Molecular History Research Center

Pseudogenes

So, assuming the Biblical scenario for the moment, let's ask the question: What could have caused man's dramatic change? From David Baltimore's analysis, we might understand that the parasitic nature of the genome could be degrative in nature. The reverse-transcribed elements that are being mentioned are: retroviruses (HIV aids), LINES (LINE-1 sequences), SIGNS (alu sequences), and processed pseudogenes.

    Instructional Note: LINES, SIGNS, processed pseudogenes, and retroviruses are all retroposons. The retroposon process is when a DNA sequence is transcribed, making a mRNA copy. The copy is converted into DNA by reverse transcriptase then the DNA piece is inserted back into the chromosome DNA. All the following groups replicate or more by the same method.

    Processed pseudogenes are genes which have been moved from their original location. The information of the process mRNA gets inserted back into the DNA at some other place on the chromosome. The flow diagram below shows the processed pseudogene as an example.

    SINEs (Short Interspersed Elements) and LINEs (Long Interspersed Elements) are both able to replicate themselves, thus making multiple copies on the Chromosomal DNA. 10% of human DNA is composed of SINEs and 20% of human DNA is composed of LINEs. Alu, a SINE sequence is very common in the human genome. The fact that these structures are able to replicate is thought by many to explain why there are so many copies in our DNA. LINEs also contain a few genes in addition to the replication mechanism that is found in SINEs.

    Retroviruses such as HIV are very similar to viruses except they replicate by the retroposon process.

Another possible answer may be found in classical, or unprocessed pseudogenes. Unprocessed pseudogenes are apparent genes which are deficient in some way, thus not allowing them to function as genes any longer. Some think of them as defective genes, however, others feel that there is reason to hold off on pronouncing unprocessed pseudogenes as being defective genes. It is felt that one day a function may be found for Pseudogenes.

The following link will introduce you to the controversy surrounding pseudogenes from a creationist's perspective. Not only are pseudogenes found throughout our DNA but many of them are found in exactly the same positions as in other organisms such as the chimpanzee. Having the same pseudogenes at the same positions in different species is a real problem for Creationists since pseudogenes apparently cannot be selected. They apparently do not function and thus would be classified as "junk DNA" by many evolutionists who assert that the presence of the same Pseudogenes in different species is evidence for the existence of some common ancestor. If Pseudogenes do not have a function than why do they seem to be preserved in the same manner across different species? (A separate page will open on your browser.)

The Data Could Lead to Three Possibilities:

1. We could use evolution as the mechanism to explain the common existence of Pseudogenes. A common ancestor would explain why our Pseudogenes are so similar to the chimpanzee. However. this position does not fit within the creationary paradigm we want to work in.

Unfortunately science is unable to prove positions absolutely, especially positions that deal with historical data. So we will continue to depend on assumptions to determine which of the options are more correct. No matter what position we take, we will have to depend on assumptions that are based on our philosophy or beliefs of origins. But we must not forget that, at least for the present, the evolutionary solution does seem to answer the problem.

2. Dr. Gibson's caution proves to be well founded and a function for the Pseudogenes is discovered. If Pseudogenes have a purpose; then, their presence cannot represent a corruption of DNA code. So we would have to look elsewhere for an answer to the degradation of man. At least the existence of the same Pseudogenes at the same positions in different species could be explained by having the original Genesis kinds be similar in design.

Some Pseudogenes have an extremely large number of differences from its functioning counter parts. These might be argued, due to a lack of knowledge, that there could be some unknown function. However, some Pseudogenes only have a very low number of differences. These examples would be harder to explain. Their structure is essentially that of a gene. They have all the characteristics of a functioning gene except for a few positions making it non-functional.

3. No function for Pseudogenes in their present form is ever discovered. Pseudogenes would then be suspected as being defective genes which have contributed to the degradation of man. A very serious problem however would be to explain the presence of similar Pseudogenes in different species. The absence of a mechanism to produce very similar Pseudogenes in a parallel process is the source of the headache for Creationists. It was the realization of this problem that originally caused some to wonder whether Pseudogenes could have a function after all.

It should be remembered that there are many papers in the literature that suggest various functions for specific pseudogenes. (Many of these are referring to processed pseudogenes and not the classical, non-processed pseudogenes which is the subject of our study.) These functions for the various pseudogenes would have to be classified as functions that have occurred by chance and are not of the original type of function as was dictated by the Creator.

