Tuesday, June 2, 2015
Block Duplication & 2R Hypothesis
Recently, I debated Dr. Dan Larhammar of Uppsala University on the subject of evolution relating to biology and genetics. Dr. Larhammar is a proponent of the 2R Hypothesis which is the belief that the genomes of many organisms experienced duplication events in the distant past. What this means is that a genetic error took place which copied the entire DNA then bound both DNA molecules together to form a single, much larger genome. 2R Hypothesis has been a controversial idea since it was first put forth in the 1970's, even amongst some geneticists who are believers of evolution theory. Some published scientific whitepapers have questioned the validity of 2R Hypothesis since the early 1980's.1
Like most evolutionist scientists and university professors today, he also believes that the genetic redundancy which exists in the genomes of most plants and animals is a result repeated block duplications over vast ages of time during the process of evolution and provides raw material for evolution by producing new copies of genes that are free to mutate and take on other functions. This assumption is held because there are many redundant genes in the genomes of various creatures, and the evolutionist assumes that genetic similarities between gene families in different species (i.e. human and fly) is evidence that the species are related over time. Block duplication is a known but uncommon genetic error in which sections of DNA are duplicated and joined by mutation during cell duplication, resulting in what is called polyploidy.
However, polyploidy cannot be the reason for the genetic redundancy in the genomes of creatures. There are many problems associated with these ideas, which evolutionists typically gloss over and ignore, as they do the degenerative effects of mutation in general in order to believe that mutation is the designer of the marvelous genetic material of creatures. While block duplication may occur occasionally in extant organisms, it has negative consequences, and like genetic mutation in general, it is not plausible to believe that a genetic error process which causes many degenerative effects is the result of all of the genetic redundancy known to exist in the genomes of various creatures for the following reasons, and others not listed:
A. It has been known for many decades that random gene duplication mutation in general is degenerative, contrary to the absurd belief of evolutionists that it is a designer of new information which codes for new viable anatomical features and biological functions.2,3,4,5,6,7,8,9,10
B. Since block duplication mutation is degenerative to an organism, entire genomic duplication is deadly or highly degenerative.
C. If block duplication were the explanation for the genetic redundancy and similarity between species, it could only be because numerous block duplication had taken place over vast ages. However, the effect of block duplication is highly degenerative, so it is not plausible that many repeated block duplications could take place to produce viable, healthy genomes which Natural Selection would select as the phenotype of the organism.11,12,13
D. Block duplication is known to cause a loss of genetic information at the loci where the block is spliced into the genome because genes at the loci are broken. This loss of genetic information caused by block duplication is known to be the cause of disease.11,12,13 Over the vast ages of the evolution theory, this would result in a very high number of genes being lost during block duplication or chromatid recombination.2,11,12,13
E. Since regulatory sequences may be dozens, hundreds, or thousands of base pairs away from the sequences which they regulate, one would have to believe that contrary to the odds, an almost magical perfection occurred each time a block duplication took place so that all related regulatory sequences were not broken and were duplicated with the sequences which they regulate. Unless one believes this, repeated block duplication would rapidly degenerate the genome.2,14
F. Believing that block duplication explains the redundant genetic similarities between species requires one to believe that a process which causes genetic disorder is instead a designer of new viable features and functions.2,11,12,13
G. While duplicated sequences may in the imagination of the evolutionist provide raw material for mutation to transform into new information that codes for new features and function for evolution to occur, the simple truth is that gene duplication causes diseases and malformations, and duplicate genes would only become more potential for increased degenerative random mutation. Repeated instances of block duplication could only continuously increase disease in any given species over time.12,15
H. It has been shown with many studies that random mutation is degenerating the genomes of all life, moving all species towards extinction.
Evolutionists refuse to accept scientific knowledge which refutes their theory. Most specifically, they refuse to accept the astonishing volume of consistent and correlating evidence accumulated over many decades that random genetic mutation is degenerative to genomes. Despite the overwhelming body of scientific evidence, evolutionists continue to hold to the long-disproven idea that random mutation and chromosome errors are the producers of raw material which subsequent mutations then transform into new information which codes for all manner of anatomical biological designs and interdependent biological functions. It is a sad sort of state which one can liken to a dying person refusing to let go of the pitcher of poison they have been drinking while medical personnel tussle with them over it, repeating to them, "But it's poison! You must give it up!".
When will it ever end? Eventually, it must. There will come a time when scientists who are willing to believe that there cannot be a divine cause for man's existence will give up the absurd idea that random genetic mistakes are the most ingenious designers known to exist, and capable of designing technology at the molecular scale which vastly exceeds mankind's abilities. It will be shame and embarrassment that does it. Unfortunately, when this time comes, they will not acknowledge our Creator, Jesus Christ, but will instead point to the heavens, as some are already doing, and tell us that aliens are responsible for the existence of mankind. This will only push the problem away from the earth however, as one must then ask, "Who created the aliens?"
