Prediction of a universal common ancestor falsified: different key proteins in DNA polymerase in prokaryotes ( bacteria ) and archaea (as well as eukaryotes) are unrelated
http://reasonandscience.heavenforum.org/t1831-prediction-of-a-universal-common-ancestor-falsified-different-key-proteins-in-dna-polymerase-in-prokaryotes-bacteria-and-archaea-as-well-as-eukaryotes-are-unrelated?highlight=falsified
Several lines or reasoning are brought forward to back up common ancestry, and a last unversal common ancestor ( LUCA ). Different key proteins in DNA polymerase ( the DNA duplication process ) in prokaryotes ( bacteria ) and archaea (as well as eukaryotes) are unrelated. This finding falsifies the claim of LUCA.
DNA replication
http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/Replication_Process
What was the chemical pathway for an "RNA world" to transform into a "DNA/protein world." ?
DNA replication must not have been present in LUCA because the DNA replication machinery in today’s species reveals too many differences.
Furthermore the aminoacyl tRNA synthetases fail to form an evolutionary tree. So evolutionists must believe HGT caused the confusion. There is no independent evidence that HGT changed around the aminoacyl tRNA synthetases. The evidence simply is the failure to find an adequate evolutionary tree to explain these enzymes.
DNA polymerase is a polypeptide enzyme
http://www.nature.com/scitable/topicpage/cells-can-replicate-their-dna-precisely-6524830
DNA polymerase is the most accurate enzyme. It creates an exact copy of your DNA each time, making less than one mistake in a billion bases. This is far better than information in our own world: imagine reading a thousand novels, and finding only one mistake. The excellent match of cytosine to guanine and adenine to thymine, the language of DNA, provides much of the specificity needed for this high accuracy. But DNA polymerase adds an extra step. After it copies each base, it proofreads it and cuts it out if the base is wrong.
https://www.youtube.com/watch?v=OnuspQG0Jd0
http://web.archive.org/web/20090126042355/http://darwinspredictions.com/#_1.3_Evolution’s_falsifications
Introduction
Despite the fact that the origin of life belongs to abiogenesis, many propose evolution as the driving force to produce the first living cell, despite the fact that evolution only works after replication begins. The following article deals with the proposal that evolution could be the driving force for the arise of the DNA replication process.
In the twentieth century scientists discovered a great deal about the inner workings of the cell. These details, involving DNA, the genetic code, protein synthesis and an army of molecular machines, revealed many commonalities across the species, and many complex and convoluted designs.
Consider for example DNA replication, a common and central feature of all known cellular life. Cells are the basic unit of life and to replicate themselves they make a copy of the DNA they contain. The DNA consists of pairs of long molecular strands, and a small army of proteins performs a series of fascinating and complex tasks to make a copy of each pair of strands.
This process is essentially the same in all species and begins by separating the two DNA strands at designated starting points. Each strand then serves as a template upon which a new copy of the other, complementary strand, is synthesized. In the end, the result is two pairs of strands where originally there was just one pair. One intriguing aspect of this operation is that the synthesis is performed in opposite directions on each strand. That is, as the strands are unzipped a “Y” is formed. On one of the single strands, the proteins synthesize a new strand, continuously moving toward the intersection of the “Y” as the DNA strands are unzipped. This way, as more strand becomes exposed it quickly is covered with its new paired strand.
On the other single strand, however, the proteins synthesize a new strand in the opposite direction, away from the unzipping action. This makes sense because paired DNA strands are chemically anti-parallel. But this makes for a complex process. As the strand is exposed due to unzipping, the proteins start close to the intersection of the “Y,” at the location that has most recently been exposed. The proteins then move away from the intersection as they synthesize a new paired strand.
At some point the proteins halt, move back toward the intersection of the “Y,” and begin the process again on the newly exposed section of strand. Hence on one of the strands replication is continuous (the “leading” strand), and on the other strand replication is discontinuous (the “lagging” strand). Figure 3 illustrates the process.
Figure 3 DNA replication processes on the leading and lagging strands. Several protein machines perform various tasks to complete the replication.
Figure 3 illustrates how the topoisomerase and helicase protein machines act to unwind and separate the DNA strands. Then in addition to the DNA polymerase machines which synthesize the new complementary strands, a variety of other protein machines perform various tasks in a highly coordinated manner, particularly on the lagging strand. These tasks include priming the lagging strand with temporary nucleotides, later removal of those nucleotides, gap filling and nick sealing.
Prediction
There is of course a great deal more detail to this process. For our purposes what is important is that this complex and somewhat circuitous process is found in all cellular life. It is a classic example of the type of fundamental molecular processes that evolution predicts to originate in a common ancestor. How could it evolve twice?
Furthermore, once established, such fundamental molecular processes probably could not evolve, for too much depends on them. It would be like changing the size of an inner part at the core of a finely tuned machine.
Therefore, evolution predicts that the fundamental molecular processes within the cell, that perform functions common to all life, are conserved and originate from a common ancestor. In other words, processes that are found in all species must have been present in the common ancestor of all the species.
Initially it appeared that this prediction was confirmed. All species use DNA to store genetic information, the same code to interpret that information, RNA to copy that information, the DNA replication process to pass on that information, and so forth. Evolutionists boldly proclaimed that a key prediction had been verified and that evolution had passed a crucial test. As the leading evolutionist Niles Eldredge put it:
The basic notion that life has evolved passes its severest test with flying colors: the underlying chemical uniformity of life, and the myriad patterns of special similarities shared by smaller groups of more closely related organisms, all point to a grand pattern of “descent with modification.” [1]
Similarly philosopher Michael Ruse concluded that “molecular biology has opened up dramatic new veins of support” for evolution, and the theory is now beyond reasonable doubt. “The essential macromolecules of life speak no less eloquently about the past than does any other level of the biological world.” [2] The National Academy of Sciences found that the “evidence for evolution from molecular biology is overwhelming” [3] and Christian de Duve began his ambitious history of life with a triumphant declaration:
Life is one. This fact, implicitly recognized by the use of a single word to encompass objects as different as trees, mushrooms, fish, and humans, has now been established beyond doubt. Each advance in the resolving power of our tools, from the hesitant beginnings of microscopy little more than three centuries ago to the incisive techniques of molecular biology, has further strengthened the view that all extant living organisms are constructed of the same materials, function according to the same principles, and, indeed, are actually related. All are descendants of a single ancestral form of life. This fact is now established thanks to the comparative sequencing of proteins and nucleic acids. [4]
Evolutionists believed that the fruits of molecular biology, unknown to Darwin, had resoundingly confirmed his theory. In fact, it is difficult to overestimate the confidence instilled by these findings.
Falsification
The twentieth century’s findings that the fundamental molecular processes within the cell are common to all species was superficial. In later years, as the details were investigated, nuanced differences between species emerged that defied the simplicity of the earlier claims. It seemed that such processes, such as DNA replication, could not have evolved twice, but it now appears this is exactly what must have happened if evolution is true. For too many of the key proteins involved in DNA replication are too different in the various species to be related via the usual Darwinian model of common descent.
Furthermore, scientists have also discovered different DNA replication processes, used to replicate viral and plasmid DNA. These results were not what evolutionists expected. As one evolutionist has written:
It is therefore surprising that the protein sequences of several central components of the DNA replication machinery, above all the principal replicative polymerases, show very little or no sequence similarity between bacteria and archaea/eukaryotes. [5]
In particular, and counter-intuitively, given the central role of DNA in all cells and the mechanistic uniformity of replication, the core enzymes of the replication systems of bacteria and archaea (as well as eukaryotes) are unrelated or extremely distantly related. Viruses and plasmids, in addition, possess at least two unique DNA replication systems, namely, the protein-primed and rolling circle modalities of replication. This unexpected diversity makes the origin and evolution of DNA replication systems a particularly challenging and intriguing problem in evolutionary biology. [6]
For the process of DNA replication, the evolutionary prediction that this fundamental molecular process is conserved across all life has been empirically falsified. Not only are key molecular components not conserved, but there is not one, but several types of DNA replication processes.
Reaction
The response of evolutionists to this finding is to drop the prediction and modify evolution, making it more complex. Now they say that some fundamental molecular processes within the cell, that perform functions common to all life, may not originate from a common ancestor, but perhaps evolve independently. As one paper concluded, “the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.” [5] Indeed, some evolutionists are reconsidering the assumption that all life on Earth shares the same basic molecular architecture and biochemistry, and instead examining the possibility of multiple origins of fundamentally different life forms. [7]
Hence the prediction was never really a prediction after all. The direct opposite of the prediction is what is suggested by the research, and evolution is expanded to accommodate this new finding. The theory becomes more complicated as it now must account for unexpected and seemingly contradictory findings.
References
1. Niles Eldredge, The Monkey Business (New York: Washington Square Press, 1982), 41.
2. Michael Ruse, Taking Darwin Seriously (New York: Basil Blackwell, 1986), 4.
3. National Academy of Sciences, Science and Creationism: A View from the National Academy of Sciences, 2d ed. (Washington D.C.: National Academy Press, 1999), 20.
4. Christian de Duve, Vital Dust (New York: BasicBooks, 1995), 1.
5. D. Leipe, L. Aravind, E. V. Koonin, “Did DNA replication evolve twice independently?,” Nucleic Acids Research 27 (1999): 3389-3401.
6. E. V. Koonin, “Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases,” Biology Direct 18 (2006): 1-39.
7. Carol E. Cleland, “Epistemological issues in the study of microbial life: alternative terran biospheres?,” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 38 (2007): 847-861.
Further reading :
http://reasonandscience.heavenforum.org/t1725-dna-polymerase#2742
http://reasonandscience.heavenforum.org/t1831-prediction-of-a-universal-common-ancestor-falsified-different-key-proteins-in-dna-polymerase-in-prokaryotes-bacteria-and-archaea-as-well-as-eukaryotes-are-unrelated?highlight=falsified
Several lines or reasoning are brought forward to back up common ancestry, and a last unversal common ancestor ( LUCA ). Different key proteins in DNA polymerase ( the DNA duplication process ) in prokaryotes ( bacteria ) and archaea (as well as eukaryotes) are unrelated. This finding falsifies the claim of LUCA.
DNA replication
http://en.wikibooks.org/wiki/Structural_Biochemistry/Nucleic_Acid/DNA/Replication_Process
What was the chemical pathway for an "RNA world" to transform into a "DNA/protein world." ?
DNA replication must not have been present in LUCA because the DNA replication machinery in today’s species reveals too many differences.
Furthermore the aminoacyl tRNA synthetases fail to form an evolutionary tree. So evolutionists must believe HGT caused the confusion. There is no independent evidence that HGT changed around the aminoacyl tRNA synthetases. The evidence simply is the failure to find an adequate evolutionary tree to explain these enzymes.
DNA polymerase is a polypeptide enzyme
http://www.nature.com/scitable/topicpage/cells-can-replicate-their-dna-precisely-6524830
DNA polymerase is the most accurate enzyme. It creates an exact copy of your DNA each time, making less than one mistake in a billion bases. This is far better than information in our own world: imagine reading a thousand novels, and finding only one mistake. The excellent match of cytosine to guanine and adenine to thymine, the language of DNA, provides much of the specificity needed for this high accuracy. But DNA polymerase adds an extra step. After it copies each base, it proofreads it and cuts it out if the base is wrong.
https://www.youtube.com/watch?v=OnuspQG0Jd0
http://web.archive.org/web/20090126042355/http://darwinspredictions.com/#_1.3_Evolution’s_falsifications
Introduction
Despite the fact that the origin of life belongs to abiogenesis, many propose evolution as the driving force to produce the first living cell, despite the fact that evolution only works after replication begins. The following article deals with the proposal that evolution could be the driving force for the arise of the DNA replication process.
In the twentieth century scientists discovered a great deal about the inner workings of the cell. These details, involving DNA, the genetic code, protein synthesis and an army of molecular machines, revealed many commonalities across the species, and many complex and convoluted designs.
Consider for example DNA replication, a common and central feature of all known cellular life. Cells are the basic unit of life and to replicate themselves they make a copy of the DNA they contain. The DNA consists of pairs of long molecular strands, and a small army of proteins performs a series of fascinating and complex tasks to make a copy of each pair of strands.
This process is essentially the same in all species and begins by separating the two DNA strands at designated starting points. Each strand then serves as a template upon which a new copy of the other, complementary strand, is synthesized. In the end, the result is two pairs of strands where originally there was just one pair. One intriguing aspect of this operation is that the synthesis is performed in opposite directions on each strand. That is, as the strands are unzipped a “Y” is formed. On one of the single strands, the proteins synthesize a new strand, continuously moving toward the intersection of the “Y” as the DNA strands are unzipped. This way, as more strand becomes exposed it quickly is covered with its new paired strand.
On the other single strand, however, the proteins synthesize a new strand in the opposite direction, away from the unzipping action. This makes sense because paired DNA strands are chemically anti-parallel. But this makes for a complex process. As the strand is exposed due to unzipping, the proteins start close to the intersection of the “Y,” at the location that has most recently been exposed. The proteins then move away from the intersection as they synthesize a new paired strand.
At some point the proteins halt, move back toward the intersection of the “Y,” and begin the process again on the newly exposed section of strand. Hence on one of the strands replication is continuous (the “leading” strand), and on the other strand replication is discontinuous (the “lagging” strand). Figure 3 illustrates the process.
Figure 3 DNA replication processes on the leading and lagging strands. Several protein machines perform various tasks to complete the replication.
Figure 3 illustrates how the topoisomerase and helicase protein machines act to unwind and separate the DNA strands. Then in addition to the DNA polymerase machines which synthesize the new complementary strands, a variety of other protein machines perform various tasks in a highly coordinated manner, particularly on the lagging strand. These tasks include priming the lagging strand with temporary nucleotides, later removal of those nucleotides, gap filling and nick sealing.
Prediction
There is of course a great deal more detail to this process. For our purposes what is important is that this complex and somewhat circuitous process is found in all cellular life. It is a classic example of the type of fundamental molecular processes that evolution predicts to originate in a common ancestor. How could it evolve twice?
Furthermore, once established, such fundamental molecular processes probably could not evolve, for too much depends on them. It would be like changing the size of an inner part at the core of a finely tuned machine.
Therefore, evolution predicts that the fundamental molecular processes within the cell, that perform functions common to all life, are conserved and originate from a common ancestor. In other words, processes that are found in all species must have been present in the common ancestor of all the species.
Initially it appeared that this prediction was confirmed. All species use DNA to store genetic information, the same code to interpret that information, RNA to copy that information, the DNA replication process to pass on that information, and so forth. Evolutionists boldly proclaimed that a key prediction had been verified and that evolution had passed a crucial test. As the leading evolutionist Niles Eldredge put it:
The basic notion that life has evolved passes its severest test with flying colors: the underlying chemical uniformity of life, and the myriad patterns of special similarities shared by smaller groups of more closely related organisms, all point to a grand pattern of “descent with modification.” [1]
Similarly philosopher Michael Ruse concluded that “molecular biology has opened up dramatic new veins of support” for evolution, and the theory is now beyond reasonable doubt. “The essential macromolecules of life speak no less eloquently about the past than does any other level of the biological world.” [2] The National Academy of Sciences found that the “evidence for evolution from molecular biology is overwhelming” [3] and Christian de Duve began his ambitious history of life with a triumphant declaration:
Life is one. This fact, implicitly recognized by the use of a single word to encompass objects as different as trees, mushrooms, fish, and humans, has now been established beyond doubt. Each advance in the resolving power of our tools, from the hesitant beginnings of microscopy little more than three centuries ago to the incisive techniques of molecular biology, has further strengthened the view that all extant living organisms are constructed of the same materials, function according to the same principles, and, indeed, are actually related. All are descendants of a single ancestral form of life. This fact is now established thanks to the comparative sequencing of proteins and nucleic acids. [4]
Evolutionists believed that the fruits of molecular biology, unknown to Darwin, had resoundingly confirmed his theory. In fact, it is difficult to overestimate the confidence instilled by these findings.
Falsification
The twentieth century’s findings that the fundamental molecular processes within the cell are common to all species was superficial. In later years, as the details were investigated, nuanced differences between species emerged that defied the simplicity of the earlier claims. It seemed that such processes, such as DNA replication, could not have evolved twice, but it now appears this is exactly what must have happened if evolution is true. For too many of the key proteins involved in DNA replication are too different in the various species to be related via the usual Darwinian model of common descent.
Furthermore, scientists have also discovered different DNA replication processes, used to replicate viral and plasmid DNA. These results were not what evolutionists expected. As one evolutionist has written:
It is therefore surprising that the protein sequences of several central components of the DNA replication machinery, above all the principal replicative polymerases, show very little or no sequence similarity between bacteria and archaea/eukaryotes. [5]
In particular, and counter-intuitively, given the central role of DNA in all cells and the mechanistic uniformity of replication, the core enzymes of the replication systems of bacteria and archaea (as well as eukaryotes) are unrelated or extremely distantly related. Viruses and plasmids, in addition, possess at least two unique DNA replication systems, namely, the protein-primed and rolling circle modalities of replication. This unexpected diversity makes the origin and evolution of DNA replication systems a particularly challenging and intriguing problem in evolutionary biology. [6]
For the process of DNA replication, the evolutionary prediction that this fundamental molecular process is conserved across all life has been empirically falsified. Not only are key molecular components not conserved, but there is not one, but several types of DNA replication processes.
Reaction
The response of evolutionists to this finding is to drop the prediction and modify evolution, making it more complex. Now they say that some fundamental molecular processes within the cell, that perform functions common to all life, may not originate from a common ancestor, but perhaps evolve independently. As one paper concluded, “the modern-type system for double-stranded DNA replication likely evolved independently in the bacterial and archaeal/eukaryotic lineages.” [5] Indeed, some evolutionists are reconsidering the assumption that all life on Earth shares the same basic molecular architecture and biochemistry, and instead examining the possibility of multiple origins of fundamentally different life forms. [7]
Hence the prediction was never really a prediction after all. The direct opposite of the prediction is what is suggested by the research, and evolution is expanded to accommodate this new finding. The theory becomes more complicated as it now must account for unexpected and seemingly contradictory findings.
References
1. Niles Eldredge, The Monkey Business (New York: Washington Square Press, 1982), 41.
2. Michael Ruse, Taking Darwin Seriously (New York: Basil Blackwell, 1986), 4.
3. National Academy of Sciences, Science and Creationism: A View from the National Academy of Sciences, 2d ed. (Washington D.C.: National Academy Press, 1999), 20.
4. Christian de Duve, Vital Dust (New York: BasicBooks, 1995), 1.
5. D. Leipe, L. Aravind, E. V. Koonin, “Did DNA replication evolve twice independently?,” Nucleic Acids Research 27 (1999): 3389-3401.
6. E. V. Koonin, “Temporal order of evolution of DNA replication systems inferred by comparison of cellular and viral DNA polymerases,” Biology Direct 18 (2006): 1-39.
7. Carol E. Cleland, “Epistemological issues in the study of microbial life: alternative terran biospheres?,” Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 38 (2007): 847-861.
Further reading :
http://reasonandscience.heavenforum.org/t1725-dna-polymerase#2742
