Intelligent Design, the best explanation of Origins

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Intelligent Design, the best explanation of Origins » Palaentology » Cambrian/mutations/genetic entropy and more confirm creation and ID/debunk Darwinism Jerry Bergman, Ph.D.

Cambrian/mutations/genetic entropy and more confirm creation and ID/debunk Darwinism Jerry Bergman, Ph.D.

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Dr. Jerry Bergman was an atheist/Darwinian like many leading creationists/IDers used to be. He realized like many on both sides have found strong evidence for ID/creation in the records of nature and many powerful reasons to reject Darwinism. Excerpts of his article about how way over 99% of mutations involve loss of genetic information or neutral changes and how even beneficial mutations are by loss of genetic information and usually cause weaker species are below.

This and so much other research like it make Darwinism completely indefensible as a way to explain the diversity of life. It's like claiming that you have traveled to Mars and back with no space vehicle or any mechanism to get there, while creation science and ID have always had the most powerful mechanism known to man to produce complex functioning systems, intelligent Creator(s). Just a couple things before that.

1) Cambrian layer (and most of the fossil record): Even Darwinians agree that the fossil record is the opposite of what Darwinism expects and many scientists agree it matches what creation scientists claimed/expect in regard to how the major body plans were created first and then diversified from there.Dr. Valentine is one of the world's best experts on this topic

“Darwin had a lot of trouble with the fossil record because if you look at the record of phyla in the rocks as fossils why when they first appear we already see them all. The phyla are fully formed. It’s as if the phyla were created first and they were modified into classes and we see that the number of classes peak later than the number of phyla and the number of orders peak later than that. So it’s kind of a top down succession, you start with this basic body plans, the phyla, and you diversify them into classes, the major sub-divisions of the phyla, and these into orders and so on. So the fossil record is kind of backwards from what you would expect from in that sense from what you would expect from Darwin’s ideas."

James W. Valentine - as quoted from "On the Origin of Phyla: Interviews with James W. Valentine" - video
http://www.arn.org/arnproducts/php/video_show_item.php?id=7

This was noted in the past too and it's a back breaking problem for Darwin now AND one that confirms creation science/ID. "it remains true, as every paleontologist knows, that most new species, genera, and families and that nearly all new categories above the level of families appear in the record suddenly and are not led up to by known, gradual, completely continuous transitional sequences." Major Features of Evolution (1953) p.360

Another Darwinian makes it clear that there is nothing in geology that goes contrary to the view of creationists:
“We need to remember that the only evidence about the way events occurred in the past is found in the geological records. However sophisticated advances in molecular genetics and molecular engineering may become eventually, the fact that a genetic change or even a new species might be generated eventually in the laboratory does not tell us how new species arose in the past history of the earth. They merely provide possible mechanisms. At the present stage of geological research,

**we have to admit that there is nothing in the geological records that runs contrary to the view of conservative creationists, that God created each species separately, presumably from the dust of the earth.**

My own view is that this does not strengthen the creationists' arguments." Dr. Edmund J. Ambrose, Emeritus Professor of Cell Biology University of London, evolutionist, The Nature and Origin of the Biological World, John Wiley and Sons, 1982, p. 164

His last sentence is about the ultimate confirmation bias I have seen. He says that the fossils line up well with creationist expectations..and decides that evidence he like doesn't matter/can't be counted, even though in every other field it is. There are new questions that do arise from time to time for both sides..but they are habitually resolved in favor of creation science/ID and have been for 1000s of years.Another leading Darwinian rejects Darwinism:

"Darwinian evolutionary theory was my field of specialization in biology. Among other things, I wrote a textbook on the subject thirty years ago. Meanwhile, however I have become an apostate from Darwinian theory and have described it as part of modernism’s origination myth. Consequently, I certainly agree that biology students at least should have the opportunity to learn about the flaws and limits of Darwin’s theory while they are learning about the theory’s strongest claims." - Dr. Stanley Salthe, Professor Emeritus, Brooklyn College of the City University of New York

"Very few leading evolutionary biologists today think that natural selection and random mutation are sufficient to produce the new forms of life we see arising in the history of life,” Meyer said.” http://www.worldmag.com/2014/04/scientists_stunned_by_the_public_s_doubt_of_darwin

2) Creation science has always had positive evidence of many kinds, including the Cambrian explosion, most/all of the fossil record, powerful evidence for the flood and so much more. Some is here: Presenting the Creation Model by Patrick Briney, Ph.D. A microbiologist who was a Darwinian until his studies in university. He has many specific predictions and models