So when it is said that no function for pseudogenes is ever discovered, We must be aware of the difference from the original created kind of function which would be beneficial and those functions that arise by chance which could either be beneficial or detrimental to the organism.

Pseudogenes From an Evolutionary context

A well written review article concerning pseudogenes and the creation/evolution controversy surrounding these pseudogenes has been submitted by Dr. Max. His paper is published right on the internet and you can get to it by clicking the link below. (A separate page will open on your browser.)

His paper is much larger in scope than Dr. Gibson's paper and you will gain a well rounded background to the pseudogene controversy by reading it. In spite of his strong evolutionary position, I am surprised at how similar our viewpoints actually are. In addition, he has put together material that one can only do if they have been in the field for a long time. Yet we do differ on the type of answer that will eventually solve the problem. I think you will enjoy the paper, read it.

On his front page you will see references to other creationists who have tried to counter Max's position. Unfortunately, they have done a rather poor job. I think that a lot of "standard answers" that creationists use need to be modified or changed as knowledge increases. If our answers do not answer the problem, then we need to acknowledge it! It is only when we see the weakness in our answers will we ever get better answers.

We also need to be especially sensitive to new possibilities as hinted in recent scientific discoveries that fit with the Bible. Often what scientists espouse as being strong evidence for evolution also can fit in creationary thinking as well!

Updates and Thoughts

Look forward to seeing updates at this web site on future Pseudogene research.

I have been looking at some interesting patterns found in Pseudogenes. Their presence suggests some very interesting possibilities. I am presently gathering funds to pay for the services of a statistician so that the work can be completed. Only when something is published will it be reported on this web page. However, At that time there will be a flood of information that will be added to this site. There will be a greater depth of data and information available to you on this site than is possible in a pithy scientific paper. Michael E. Brown 11/17/98

The following letter and my answer illustrates the direction my research is taking me.
Michael E. Brown 3/17/99

Dear Mike,

This came on the asa net. Do you have an explanation ?

Hi list,

Dick Fischer's ORIGIN'S SOLUTION mentions the dreaded endogenous retroviral sequence common to both chimp and human DNA as a strong lobbyist for common descent. Anybody have any other reasonable explanation?

(Name withheld)

Hi ,

This is an extremely important question that Creationists have to face. It is exactly the same question that I sought to answer with my research on Pseudogenes. In my talk at Andrews University, I introduced the idea of "Common Mechanism" as an alternative to "Common Descent". I also discussed evidence that shows "Common Mechanism" is being a possible answer to the origin of the many common sequences found in different species.

The common sequences that have given us problems in the past are sequences that don't seem to have a function for the organism. Common sequences that are easily identified as being functional, can easily be explained as existing because God designed them in the same way. I don't like the term "Common Designer, " because it has connotations of a deficient God who designs different animals in the same way because he is running out of ideas, or because it is too much effort to redesign the different animals.

A rocket designer designs a rocket. It works. Now he is asked to design a larger rocket. What he does is to use what he has already learned from his previous experience to save on effort and time. His larger rocket is going to look much like the smaller one. That is what Common Designer means. It takes too much effort not to use what has already be done before.

The question is, do we want to say the same thing about God? Is God designing the various animals in such a similar fashion because it would be too much effort to completely design a completely different design? Like the rocket designer?

I don't think so. I think this is our chance to start looking for alternative ideas. Instead of thinking of God as a designer, maybe we should think of Him as an artist (well, maybe both). If we go into a new house, maybe Mexican style, we might expect the whole house to have common features throughout. We would expect to see various artistic themes throughout the whole house. Also we would expect to see various differences in the house that is due to artistic variations of the Mexican themes found in the house.

I might expect God to have created the Earth in the same way. The animals (and plants) have many common features which I attribute as being artistic themes. Also, all one has to do is to look at a comparative anatomy text book to see the artistic variations of themes God has placed in this world.

I might expect the same artistic theme aspect of God's creation to be as deep as the very molecules we are made of. This could also include proteins and DNA.

I introduced this whole issue in my talk at Andrews.

back to the other issue. . .

The b-hemoglobin Pseudogene is a excellent example of a functionless portion of the genome. