I find it interesting that many Creationists, while they believe in the idea that a general increase of entropy, in our Biosphere, is occurring; they also tend to state that everything in living systems has a specific purpose. If entropy is indeed increasing, might we expect to see the results of degradation in various parts of cellular organisms?
Instructional Note: I will be talking about different types of pseudogenes. There are two major types of pseudogenes; 1) Classical non-processed pseudogenes and 2) Processed pseudogenes (how they are thought to form is illustrated in the chart below).
Classical non-processed pseudogenes are genes that are thought to have once been functional but now have become defective. The non-processed pseudogene has not moved. It is still in its original place on the DNA molecule but it is thought that normal mutational changes have made most non-processed pseudogenes defective. Of course, the assumed mutational rate of the DNA bases would take millions of years to see the high number of suspect mutations that we see in today's non-processed pseudogenes. This is a problem and it is part of the subject of my research. There is also the problem of shared mutations or mistakes among very similar animals, but we will talk about that later on this web page. Other creationary scientists believe that there might be a function to pseudogenes after all and that there is no problem. So my research deals with non-processed pseudogenes.
Processed pseudogenes are genes which have been copied and placed in another location on the DNA. But the copy is often defective, thus they are called processed pseudogenes. Many normal genes in Eukaryotic organisms have both introns and exons. Exons are the parts of the genes which are expressed. They code for the actual protein. On the other hand, Introns, indicated by the blue color in the chart below, are not expressed at all. So when a mRNA copy of the gene is made, the introns are cut out of the copy by a process called splicing. In addition, a cap and poly(A) tail is also attached to the mRNA copy. Together, both the splicing out of the introns and the adding of the Cap and tail are called processing. The mRNA is then processed.
Within the cell the normal flow of information goes from the nuclear DNA to RNA to protein. So, copies of the nuclear DNA are usually made as temporary mRNA copies. Information goes from DNA to RNA. This very process occurs in most all organisms (See the chart below). The reverse does not happen unless there is some kind of viral activity.
When a processed pseudogene is produced, however, it is mediated by viral enzymes and that allows the information flow to go backwards; From RNA to DNA. So, a mRNA that has already been processed is copied making a single-stranded (ss) DNA copy. This special step requires a special enzyme called Reverse Transcriptase and it comes from the viral-like invader. The DNA copy is called cDNA because it is a copy usually from some RNA source. The next step is to convert the single-stranded DNA into double-stranded (ds) DNA. Then it is inserted back into the DNA but at a different point either on the same chromosome or on a different chromosome (See the flow diagram below).
There are many different types of virus-like organism that can invade cells. Most people are acquainted with the idea that a cell is infected by a virus and then through some process virus particles start coming out of that cell to invade other cells. But there are other things like transposable elements or mobile elements or even simple insertion sequences. Many of these are viral-like in that they invade the cell. But what they do is to incorporate their RNA or DNA into the host Chromosomal DNA. If the invader has RNA instead of DNA, it then comes with its own enzyme (Reverse Transcriptase). That is where this enzyme comes from, it is from the viral invader.
Here is the important point: Because the cell now has these viral enzymes handy; Various other pieces of DNA and RNA, within the cell, also get inserted into the host DNA. Processed pseudogenes are thought to be just one example of what gets inserted into the DNA. The Flanking-Direct-Sequence-Repeats is a typical indication that a sequence has been added to the host nuclear DNA. (As indicated in the flow diagram below.)
I believe that I needed to explore the possibility that pseudogenes (classical non-processed) are in fact defective non-functioning genes. The presence of pseudogenes can be explained within both paradigms, whether entropy is increasing (Creationary) or decreasing (Evolutionary). However, if every part of the cell does indeed have a specific purpose, as is stated by some Creationists, it would be very hard to explain the presence of pseudogenes in the DNA of living organisms. At least with our present knowledge of pseudogenes.
In the literature today, there has been some reports that various pseudogenes do seem to have some kind of function. However, most of these examples involve processed pseudogenes and are thought to have come about by random occuring events usually involving some time that is much longer than what the Creationary paradigm will allow.
However, it must also be remembered that in the Creationary paradigm, just because a pseudogene affects some other cellular parameter, it does not mean that what we see is the original function as created from the Hand of God.
If life is slowly increasing in entropy, we would expect to find various genes with a weakened function or even having none of the original created function. In addition, some other accidental function could possibly be set up in the process, as in the example of the insertion of a new processed pseudogene. The cell is a highly reactive place with an untold number of reactions taking place all throughout the cell. If a gene has been modified, It seems likely that its partially broken down presence will probably affect other processes in the cell by happenstance. These so called new functions may or may not be beneficial to the cell. They may only be partially beneficial.
Because most Creationists believe that pseudogenes have some specific unknown purpose, they like very much the influx of papers supporting the idea of function. However this so-called function could just be the result of a highly reactive cellular environment on random interactions. It might not be an example of the original highly designed functions that we might expect of the Creator which other Creationists are searching for.
So just because various pseudogenes are reported to have some function in the cell, is not sufficient enough reason to state that the original created function has been found.
Ever since I have read the initial report of the Human Genome project and their description of what they found (Nature 15 February 2001); I have become more excited knowing that the Human Genome (and the DNA of other organisms) shows great promise in giving us the evidence for the degradation of the genetic code since Creation week.
David Baltimore, in his paper Our genome unveiled, Nature 409, 814-816, 15 February 2001 notes that out of the, 3.2 Gigabases, that is the estimated total size of our genome; as much as 45% of our DNA is probably parasitic in nature. He states that "In places, the genome looks like a sea of reverse-transcribed DNA with a small admixture of genes. " He continues: "By contrast, the puffer fish - another vertebrate - has a genome that contains very few repeats. But it encodes a perfectly functional creature, so it seems likely that most of the repeats are simply parasitic, selfish DNA elements that use the genome as a convenient host."
I think this understanding that David has, in classifying this portion of the DNA as parasitic, can fit well within the creationary paradigm. We might expect the genetic DNA code of organisms to become more corrupted as time increases. That is exactly what is illustrated in these sequences. The puffer fish helps to support the idea that these reverse-transcribed DNA sequences are not needed for a eukaryotic vertebrate genetic system to function. They are probably parasitic in nature.
So, I believe that both classical non-processed pseudogenes and processed pseudogenes could be the result of degradation from the original creation.
What would be the nature of the degradation in organisms? Would Island Speciation throw some light on this question. The Bible seems to suggest a few definite ways that man has degraded.
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Officially posted June 19, 1998
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