" I am excited about creation science as a field of study because it offers a cohesive model of everything that exists, consistency with scientific laws, and a wide open field for pioneering investigators. There are several creation models being researched and compared, and much speculation and modeling are taking place. This healthy practice of science is revealing a fresh perspective on the world’s origins. Most importantly, the creation model has a legitimate role in science. Evidence of initial events points to supernatural origins. The purpose of this presentation is to show why creation models are reasonable and credible models of science." www.uark.edu/~cdm/creation/presentation.htm

And another:
Creation vs. Evolution: Why a Model Is Essential by Dr. Hugh Ross
"My new book, Creation as Science, summarizes our testable creation model and includes an appendix (F) where I make 90 predictions of what scientists will discover in their future research and contrast our predictions with those arising from three other creation/evolution models.
www.reasons.org/articles/creation-vs.-evolution-why-a-model-is-essential

Dr. Hugh Ross has a team of scientists how have been making predictions based on creation science for decades and then using the objective methods of science to find confirmation of them (just like Einstein did his question to show that relativity was true). They've had 100s of stunningly successful confirmations of their predictions and turn up more every week, and sometimes more every day.
TODAY'S NEW REASON TO BELIEVE
http://www.reasons.org/explore/type/todays-new-reason

Here are 131 categories of evidence for creation science by Dr. Walter Brown, a former Darwinian with a Ph.D. from MIT. They are summarized shortly, but there are more details in notes or chapters:
http://www.creationscience.com/onlinebook/PartI.html

Another one is here:
http://www.carewinnipeg.com/books/97-100-reasons-to-choose-biblical-creation-over-evolution

So don't ever think that creation science is only criticizing Darwinism. That's never been true.

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Darwinism and the Deterioration of the Genome Jerry Bergman, Ph.D.http://www.trueorigin.org/mutations01.aspBEST QUOTES:A) "All of the beneficial mutations located in my search of the literature involving almost 20 million references were loss mutations and mutations such as sickle cell anemia that have a beneficial effect only in very special circumstances. In most situations they have a decidedly negative effect on the organism’s health. Not a single clear example of an information-gaining mutation was located. It was concluded that molecular biology research shows that information-gaining mutations have not yet been documented. While such negative findings do not in and of themselves prove creation, they support the conclusion that an Intelligent Designer formed the original genomes of each created kind."B) "NeoDarwinists estimate that as many as 99 percent of all species that have ever lived are extinct (Margulis and Sagan, 2002, p. 52; Raup, 1977, p. 50). Although some claim the number is far lower, assuming this estimate to be valid would put the number of species that have ever lived at over 200 trillion!

Given the estimate that roughly an average of 1,000 transitional forms are required to evolve a species (a number that is a rough estimate and is dependant on various assumptions)—this would mean that 2x1017 transitional forms have existed. If 1,000 mutations are required for each transitional form, this would translate into 2x1020 beneficial mutations that are required. And not one clear beneficial mutation or transitional form has yet been convincingly demonstrated, although likely some do exist. The paucity of clearly helpful mutations must be considered in context with the estimate that 2x1020 mutations that are required to produce the natural living world existing today and the number of animals that are speculated to have once existed."Changes by LOSS of genetic information are common and can happen super fast as research has shown. Changes to new genera and family the by addition of genetic information are extremely rare if they happen at all. This is a back breaker for Darwinism and a strong support for creation.

PAPER EXCERPTS

Abstract
An evaluation of DNA/RNA mutations indicates that they cannot provide significant new levels of information. Instead, mutations will produce degradation of the information in the genome. This is the opposite of the predictions of the neoDarwinian origins model. Such genome degradation is counteracted by natural selection that helps maintain the status quo. Degradation results for many reasons, two of which are reviewed here. 1) there is a tendency for mutations to produce a highly disproportionate number of certain nucleotide bases such as thymine and 2) many mutations occur in only a relatively few places within the gene called “hot spots,” and rarely occur in others, known as “cold spots.” An intensive review of the literature fails to reveal a single clear example of a beneficial information-gaining mutation. Conversely, thousands of deleterious mutations exist, supporting the hypothesis that very few mutations are beneficial. These findings support the creation origins model.

Bias in Mutational Types
Studies of bacterial mutations has found that a pervasive bias toward deletions rather than insertions exists (Andersson and Andersson, 1999; Gregory, 2004). Zhang and Gerstein found deletions were about three times more common than insertions (2003, p. 5338). Another study found a “virtual absence of insertions and a remarkably high incidence of large deletions” (Petrov and Hartl, 1997, p. 279). This deletional bias produces a strong tendency to lose base pairs, which results in a clear genome deterioration that must be selected against by natural selection and other mechanisms for a life form to survive. This, again, illustrates a conserving role for natural selection. The same bias favoring loss above insertion has been found true for other types of mutations, including point mutations, nonsense mutations, and other mutation types.

