year or so that wolves have been in large contact with humans and started genetic changes that produced all the subspecies of dogs we see and those sub species, most scientist will agree are artificially selected and inbreed to obtain specific traits. All these traits are not “new genetic information” but instead caused by slight changes in genetic information that control the expression of particular genes. This is why we can select for certain traits. There is a lot of research going on in this area. We see the same type of changes in another genus. Vulpes (aka Foxes) , in the family Canidea. The same changes can be found. Populations of different species in vulpes can selectively breed to be more docile thus tend to do better around human populations. Besides becoming more docile, which means not only are they less likely to attack humans thus humans are less likely to retaliate and kill them, they get characteristic changes that we see between wolves and domesticated dogs. Ears tend to go floppy, tails tend to turn up, and coats start to take on a much more diverse set of pattern and colors. These are what I call secondary traits. We notice them more because they are very visual but they just happen to be traits that are controlled by the same genes that are responsible for aggression. Foxes and wolves around human societies then have the chance to fill a niche. First as a scavenger, around human societies, then eventually being adopted into the human society. Eventually will dogs and wolves be, once again, classified as separate species? I believe so. This is because genetically they will eventually become incompatible. This may take a few million years but its bound to happen just by the accumulation of normal, very well understood, “micro evolutionary events”. Will they still be “wolves” and “dogs”? Yes but you’ll see the classification of Canis Lupus go to the level of Genus and the populations that have been genetically isolated for long periods of time become species instead of sub species. We don’t expect to see a “on/off” point where they suddenly can’t interbreed but just a slow change in viability/fertility rates of offspring. We see that now within the genus of Equus where different species like Equus caballus (domestic horse) and Equus asinus (donkey) where the viability rate of hybrid offspring between these 2 species (mules) is fairly high but the fertility rate is extremely low. We look at Equus caballus and Equus quagga and we see the viability rate of their hybrid offspring (Zebroids) drastically lower then that of mules. There are actually 3 species of zebra and they are much more genetically different then donkeys and domestic horses. Their hybrid offspring are often not viable and depending on the hybrid the fertility rates can be rare to nonexistent. At the other end of the spectrum there is the Equus Przewalskii/ Equus caballus hybrid that not only has an extremely high viability rate but are almost always fertile. You may then ask “Why are they a separate species?” This is a valid question. At the time that they where classified there where enough differences between the two to make them two separate species. Genetically speaking they are different to horses too. They have 66 chromosomes while domestic horses have 64, FYI Donkeys have 62. Even with this chromosomal difference the offspring are still highly viable and fertile. Genetic studies show that Equus przewalskii and Equus caballus do not form a monophyletic clade. They are more akin to the relationship between sisters in the “tree of life” then one evolving from the other. Fixed nucleotide differences on the Y chromosome indicate clear divergence between Equus przewalskii and Equus caballus B. Wallner, G. Brem, M. Müller, R. Achmann Animal Genetics 2003 34:6 453 Thus they are still separate species just as many of the “big cats” are separate species even though they technically can interbreed with high viability/fertility rates. We can see while it has been about 15,000 years in the making we can do the same in just a handful to a dozen generations of selective breeding. Yes Dogs and Wolves are still really just wolves or more specifically they are just Canis lupus. This doesn’t mean we shouldn’t try to learn about the causes of the changes. All this said Scientist still don't know all the answers and most would say that when science knows all the answers there will be no need for scientists. So we are still learning. We are still finding out what causes different changes. It is turning out from genetic research that the big differences between chimps and humans isn’t some grand genetic change but actually just genes being expressed at slightly different times and amounts during development. It is studies into this area that will eventually tell us why we have bigger brains. Why we are more akin to bonoboos then chimps in our social interactions and many other things. Will it tell us why we have a broken vitamin C gene? Will that be a “secondary trait” to us becoming more intelligent? Could our increased intelligence be a “secondary trait” to the broken vitamin C gene? Who knows but if we don’t try to look for an answer we will never find one weather it is there or not. Thankfully when we do look for answers we do find them and our knowledge increases. I don’t, in any way, see this as a strike against “God”. What seems random and undirected to us would not be random and undirected to a “God” Is 55:8 For my thoughts are not your thoughts, neither are your ways my ways, saith the LORD WayneFrancis

