Junk Science and Junk DNA

If the reader gets lost in this chapter, be of good cheer because you are in company with some of the best minds of science. So-called junk DNA is kind of like what they call vestigial organs. There used to be over a hundred in the human body that were supposed to prove that God didnít know what he was doing. Unfortunately for the atheist the list has been narrowed down about 90%. It seems that the junk DNA that atheists hailed as the ultimate proof of Godís ineptitude is also proving that the know-it-allís do not know the hundredth part of what goes on in a human organism. Like all of us, they can watch things happen but they can only guess what exactly it is that makes it do that. If reality was proved otherwise, then we certainly would not have to worry about the many diseases that still trouble us.

Iíll keep this as simple as I can, but you can be assured that everything that I describe here is anything but simple. After nearly half a century of study of the human genome, and billions of dollars of research money, it appears that we know less now than when we started about DNA and how the information contained in it is used in the human organism. We thought that we broke the code that would ultimately reveal all of the mysteries of life but we have found that there is another much more complicated and mysterious mechanism within DNA including the so called junk that has heretofore been largely disregarded as nearly useless. It was useless because we did not understand its function. In todayís pseudo science that is how they do things. Any evidence that tends to prove that man himself is not God is called junk.

So we are just talking about a small portion of the total DNA right? Wrong. We are talking about 95% of it. We have broken the code that interprets just 5% of the total amount of information contained in DNA. Even that 5% presents countless mysteries of how that information is manipulated and altered within the human body. It is not like reading a recipe book and baking a cake like Richard Dawkins would have us believe. This "recipe book" is more like 5,000 stacks of books in a huge pile. It is written in a language that we do not understand and we do not have the slightest idea what parts of this pile of "junk" information are used for what. But it is not as simple as that, really. Even if we did know what part of the pile was appropriate, we do not know at what times that information is turned on and off or how it is otherwise regulated.

In other words, the 30,000 or so genes that we have found (or rather computer simulation supposedly found) in the human genome are only one small piece of the puzzle. The other pieces are scattered hither and yon and are virtually hidden from our view. Of course the whole puzzle is microscopic, and the pieces change their shapes from time to time, and disappear and reappear mysteriously just to keep us on our toes. But anyway, enough of my inadequate analogies, letís hear from some experts here.

Ever heard of a "transposon"? Transposons are different sections of the DNA that can move around to different positions in the genome of a single cell. Some call them "jumping genes," They are cut out and then pasted into different sections, thereby altering the sequence of information within the DNA. It is kind of like reading a novel, and just about the time you get to the exciting part you find that the next 10 pages have been removed. Now what? Well maybe somebody pasted them into your motherís old cookbook that you think is in the attack. So you look through all of the books, and you finally find the pages, and as you continue to read you find more pages missing, and so on.

The transposons can delete information from the DNA or they can mutate it or they can translocate it. Slippery little devils arenít they? Now letís look at "retrotransposons." They are similar to transposons but they work on the RNA. You may remember that this RNA is essentially a copy of the DNA, but not always. After the RNA has made its copy, parts of it may be cut out and pasted. Where do you think they are pasted? No, bad guess, they are pasted back into the DNA thereby altering the instructions that were in it initially. Many retrotransposons have "long terminal repeats" (LTRís) at their ends that may contain over 1,000 base pairs each. About 40% of the entire human genome consists of retrotransposons. It is all much more complicated than I am making it sound here. We have not even mentioned LINES (long interspaced elements), or SINES (short interspaced elements) and quite a few other things, but I think you get the point. Even if you do get the point however, all of this information really does not help us much because we are still only in the books! We havenít even got to how this confusing jumble of information is used and manipulated once its meaning is discovered.

A completely different field of research is needed to determine how the cell further manipulates the information and variously interprets it depending on the myriads of environmental possibilities available within an organism. For instance there is "feedback" information to consider. That is intercommunication within the body which gives new instructions to appropriate cells which in turn alter the function of other cells which in turn change the information in another and so on. Simply trying to break the code will not yield the answers to the countless problems that are encountered. The myriad of combinations of amino acids contained in myriads of proteins represent coded information. This opens up a new field of research called "proteonics." What exactly are these coded proteins doing when they disappear into the organism? Which ones do what where, and for how long? What tells them to start and stop, etc.?