Research Has Also Demonstrated Bias in Mutation Direction
Some non-random mutational base changes are more likely to occur than others. Genetic recombination studies have found, for example, that heterozygous organisms “produce an excess of one allele in their gametes” resulting in biased gene conversion and resultant genome deteriation (Eyre-Walker, 2002, p. 177). Studies of bias revealed that nucleotide mutation tended to go one way more frequently than the other (Freeman and Herron, 2001). Eyre-Walker (2002, p. 178) found that “there are many more GC —> AT than AT —> GC mutations, particularly in genes with high GC3” content. If this bias occurs even to a small extent, mutations would produce more and more thymines until eventually thymies would dominate the genome. Furthermore, entropy would increase more rapidly if the four DNA bases were used rather than Dawkins’ 26 letters. The reason is that far more changes are required to reach homogeneity with 26 letters than with four.

Mutation Hot Spots
Studies of mutations have shown that mutations are much more common in some areas of the genome termed “hot spots” than in others known as “cold spots” (Jorde, et al., 1997; Stadler, 1942; Zhang, et al., 2004; Mira, et al., 2001). In these mutation studies, workers have found that a large percentage of known mutations occur in only a small number of possible loci. Freeman and Herron (2001) found that only two mutations accounted for 94.4% of the 319 mutations identified in one gene.

A worker in another study of mutations in a human germline of the tumor suppressor anti-oncogene gene p53 found that, of the approximately 400 codons whose mutations were mapped, only 35 mutations were at sites other than in four codons, numbered 175, 245, 248, and 243 (Vogelstein and Kinzler, 1998, p. 398). Similar observations have been made for other types of cancer genes and many non-cancer genes. Origin by natural selection cannot account for the existence of hot spots. These hot spot patterns are found in both germline (inherited) and somatic mutations (Vogelstein and Kinzler, 1998, p. 398).

One of the most common mutational hot spots is the CG dinucleotide, which is involved in mutations about 12 times more often than other dinucleotide sequences (Jorde, et al., 1997). Another hot spot cluster involves the ras gene/mutations which are at codons 12, 13, and 61 (Clark and Russell, 1999, p. 196). Bonaventure, et al. (1996, p. 148), found that “more than 98%” of all cases of achondroplasia are a result of mutations in the transmembrane receptor domain that often involves a missence substitution in the first tyrosine kinase domain of the receptor. Another example is that about 70 percent of all cystic fibrosis patients have the same defect—a small deletion of 3 bases that code for phenylalanine—which is another hot spot (Clark and Russell, 1999, p. 179).

Although some of these examples that appear to be mutational hot spots actually result from the fact that many mutations are inherited, most are true hot spots. Approximately one-third of all cystic fibrosis cases result from a novel mutation in one location on the gene, indicating that the area is a true hot spot, and is not the result of the parent’s carrying cystic fibrosis alleles. Evidently all genes contain hot spots, although new sequences and further study of individual variations may reveal some exceptions.

One major hot spot area occurs where DNA sequences contain repetitive or short, repeated, similar sequences. Small insertion mutations are relatively common events, often occurring due to “slippage” or “stuttering” of DNA polymerase enzymes during DNA replication. These cause various mutations such as “triplet-repeat, expansion disorders.” As is true when editors scan a manuscript, spelling errors in words with multiple letters such as “addresses,” or “assesses,” often are missed, and misspellings such as “accessses” or “assessors” are allowed to slip by (Lewis, 1997). Another possible cause for the increased incidence of repeat DNA sequence mutations is that symmetrical or inverted repeat sequences allow abnormal base pairing to occur within a strand when local DNA strands unwind to prepare for replication. This condition can interfere with both replication and repair enzyme functions, thereby increasing the likelihood of errors.

An example is the clotting factor IX gene, which, when damaged, causes the hemophilia B blood clotting disorder. Mutations in this gene occur up to 100 times more often at 11 specific sites within the gene that have relatively long CG dinucleotide repeats. Similarly, an inherited form of the bone-weakening condition, osteoporosis, is usually caused by an extra thymine that is inserted into a specific three base homopolymer of thymine in the normal gene (Lewis, 1997). The result is a tendency to produce nucleotide “stuttering” at this hot spot. In Dawkins’ example (1986), this would be illustrated by the degeneration of changing weasel into weasssel.

The mutational probability varies by as much as 50% from one gene to another gene. A study by Stadler found that in corn the number of mutations ranges from zero to 492 per million gametes, depending on the gene (Freeman and Herron, 2001).