1. 2R or not 2R: testing hypotheses of genome duplication in early vertebrates, Hughes AL1, Friedman R. 1983 "Comparison of gene family size in the human genome and in invertebrate genomes shows no evidence of a 4:1 ratio between vertebrates and invertebrates. Furthermore, explicit phylogenetic tests for the topology expected from two rounds of polyploidization have revealed alternative topologies in a substantial majority of human gene families. Likewise, phylogenetic analyses have shown that putatively duplicated genomic regions often include genes duplicated at widely different times over the evolution of life. The 2R hypothesis thus can be decisively rejected."
2. "It is also important to remember that, in terms of natural selection, “beneficial” means any mutation that leads to greater reproduction, without regard to long-term goals. Under many conditions, that can mean that any mutation that increases efficiency, including mutations that inactivate or delete genes, will be favored [39-41]. Even though genetic information is being lost, such mutations would still be considered “beneficial.” That loss of information is a common evolutionary outcome has been shown repeatedly . Wilf and Ewens’s model, however, assumes that all beneficial mutations lead to more and more “advanced” forms." -- Time and Information in Evolution, William A. Dembski, Winston Ewert, Ann K. Gauger, and Robert J. Marks II, Bio-Complexity 4(2012)
4. "Distribution of fitness effects caused by random insertion mutations in Escherichia coli Excerpt: "At least 80% of the mutations had a significant negative effect on fitness, whereas none of the mutations had a significant positive effect."
5. "It is good to keep in mind ... that nobody has ever succeeded in producing even one new species by the accumulation of micromutations. Darwin's theory of natural selection has never had any proof, yet it has been universally accepted." - Prof. R Goldschmidt PhD, DSc Prof. Zoology, University of Calif. in Material Basis of Evolution Yale Univ. Press
6. "Not even one mutation has ever been observed that adds a little information to the genome." - Dr. Lee Spetner, a scientist and teacher at Johns Hopkins University, Not by Chance! Shattering the Modern Theory of Evolution
7. "The actual rate of beneficial mutations is so extremely low as to thwart any actual measurement." - Bataillon, 2000, Elena et al, 1998
8. "But in all the reading I've done in the life-sciences literature, I've never found a mutation that added information. All point mutations that have been studied on the molecular level turn out to reduce the genetic information and not increase it." - Lee Spetner - Ph.D. Physics, MIT, Not By Chance: Shattering the Modern Theory of Evolution
9. "In medical circles, mutations are universally regarded as deleterious. They are a fundamental cause of ageing,1,2 cancer 3,4 and infectious diseases 5." - Alexander Williams, Botanist, Research Associate at the Western Australian Herbarium specializing in the taxonomy of grasses, Journal of Creation 22(2):60–66 August 2008
10. Haldane’s dilemma: "The severe contradictions that these findings pose for neo-Darwinian theory corroborate what has become known as Haldane’s dilemma. J.B.S. Haldane was one of the architects of neo-Darwinism who pioneered its application to population biology. He realized that it would take a long time for natural selection to fix an advantageous mutation in a population—fixation is when every member has two copies of an allele, having inherited it from both mother and father. He estimated that for vertebrates, about 300 generations would be required, on average, where the selective advantage is 10%. In humans, with a 20-year generation time and about 6 million years since our last common ancestor with the chimpanzee, only about 1,000 such advantageous mutations could have been fixed. Haldane believed that substitution of about 1,000 alleles would be enough to create a new species, but it is not nearly enough to explain the observed differences between us and our closest supposed relatives.
The measured difference between the human and chimpanzee genomes amounts to about 125 million nucleotides, which are thought to have arisen from about 40 million mutation events. If only 1000 of these mutations could have been naturally selected to produce the new (human) species, it means the other 39,999,000 mutations were deleterious, which is completely consistent with the reviews showing that the vast majority of mutations are deleterious. Consequently, we must have degenerated from the apes, which is an absurd conclusion." - Alexander Williams, Botanist, Research Associate at the Western Australian Herbarium specializing in the taxonomy of grasses, Journal of Creation 22(2):60–66 August 2008
11. Thalassemia is a genetic blood disorder which causes people to be unable to make enough hemoglobin, causing severe anemia. When hemoglobin is lacking in the red blood cells, oxygen can't get to all parts of the body and organs become starved for oxygen and unable to function properly. Gamma thalassemia resulting from the deletion of a gamma-globin gene, P K Sukumaran, T Nakatsuji, M B Gardiner, A L Reese, J G Gilman, and T H Huisman
12. DNA Deletion and Duplication and the Associated Genetic Disorders, Suzanne Clancy, Ph.D. & Kenna M. Shaw, Ph.D. 2008 Nature Education "Duplications may affect phenotype by altering gene dosage. For example, the amount of protein synthesized is often proportional to the number of gene copies present, so extra genes can lead to excess proteins. Because most embryonic developmental processes are heavily dependent on carefully balanced levels of proteins, duplications resulting in extra gene copies (Figure 1) can therefore lead to developmental defects such as those seen in the Drosophila Bar eye mutation."
13. Repeated duplications have been associated with cancer: Lucito, R., Healy, J., Alexander, J., Reiner, A., Esposito, D., Chi, M., Rodgers, L., Brady, A., Sebat, J., Trope, J., West, J.A., Rostan, S., Nguyen, K.C., Powers, S., Ye, K.Q., Olshen, A., Venkatraman, E., Norton, L. and Wigler, M., Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation, Genome Res. 13(10):2291–2305, 2003.
14. DNA Study Forces Rethink of What It Means to Be a Gene, Eliizabeth Pennisi, Science 15 June 2007, Vol. 316 no. 5831 pp. 1556-1557: "According to a painstaking new analysis of 1% of the human genome, genes can be sprawling, with far-flung protein-coding and regulatory regions that overlap with other genes."
15. Yingguang Liu and Dan Moran: "(1) gene duplications are aberrations of cell division processes and are more likely to cause malformation or diseases rather than selective advantage; (2) duplicated genes are usually silenced and subjected to degenerative mutations; (3) regulation of supposedly duplicated gene clusters and gene families is irreducibly complex, and demands simultaneous development of fully functional multiple genes and switching networks, contrary to Darwinian gradualism."
"In most dioecious (possessing either male or female organs) animals and humans, however, polyploid embryos typically suffer generalized malformation and die during development.8 It is not only sex determination per se (as was proposed by Muller), but more importantly, the delicate balancing between homologous genes, that is disrupted in polyploid individuals of higher animals. For instance, parental imprinting (differences in the expression of maternal and paternal genes) by DNA methylation may be disrupted as the cell endeavors to silence extra chromosomes by extensive methylation."
"Disharmonious interactions between homologous genes are thought to be the reason for most cases of hybrid sterility in allodiploid animals. In plants, neoallopolyploid genomes are often unstable, displaying ‘sterility, lethality, and phenotypic instability’."
"Polyploidy is seen in ferns, flowering plants and some lower animals.7,8 It is usually associated with hermaphroditism, parthenogenesis (mother producing young asexually), or species without disparate sex chromosomes."
16. Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over? Alexey S. Kondrashovf, Journal of Theoretical Biology, Volume 175, Issue 4, 21 August 1995, Pages 583–594
17. Rates and Fitness Consequences of New Mutations in Humans, Peter D. Keightley, 2012, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh
18. All multicellular organisms are undergoing inexorable genome decay from mutations because natural selection cannot remove the damage: Baer, C.F., Miyamoto, M.M. and Denver, D.R., Mutation rate variation in multicellular eukaryotes: causes and consequences, Nature Reviews Genetics 8:619–631, 2007.
19. "The decay in the human genome due to multiple slightly deleterious mutations each generation is consistent with an origin several thousand years ago." -- Sanford, J., Cornell University Geneticist, inventor of the Gene Gun, Genetic entropy and the mystery of the genome, Ivan Press, 2005
20. "Thus, all multicellular life on earth is undergoing inexorable genome decay because the deleterious mutation rates are so high, the effects of the most individual mutations are so small, there are no compensatory beneficial mutations, and natural selection is ineffective in removing the damage." - Alexander Williams, Botanist, Research Associate at the Western Australian Herbarium specializing in the taxonomy of grasses, Journal of Creation 22(2):60–66 August 2008
21. Human Molecular Genetics, 4th Edition, April 02, 2010, Chapter 9: instability of the human genome: mutation and repair, Tom Strachan and Andrew Read, Garland Science
22. Human mutation rate revealed, Next-generation sequencing provides the most accurate estimate to date, Elie Dolgin, August 2009, Nature: Every time human DNA is passed from one generation to the next it accumulates 100–200 new mutations, according to a DNA-sequencing analysis of the Y chromosome.
23. Estimate of the Mutation Rate per Nucleotide in Humans, Michael W. Nachman and Susan L. Crowell, Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, Corresponding author: Michael W. Nachman, Department of Ecology and Evolutionary Biology, Biosciences West Bldg., University of Arizona, Tucson, AZ
24. "Thus the estimate from the Biochemical Method is 130 mutations per generation." - Larry Moran, Professor in the Department of Biochemistry at the University of Toronto
25. 70 new mutations per generation: Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing, Published Online March 10 2010, Science 30 April 2010: Vol. 328 no. 5978 pp. 636-639
26. Rate, molecular spectrum, and consequences of human mutation, Michael Lynch: Although the human per-generation mutation rate is exceptionally high, on a per-cell division basis, the human germline mutation rate is lower than that recorded for any other species."
27. 89 new mutations per person per generation : Rate, molecular spectrum, and consequences of human mutation, Michael Lynch