So far there has been several uses found for this junk DNA in case anyone still thinks that it is an unimportant diversion. It has been shown to be an essential part of the structure of the nucleus. Statistical analysis of long sections of this so-called junk has shown that it resembles human language. Isnít that fascinating? It is very possible that the 3-letter code of DNA that basically determines how a protein is made is only a scratch on the surface compared to a real language contained in a code that may be known only to God. A real language! To me this stuff is just amazing, but there is more. Letís hear directly from the experts on this subject:

"When you take human language texts and create a histogram plotting the log of the frequency of occurrence of words against the log of the rank, the resulting plot is always linear with a slope of -1 for every human language. Likewise, when you perform the same plot for coding and non-coding DNA, the plot for the non-coding DNA exhibits a nearly perfect linear relationship (much better than that seen for the coding regions of DNA). The purpose or function of this "DNA language" was not determined. Another study showed that DNA contains large areas with unexplained patterns (4). Such patterns could not be the result of random chance as stated by Dr. H. Eugene Stanley (Boston University), "it is almost incredible that the occupant of one site on a gene would somehow influence which nucleotide shows up even 100,000 bases away."

Another function of the junk DNA is to maintain the integrity of the Chromosomes during cell division. "Specific non-coding (junk) DNA sequences within selected Chromosome domains participate in more complex levels of Chromosome folding, and index different genetic compartment for orderly transcription and replication." I really donít think we should call this stuff junk anymore, do you? "The unique 3d structure created by this mysterious DNA also controls the expression of specific genes in cells of differentiated cell types. This so called non-coding DNA is essential in other ways such as regulation of functions and recognition of amino acids during the protein translation process, fetal development and embriogenesis, proper framing for translation of proteins." If it werenít for the "junk" DNA the cell would produce "junk" proteins.

"A recent study has shown that genes (as many as five at a time) are found within the introns of other genes (24). This kind of arrangement results in the simultaneous expression of all of these genes during transcription of the gene in question... Some of the noncoding DNA is loop code for single-stranded RNA-protein interactions. The codes are degenerate and corresponding messages are not only interspersed but actually overlap, so that some nucleotides belong to several messages simultaneously. Tandemly repeated sequences frequently considered as functionless "junk" are found to be grouped into certain classes of repeat unit lengths, indicating functional involvement of these sequences. It is likely these tandem repeats play the role of weak enhancer-silencers that modulate, in a copy number-dependent way, the expression of proximal genes..."
"Well over 700 studies have demonstrated the role of non-coding DNA as enhancers for transcription of proximal genes."
"Another 60+ studies have demonstrated the role of non-coding DNA as silencers for suppression of transcription of proximal genes. The presence of silencer genes has been shown to down-regulate the apolipoprotein A-II gene, the osteocalcin gene, the 2-crystallin gene, the CD4 gene, the beta globin gene, the gene for the neuron-glia cell adhesion molecule, Ng-CAM, the renin gene, the keratin 18 gene, the platelet-derived growth factor A-chain gene, and dozens of other genes."

There are several other functions that I wonít bother with here because I think that most people have got the point by now. I really do not see how anyone cannot see intelligent intervention in all of this. Even if you donít see it here I think it is rather obvious that mankind has just begun to understand the mysteries of life. For years we have been led to believe that scientists had all of the answers to life as they were contained in DNA. Now the story must be changed again in order to fit with the latest mystery. One honest researcher answered the mystery by saying that there is a century of work left to do. I donít think that he is even half right. As Michael Behe says, they will only find another black box full of more complexity and mystery.

I cannot help but to comment here about a certain news item that came out on February 21, 2001, shortly after the rough draft of the human genome was published. While much of the scientific world was scratching their head over the implications of the brevity of the known part of the human genome, a certain Arthur Caplan, Ph. D. authoritatively posted his arrogant conclusions on the MSNBC website under the headline, "Darwin Vindicated":

The genome reveals, indisputably and beyond any serious doubt, that Darwin was right - mankind evolved over a long period of time from primitive animal ancestors. Our genes show that scientific creationism cannot be true. The response to all those who thump their bible and say there is no proof, no test and no evidence in support of evolution is, "The proof is right here, in our genes." ...The core recipe of humanity carries clumps of genes that show we are descended from bacteria. There is no other way to explain the jerry-rigged nature of the genes that control key aspects of our development.