Another factor that influences the frequency of gene mutations is the size of the gene. All other things being equal, the longer the gene, the greater the statistical expectation of a mutation. The genes in which mutations cause both cystic fibrosis and phenylketonuria are abnormally large. These two diseases are among the more common genetic defects found today (Clark and Russell, 1999, p. 176). Factors such as the specific location of the gene in the chromosome, its structure, and its proximity to histones likewise affect the frequency of mutations. These empirical findings are also of a major concern for medicine. They explains why over 1,085 diseases are caused by mutational errors (McKusick, 2002).

A clear trend exists for mutations to degrade the genome, resulting in a loss of information. This is because the strong tendency of mutations is to shift the genome content in the direction of less useful information (e.g., a higher proportion of pyrimidines, specifically thymine). This change creates a serious problem for the mutation/selection model, and helps to explain why the vast majority of mutations have a detrimental effect on the functionality of the final protein coded by the DNA.

These are a few of the many reasons why mutations tend to produce non-random patterns. Non-randomness results in deterioration of the genome because when a greater likelihood exists that certain combinations of nucleotides will be produced than others, certain base combinations become increasingly frequent. This process produces more and more nonfunctional proteins. These are all reasons why most of the expressed mutations are lethal or detrimental.

Systems and Mechanisms Designed to Reduce Degradation
One reason why mutations are kept at bay is that the coding regions of the genome are repaired much more effectively than most noncoding regions, and several repair systems are active only on transcriptional genes (Freeman and Herron, 2001). Freeman and Herron (2001) write that the “most transcriptionally active genes are repaired most effectively,” and that the “accuracy appears to be the greatest where mutations could be the most damaging” (p. 85). It could be logically asserted that this accuracy is a tribute to design, not evolution. Many deleterious mutations are eliminated by natural selection and this too helps to protect the genome from deterioration.

Dawkins and others have argued that the tendency of the genome to degrade is not fatal to neoDarwinian theory. Their main defense is that selection pressure works against these strong deteriorative tendencies. NonDarwinists have long recognized this protection by natural selection, as summarized in Bergman, 2001. The tendency of the genome to degrade, however, militates against its ever producing a functional gene upon which selection could occur. A living organism that can survive in a specific environment must first exist for selection to occur. Dawkins’ mechanism cannot function until a living, functioning organism first is present. Even if DNA could somehow replicate outside of a living cell, it would rapidly degenerate for the reasons discussed above. DNA is a very unstable chemical molecule. Without complex systems to constantly repair and maintain the genome, it deteriorates readily by oxidation and other normal chemical processes.

Evidence for Beneficial Mutations
It is also widely known that beneficial mutations are extremely rare. Some workers have estimated that far less than .01 percent of all expressed mutations are helpful to the organism. As Francisco Ayala (1978) noted “mutation is the ultimate source of all genetic variation,” but useful genetic variation “is a relatively rare event....” (p.63). Dobzhansky (1957) likewise concluded that “the mutants which arise are, with rare exceptions, deleterious to their carriers, at least in the environments which the species normally encounters” (p. 385). The conclusion that very few beneficial mutations occur in nature is still held by many today. In Strickberger’s words “new mutations that have an immediate beneficial effect on the organism seem generally to be quite rare” (2000, p. 227).

In order to locate all alleged examples of beneficial mutations, I carried out a computer search of the literature. My review covered all published scientific studies that dealt with beneficial mutations. The definition of beneficial mutation used was a mutation that was regarded as beneficial by the authors surveyed. Key words used in the computer search included synonyms of beneficial, such as “favorable, helpful, usable, valuable, adaptive, good, advantageous, supportive, positive,” etc. The search of two data bases totaling 18.8 million records found that, of all articles discussing mutations, only 0.04 percent, or 4 in 10,000 articles on mutations, were located that discussed beneficial or favorable mutations. Some overlap exists in the data bases searched, consequently the actual total number of records searched was less than 18.8 million. The overlap in the search was estimated by extrapolating from the records found. Assuming that the same level of overlap exists in the entire database, a total of approximately 16 million records was searched. These searches may have missed some relevant articles but are useful to indicate trends.

All of the 126 examples located were then reviewed, focusing on evidence for information-gaining beneficial mutations. It was found that none of them contained clear, empirically supported examples of information-gaining, beneficial mutations. Most “examples” of actual, beneficial mutations were loss mutations in which a gene was disabled or damaged, all of which were beneficial only in a limited situation.
A review of both textbooks and journal articles on evolution demonstrated that the most common examples of beneficial mutations were sickle cell anemia, bacterial resistance to antibiotics, Ancon short legged sheep, viral/bacterial immunity, and a “putative beneficial mutation for lipid transport” (Galton, et. al., 1996; Strickburger, 2000).