Here is another possible example with a higher organism: http://sciencenow.sciencemag.org/cgi/content/full/2004/1013/2 "Contrary to previous belief, blind cave fish have the genes to build eyes but turn them off during development. When a body part is no longer needed, scientists usually assume that mutations accumulate in the genes controlling the structure, eventually preventing it from working or being made. “That was the dogma,” says Stephen Ekker of the University of Minnesota, Twin Cities. But because the cave fish eyes are actively killed, natural selection is probably doing its thing, says Jeffery. And that, he adds, might come as a surprise even to Darwin, who thought the cave fishes’ loss of sight might be an exception to the rules of natural selection." So it’s not simply an issue of “use it or lose it,” the article states; “new research suggests that for some cave-dwelling fishes, blindness results from the careful coordination of gene expression, not simply from lack of use." In short, the blindness is temporary (genetics wise) and might actually be the result of a system reacting to dynamic environments. I think I remember seeing an article where these fish actually regain their sight under certain circumstances...but I cannot remember where I saw that. Gumpngreen

Wayne I use "still are bacteria" to make it clear that in any event it remains a demonstration of adaption within species not origin of a new species. Moreover, this is really a case for design as the mutations appear to have far too fast for rm+ns to account for. It's likely IMO that bacteria have some native intelligence in coming up with chemicals used in self defense and digestion. After all, they've had 4 billion years to come up with it There's some interesting Scripps Institute research on e.coli that has identified a gene that controls mutation rate of other genes in response to stress. God only knows how many other bits of intelligent response to the environment bacteria have. And if bacteria have it then it's likely many other living things have similar response pathways. DaveScot

I've blogged on nylonase here: https://uncommondesc.wpengine.com/index.php/archives/348. --WmAD William Dembski

I'm glad you responded to this! I saw this for a while and I couldn't make sense of it. Benjii

WayneFrancis: (a) it is not "simple frame shifts". Pseudomonas, if you are referring to the nylon bug, actually had not only the frame shift but multiple point mutations and, I think, transposon activity. Not only that, there were _2_ enzymes involved in changing in order to make the metabolic pathway happen. I discuss it here: http://crevo.blogspot.com/2005/06/evolution-chance-and-design-to-cb940.html Also see Spetner's comments on it here: http://members.tripod.com/aslodge/id89.htm http://members.tripod.com/aslodge/id133.htm Dembski's work (and others, indirectly) is about assisted searches vs. unassisted searches. It is clear from the data that these changes are assisted searches. Even your description of it seems to indicate such: "The proteins used to metabolize different compounds have been shown to come about by simple frame shifts". Frame shifts of what? Do any frameshifts work? No. Does it have to be of specific existing enzymes? Yes. Is the bacteria frameshifting every gene in its genome? No. This is clearly an assisted, not blind, search. Thus, teleology enters the picture. I'm writing an article about these sorts of topics for a YEC website. You can read a pre-release version here: http://www.eskimo.com/~johnnyb/creation_change.html You also might take a look at Dembski's Searching Large Spaces paper: http://www.designinference.com/documents/2005.03.Searching_Large_Spaces.pdf johnnyb

DaveScot why do you use the "Still are bacteria" line. Don't you know that saying that is like saying "Still are Vertebrate" when talking comparing, let us say, a lamprey to a human. The proteins used to metabolize different compounds have been shown to come about by simple frame shifts as shown by Flavobacterium sp. KI72. This same mutation has been demonstrated in the lab with Pseudomonas aeruginosa PAO5502. These enzymes that hydrolyze Acd into Ald are not present in the parent strain and without selective pressure do not take hold in the strain. Your "Front Loading" hypothesis has been shown faulty over and over again. Please stop waving your hands about mutations really being front loaded. WayneFrancis

Setting aside for a moment the fact that bacteria have been for billions of years perfecting the art of eating everything everywhere from sulfur in boiling ocean vents to the gray matter in the freezing cold vacuum between Matzke's ears... how does Nick propose to demonstrate that the TnT eating bacteria, which by the way are still bacteria, actually evolved the TnT eating enzymes by random means instead of 1) adapting by an unknown directed process or 2) the enzymes in question were always there and it simply took decades for the right bacterial spores to land there, germinate, and begin dining. DaveScot