My my how we have placed folly in such dignity. "Jerry-rigged?" Anyway letís hear from some of the more humble researchers:

The mind set governing genetic engineering includes important mismatches with reality. The failure to realize this has lead to an underestimation of the hazards and difficulties with genetic engineering and to an unrealistic overestimation of its possibilities.
Recent findings about several "single gene" disorders indicate that they are actually caused by different genes or gene patterns resulting in the same diseases. There are actually no simple one to one relationships between genes and traits. In such cases, the attempts at treating "single gene disorders" by replacing one gene are not likely to be successful.
The expression of a gene is the result of a very complex interaction with the whole of the organism and is even influenced by external conditions. The stability of a gene is influenced by the condition of the organism. The genes are actually not well delineated entities as believed formerly. They may change character in response to the state of the organism and the same gene may even give rise to different proteins under different conditions. Therefore one cannot expect to be able to "tailor" the traits of organisms in a predictable way by insertion of "desirable" genes.
Because of the context dependence of a gene it is impossible to predict and master the effects of gene insertion. It may seem that the desired property has been added... But in addition, a number of unexpected other changes may have occurred. There are also other factors that add to the likeliness of unexpected changes. - Including possible appearance of some harmful substance that may be difficult to detect reliably because of the limitations of present safety assessment technologies.
No gene works in isolation. It is thus a well proven fact that the same gene may have different effects in different individuals, because the influences of other genes modify how it will express itself... genes may change in response to the conditions of the organism and the environmental situation. And these adaptive genetic changes may be passed over to the following generations... According to the "new genetics", the expression of one single gene into its corresponding protein is the result of a very complex process of feed-back and feedforward interactions. The expression of a gene is the result of a complicated network of interactions that involves not only the whole cell but the whole organism and even the environment.
The DNA may mutate and new pieces may be inserted or pieces may be deleted or multiplied many times. Sequences of the genetic code may be rearranged or combined with other sequences. Some genes can jump around between different places in the chromosomes. Some genes can convert other genes to their own DNA sequence. Geneticists have coined the phrases "fluid genome" to describe this behaviour of the totality of the genes, the genome. These fluid genome processes are not at all haphazard, accidental or meaningless. They occur, under the control of the cell, as adaptive responses to various conditions.
An additional problem is that genomes normally do not accept intrusions by foreign genes. This so called species barrier is mediated by different mechanisms that prevent the insertion or inactivate foreign genes into the genome. This is one of the reasons why most gene insertion attempts fail. It also contributes to the destabilisation of genes that have been successfully inserted. Because of this instability it has turned out to be difficult to create genetically stable transgenic organism strains.

Most but not all of the above quotes were from Jaan Suurkula, MD. For more information see the book, Genetic Engineering, Dreams or Nightmares 1998 by Mae-Wan Ho.

As I researched this issue of junk DNA I was pleasantly surprised to find that many reputable names in the field candidly admit to their lack of knowledge about what really goes on in the biological cell. I appreciate that honesty. I have come to another conclusion while doing the research for this book and that is that the field is full of dedicated people who are trying to help sick people. It is really a shame that the loud mouths cast doubt on an honorable profession by making ridiculous claims that are simply wishful thinking. I do not know how anyone can conclude that there is no God when we consider not only the evidence, but also that which is unknown. It can be nothing less than arrogance for someone to make the definitive statement that there is no God. It seems like we are finding more evidence of his presence everyday as the mysteries of life become more profound.

It has now become clear that certain genes do not necessarily produce certain traits. The genes are only a small part of the overall system, and depend on the whole environment that they operate in. Simply splicing genes from one place in the DNA to another is certainly not the answer. Each change causes a chain reaction that is largely unknown. These reactions may not surface for generations after the damage has been done. The human organism is far too complicated to play with as if we were God. Those who wish to do the work of a healer should do it reverently with understanding of the unknown consequences of their intervention. I think that the fields of science that are dedicated to healing sick people are noble fields. It is really a shame that so much of it is now dedicated to trying to prove that there is no God when the evidence of a creator is constantly screaming at them.