An example of a mutation that was beneficial in specific situations was damage to the Chemokine receptor 5, (CCR5), the principle co-receptor in T-cells that causes cells with CD4 receptors (primarily T-cells) to be unable to take the human immunodeficiency virus (HIV) into the cell. As a result, a person with this mutation has an abnormally high immunity to HIV infection (Huang, 1996; Wilkinson, 1998).

The Number of Mutations NeoDarwinism
Requires to Evolve a Species
A total of 1.7 million species of animals have been identified from comparative studies of preserved specimens (Blackmore, 2002). Researchers estimate that somewhere between 3 million and 30 million species now exist. The most common estimate is around 13 million (Margulis and Schwartz, 1998, p. 3; Blackmore, 2002).
According to an Amersham bioscience report (2001, p. 1), it is estimated that there are thousands of different proteins used in the human body (see also “Preteome” AAAS Science Netlinks). Nuclear pore complexes alone comprise 50 to 100 different proteins (Allen, 2000, p. 1651). All of them are produced by the estimated 35 to 45 thousand human genes that, according to neoDarwinists, evolved from other, less-complex, and often shorter genes. Shermer (2002, p. 229) estimates that “trillions of distinct modifications” were required to evolve humans alone. Presumably, each modification would require many mutations.

A significant fraction of open reading frames has been judged not to match any another sequence in the database, indicating that a significant number of all proteins may be unique to each genus of animal (Bailey, 2001; Siew and Fischer, 2003, p. 7). Thus, as many as 200 million different proteins may exist. From 150,000 to 250,000 extinct animal species have also been identified and reported in the paleontological literature. NeoDarwinists estimate that as many as 99 percent of all species that have ever lived are extinct (Margulis and Sagan, 2002, p. 52; Raup, 1977, p. 50). Although some claim the number is far lower, assuming this estimate to be valid would put the number of species that have ever lived at over 200 trillion!

Given the estimate that roughly an average of 1,000 transitional forms are required to evolve a species (a number that is a rough estimate and is dependant on various assumptions)—this would mean that 2x1017 transitional forms have existed. If 1,000 mutations are required for each transitional form, this would translate into 2x1020 beneficial mutations that are required. And not one clear beneficial mutation or transitional form has yet been convincingly demonstrated, although likely some do exist. The paucity of clearly helpful mutations must be considered in context with the estimate that 2x1020 mutations that are required to produce the natural living world existing today and the number of animals that are speculated to have once existed.

Given a low estimate of 1,000 steps required to evolve the average protein (if this were possible) over 2x1014 beneficial mutations would have been needed to evolve just the proteins that are estimated to exist today. So far only 60 species, including the nematode worm, humans, yeast, rice, mustard plant, and bacteria have had their DNA fully sequenced. As more life forms are sequenced, the above estimates may go either up or down. The same evolutionary problem exists in attempting to use mutations to explain the origin of the genes required to make fat, nucleic acid, carbohydrate families, and other compounds that are produced by living organisms and are necessary for life.

Conclusions
It is critically important to focus on questions involving molecular biology because this area is central to the whole question of neoDarwinism’s validity. Although other mechanisms have been proposed to contribute to evolution, the production of new information by mutations is at its core. Therefore, the critical analysis of proposals by Dawkins and others is essential to determine the feasibility of macroevolution by means of mutations and natural selection. An examination of Dawkins’ weasel argument showed that it utterly failed to support the conclusion that mutations can produce significant, new, gene-coding information. Numerous reasons exist, aside from those discussed here, as to why Dawkins’ example is an excellent illustration of why mutations cannot function as the major, or even a minor means, of creating new genes and new species (Read, 1999; Truman, 1999). A study of hot spots and degradation of the genome by mutations shows that macroevolution by means of mutations is, at best, quite unlikely. Many complex mechanisms including natural selection work against degeneration. The fact that the more active the gene, the more accurate the repair process will be, also mitigates against NeoDarwinism.

All of the beneficial mutations located in my search of the literature involving almost 20 million references were loss mutations and mutations such as sickle cell anemia that have a beneficial effect only in very special circumstances. In most situations they have a decidedly negative effect on the organism’s health. Not a single clear example of an information-gaining mutation was located. It was concluded that molecular biology research shows that information-gaining mutations have not yet been documented. While such negative findings do not in and of themselves prove creation, they support the conclusion that an Intelligent Designer formed the original genomes of each created kind.

https://www.youtube.com/watch?v=hq98BFku7tQ

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