Once Upon A Time There Was Darwinism

Once, There Was the Myth of "Junk" DNA

The last support for faulty or vestigial structures discussed in the last chapter is the new—but recently discredited—concept of "junk" DNA.

In the second half of the 20th century, as we saw in the last chapter, the myth of vestigial organs began to collapse. Organs formerly thought to be useless turned out to have important functions, and the myth became untenable. But evolutionists, not wanting to do without the propaganda this myth afforded, embraced a new version of it, which claimed that some of the genes containing the organs' genetic code but not the organs themselves—were vestigial. The new concept that replaced "vestigial" organs was "junk" DNA.

This term "junk" referred to some sections of the huge DNA molecule in which is encoded all of a living creature's genetic data. According to evolutionist claims, a large part of DNA is now non-functional. These parts did have a function in the so-called past, but in time, after the alleged evolutionary changes, they became vestigial—in short, "junk." The parallel with Darwinism was quite clear, and in a short time, the concept of junk DNA became one of the most repeated terms in scientific literature. But this new version of the myth did not have a long lifespan. Especially with the announcement of the results of the Human Genome Project in 2001, it was more and more loudly proclaimed in the scientific world that the whole concept was wrong, because the functions of so-called junk DNA were slowly being understood. Evan Eichler, an evolutionist scientist from the University of Washington, admitted that "The term 'junk DNA' is a reflection of our ignorance."81

Now, let's examine how the myth of junk DNA was born and how it was discredited.

The Misconception that Non-Coding DNA is Useless

To better understand this evolutionist error, we must know something about the structure of the DNA molecule.

This giant molecular chain within the cells of living creatures is often referred to as a data bank, because of the genetic information it contains. At the same time, this molecule contains a genetic code that directs how this data is employed in the body's activities. As detailed in the previous chapters, every evolutionist's attempt to explain the origin of the DNA molecule has been unsuccessful, and it's been established that the data it contains could not have come into existence at random. The DNA molecule is clearly an example of a superior Creation.

The special parts of DNA encoding our physical characteristics and physiological activities are called genes, which play a role in the synthesis of various proteins and ensure that we survive. But the totality of our genes makes up only about 10% of our DNA. The remaining 90% is known as "non-coding DNA" because it does not direct the production of any proteins.

Non-coding DNA can be categorized into some sub-groups. Sometimes, it's found squeezed between genes and is called an intron. Another kind, called repetitive DNA, is formed by repeated nucleotide sequences extending the length of the chain. If the nucleotides on non-coding DNA were arranged in a way similar to the complex series in a gene, instead of in a repetitive series, they would be called a pseudogene.

Evolutionists have lumped these non-protein-coding segments of DNA under the general heading of "junk DNA" and asserted that they are unnecessary leftovers in the so-called process of evolution. However, this endeavor has clearly been illogical: Just because these DNA segments do not code for proteins does not imply that they have no function. In order to determine these functions, we have to await the results of scientific experiments to be done on them. But evolutionist prejudice, with its longstanding misleading claims about junk DNA, has kept this logic from becoming disseminated in the public domain. In the past 10 years especially, research has shown that evolutionists are wrong and their claims imaginary. The non-coding part of DNA is not "junk" as the evolutionists claim, but on the contrary, is now accepted as a "genomic treasure." 82

Paul Nelson, who received his Ph.D. from the University of Chicago, is one of the leading exponents of the anti-evolutionist movement. In an article titled "The Junk Dealer Ain't Selling That No More," he describes the collapse of the evolutionists' theory of junk DNA:

Carl Sagan [one of the proponents of atheism] argued that "genetic junk," the "redundancies, stutters, [and] untranscribable nonsense" in DNA, proved that there are "deep imperfections at the heart of life". Such comments are commonplace in the biological literature—although perhaps less common than they were a few years ago. The reason? Geneticists are discovering functions for what used to be apparent genetic debris.83

But how did they discover that "junk DNA" is not junk after all?

1. Coding criteria relative to linguistic ability were discovered in the non-coding nucleotide sequence.

In 1994, the joint experiments on non-coding DNA carried out by molecular biologists of Harvard Medical School and physicists of Boston University revealed some striking results. Researchers studied 37 DNA sequences from various organisms and having at least 50,000 base pairs, to determine if there were any particular patterns in the nucleotide arrangement. This study showed that 90% of human DNA, which was previously supposed to be junk, actually possessed structural similarities to natural languages!84 That is, a common coding criterion found in every spoken language in the world was discovered to exist in the arrangement of nucleotides in DNA. This discovery provided no support for the thesis that the data in the so-called junk DNA was assembled by chance; on the contrary, it supported a superior Creation as the basis of life.

2. Repetitive heterochromatin shows an amazing functionality: Nucleotides that appear meaningless by themselves perform important functions together and play a role in the meiotic division.

Recently, scientists have discovered the functions of heterochromatin, one of the chromosome materials formerly thought to be junk. This code is often repeated in DNA, and since its role in the production of any protein could not be determined, it was long defined as meaningless.

Hubert Renauld and Susan Gasser of the Swiss Institute for Experimental Cancer Research comment that despite heterochromatin's significant representation in the genome (up to 15% in human cells and roughly 30% in flies), it has often been considered as "junk DNA," of no utility to the cell.85

But the latest studies have revealed that heterochromatin has some important functions. Emile Zuckerkandl of the Institute of Molecular Medical Sciences has this to say:

. . . [I]f one adds together nucleotides [DNA base pairs] that are individually nonfunctional, one may end up with a sum of nucleotides that are collectively functional. Nucleotides belonging to chromatin are an example. Despite all arguments made in the past in favor of considering heterochromatin as junk, many people active in the field no longer doubt that it plays functional roles. . . . Nucleotides may individually be junk, and collectively, gold. 86

One of these "collective" functions of heterochromatin can be seen in meiotic pairing. At the same time, studies of artificial chromosomes show that these segments of DNA have various functions.87

3. Researchers have shown a relationship between non-coding DNA and the cell nucleus—a development that spells the end of the "junk DNA" concept.

A 1999 study examining the genomes of the single-celled photosynthetic organisms known as Cryptomonads discovered that eukaryotic non-coding DNA (also called secondary DNA) was functional in the nucleus.

Characteristically, these organisms show a wide variation in size. But even if they are of varying dimensions, there always remains a direct proportion between the size of their nucleus and that of the overall cell.

Seeing the proportion between the amount of non-coding DNA and the size of the nucleus, researchers concluded that more non-coding DNA was a structural necessity required in larger nuclei. This new research was a major blow to such concepts as junk DNA and Dawkins' "selfish" DNA that dismiss the fact of Creation.88 The researchers concluded their report by saying:

Furthermore, the present lack of significant amounts of nucleomorph secondary DNA . . . refut[es] "selfish" and "junk" theories of secondary DNA.89

4. Non-coding DNA was discovered to be necessary for the chromosome structure.

In the past few years, another important role played by non-coding DNA has been discovered: It is absolutely necessary for the structure and functioning of chromosomes. Studies have shown that non-coding DNA provides the structure that lets DNA perform various functions—which it cannot in the absence of a formed structure. Scientists observed that elimination of a telomere (the DNA-protein complexes at both ends of chromosomes that grow smaller after cell division) from a yeast chromosome caused a cell cycle arrest.90 This indicates that telomeres help the cell distinguish between intact chromosomes and damaged DNA. In those cells which recovered from the arrest without repairing the damaged chromosome, the chromosome was eventually lost. This also demonstrates that telomeres belonging to non-coding DNA are necessary to maintain chromosome stability.

5. The discovery of non-coding DNA's role in the development of an embryo

There is proof that during development, non-coding DNA plays a major role in regulating the gene expression (the process by which a gene's coded information is converted into the structures present and operating in the cell).91 Various studies have shown that non-coding DNA plays a role in the development of photoreceptor cells92, of the reproductive tract93, and the central nervous system.94 All this shows that non-coding DNA plays vital roles in embryogenesis, or embryonic development.

6. Introns (considered as junk DNA segments) have been shown to play a vital role in cell functioning.

For years, evolutionists thought introns, which are squeezed between functional genes and are spliced out in the process of producing proteins, to be junk DNA, but only later discovered their importance.

At first, evolutionists thought that introns had no role in the production of proteins and regarded them as merely junk. However, research has proven that they play a vitally important role and today, introns are recognized as "a complex mix of different DNA, much of which are vital to the life of the cell."95

A short but interesting article in the science column of The New York Times exposed the errors of evolutionists with regard to introns. In "DNA: Junk or Not?," C. Claiborne Ray sums up the results of research on introns:

For years, more and more research has, in fact, suggested that introns are not junk but influence how genes work. . . introns do have active roles. 96

This article emphasizes that in the light of the latest scientific developments, supposedly "junk DNA" like introns really do play a useful role in the life of organisms.

All these developments not only reveal new information about non-coding DNA, but also clearly point to the very important fact that the evolutionist concept of junk DNA was based on lack of knowledge and "ignorance" as Evan Eichler admitted.97

The Last Support for the Myth of Junk DNA has Fallen: A Pseudogene has been Shown to be Functional

Since the 1990s, important developments have all shown that the concept of junk DNA was an evolutionist error based on lack of knowledge. Non-coding DNA, like introns interrupting the sequence of genes and repetitive DNA found as longer sequences, have been shown to be functional. There was only one kind of non-coding DNA left whose functionality was unknown: pseudogenes.

The prefix pseudo means "false, deceptive." Evolutionists gave the name "pseudogene" to a DNA segment produced by a functional gene that had apparently undergone a mutation and lost its functionality. Pseudogenes have a special significance for evolutionists, who covertly acknowledge that mutations cannot bring about evolution and have resorted to pseudogenes as a means to deceive people.

Countless experiments on living things have shown that mutations always result in a loss of genetic data. Just as a few random blows with a hammer will not lead to improvements in the running of a clock, mutations have never led to the development of new organisms, or cause existing ones to evolve. Although the theory of evolution requires an increase in genetic data, mutations always reduce and destroy them.

Evolutionists, lacking even a single demonstrable mechanism to support their theory, presented pseudogenes as by-products of a phantom mechanism functioning in an imaginary evolutionary process. They claimed that these allegedly useless DNA segments were molecular "fossils" of so-called evolution. Their only support for this claim was the lack of knowledge as to whether these genes had any real function.

That is, up until May 1, 2003.

That was when Nature magazine published a study showing the functionality of pseudogenes. In a letter titled "An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene," researchers told of their observations in mice prepared for an experiment.98 According to the information they gave, fatal mutations occurred in a line of transgenic mice as a result of genetic changes in pseudogenes called Makorin1-p1. They observed in the mice polycystic kidneys and bone deformity.

It became evident why a change in the arrangement of the pseudogene would have such a disastrous effect on the mice's organs: A pseudogene is not just functional, but necessary.

An article in Nature evaluating this research stated that this discovery challenged the popular belief of evolutionists that pseudogenes were simply "molecular fossils."99 And so, one more evolutionist myth collapsed.

Just three weeks after pseudogenes were revealed to have a biological function after all, a study in the May 23, 2003 issue of Science dealt another severe blow to the idea of junk DNA100 revealing yet another function of the non-coding DNA. Evolutionists apprised of all these developments had no other choice but to accept that the time had come to "junk" their concept of junk DNA. The title of an article by Wojciech Makalowski of Pennsylvania State University shows the change: "Not Junk After All." Makalowski sums up the situation in these words:

. . . [T]he view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure. . . These two papers demonstrate that repetitive elements are not useless junk DNA but rather are important, integral components of eukaryotic genomes. . . Therefore, repetitive DNA should be called not junk DNA. . . 101

Once upon a time, you may have heard a lot about the idea of junk DNA and the evolutionist speculations connected with it.

But as outlined here, Darwinism's last assertion of "vestigiality"—junk DNA—has passed into history, and this last flutter of Darwinism has also been discredited.

Notes

82- Gretchen Vogel, "Objection #2: Why Sequence the Junk?", Science, 16 Şubat 2001

83- Wojciech Makalowski, "Not Junk After All", Science, Volume 300, Number 5623,  23 Mayıs 2003,

84-http://www.arn.org/docs/odesign/od182/ls182.htm#anchor569108

85- "Does nonsense DNA speak it's own dialect?", Science News, Vol. 164 , 24 Aralık,1994

86- Hubert Renauld and Susan M. Gasser, "Heterochromatin: a meiotic matchmaker," Trends in Cell Biology 7 (May 1997): ss. 201-205

87- Emile Zuckerkandl, "Neutral and Nonneutral Mutations: The Creative Mix-Evolution of Complexity in Gene Interaction Systems,' Journal of Molecular Evolution 44 (1997): S2-8.

88- Hubert Renauld and Susan M. Gasser, "Heterochromatin: a meiotic matchmaker," Trends in Cell Biology 7 (May 1997): 201-205.

89- Bencil DNA tezi: Evrimcilerin, kodlamayan DNA'nın sözde evrimsel oluşumunu açıklamada başvurduğu bir tez. Bu tez, canlıların işlevini yitirmiş DNA parçaları arasında bir tür rekabet olduğunu savunan hayali iddiadır. Bu yazıda da gösterildiği gibi, Crytomonad'lar üzerinde yapılan bu çalışmayla çürütülmüştür.

90- Beaton, M.J. and T. Cavalier-Smith. 1999. Eukaryotic non-coding DNA is functional: evidence from the differential scaling of cryptomonal genomes. Proc. R. Soc. Lond. B. 266:2053-2059
91- Sandell LL, Zakian VA. 1994. Loss of a yeast telomere: arrest, recovery, and chromosome loss. Cell 75: 729-739.

92- Ting SJ. 1995. A binary model of repetitive DNA sequence in Caenorhabditis elegans. DNA Cell Biol. 14: 83-85.

93- Vandendries ER, Johnson D, Reinke R. 1996. Orthodenticle is required for photoreceptor cell development in the Drosophila eye. Dev Biol 173: 243-255.

94- Keplinger BL, Rabetoy AL, Cavener DR. 1996. A somatic reproductive organ enhancer complex activates expression in both the developing and the mature Drosophila reproductive tract. Dev Biol 180: 311-323.

95- Kohler J, Schafer-Preuss S, Buttgereit D. 1996. Related enhancers in the intron of the beta1 tubulin gene of Drosophila melanogaster are essential for maternal and CNS-specific expression during embryogenesis. Nucleic Acids Res 24: 2543-2550.

96- R. Nowak, "Mining Treasures from 'junk DNA ", Science 263 (1994): 608.

97- "DNA; Junk or Not", The New York Times, 4 Mart 2003

98- Gretchen Vogel, "Objection #2: Why Sequence the Junk?", Science, 16 Şubat 2001

99- Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A., and Yoshiki, A. 2003. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423:  91-96.

100- Lee, J. T. 2003. Molecular biology: Complicity of gene and pseudogene [News and Views]/78 Emile Zuckerkandl, "Neutral and Nonneutral Mutations: The Creative Mix-Evolution of Complexity in Gene Interaction Systems,' Journal of Molecular Evolution 44 (1997): S2-S8.ature 423: 26-28.

101- "The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu Exons ", Galit Lev-Maor, et al. Science, Volume 300, Number 5623, Issue of 23 May 2003, ss. 1288-1291

102- Science, 23 Mayıs 2003