We have not even discussed half of the mysteries that remain in regard to the human genome. We did not even mention histones. These were formerly believed to be simply the structural part of the DNA ladder. Now some are finding reason to believe that even this part of the DNA contains a coded language (see "The Language of Coavalent Histone Modifications" Quantum Wave Predominance in Proteins, Nanobiology, 1993, p2, 31-33). by, Brian D. Strahl and C. David Allis, Nature Vol. 403 p. 41-45, 2000). Others are discussing the possibility that the entire field will have to look toward the quantum physical level. As gravity supposedly works by way of invisible waves, it is now seriously believed by some that the biological processes in a living organism also work according to similar laws. Einstein upset much of established science with his findings, so now it is speculated that these laws that he and others discovered also play a part in the life process.

Life is not as simple as some would have us believe. Our life is not now coded and categorized by the genome project. It is not now just a matter of a little more work before we have it all figured out. The unwarranted assumption that there is no God is based entirely on a lack of evidence and the examination of a few pieces of a puzzle that is intricately connected to more puzzles of an ever-changing nature. How can a rational person call a hugely complicated system that has not been explored to a fraction of its intricacy a pile of largely "useless junk"? What would cause a biologist, of all people, who is keenly aware of the unknown complexity of a living organism, to conclude that the portion that he does not understand is useless "noise"?

Some years ago a European car manufacturer decided to improve on a certain General Motors transmission. After disassembling the GM product they discovered a certain clutch mechanism that they thought should be machined more thoroughly because it was too rough for the exacting standards that were to be incorporated into the improved product. After reassembly the transmission did not work properly. As it turned out the roughness was included in the original design and it was essential to the proper operation of the transmission. The engineers at GM knew exactly what they were doing, and the so called flaw was intentional. This attempt at improvement was an honest mistake made by people who were interested in producing a quality product. But can we say the same about someone who spends his entire life trying to destroy rational belief in a creator while at the same time repressing the fact that his "proof" amounts to that which he does not know? Is this modern science - speculation of the unknown presented as proof? If it is, then its detractors are justified in calling it "blind faith in myths" that are perpetuated at the expense of rational judgment.

DNA is not life. It is not the recipe for making life except in a tangential way. This shows the problem with taking otherwise sound analogies too far. DNA was first compared to a blue print like a building plan. That was a good start. Then it was called an encyclopedia, and that added to the explanation some. As the intricacy of living organisms was explored further it was called by some a dictionary which must be accessed by an intricate mechanism that picks and chooses information contained therein according to various feedback mechanisms, environmental factors and even the thought processes of the individual. I really do not know exactly what DNA will or can do in every instance and neither does anyone else. The proper analogy, however, at this point would seem to lean toward all of the above. Combine this intricacy with the complexity and information that exists apart from the actual manipulation of the information in DNA. Did you know that even todayís modern computers canít keep up with the intricacy? The computer models that you hear about that "prove" one thing or the other often represent only a stripped down version of reality. All of the "junk" has been removed from consideration. The determination of what is and what is not junk is of course made by junk evolutionary science, which concluded that God himself is so much junk that should not be considered before even one experiment is undertaken.

Now I can almost hear the retort: But if a supernatural explanation is considered it is not science. My response to that is exactly one of the overall points of this book - Modern science has no place in determining whether God does or does not exist. All appeals to this modern version of science to prove that God may not, cannot or apparently does not exist are inherently absurd because the evidence of a creator is by definition excluded from consideration. Nevertheless the proper use of real science, when it considers known laws, facts, and the common experience of mankind validated by generations of experimentation without exception, proves that intelligence is necessary to create life. There may have been some wiggle room when life was thought of as various globs of goo. But with the discovery of DNA, the entire structure of atheism collapsed. There is a God. Get used to reality.

© 2003 by Raymond F. Hendrix. All rights reserved.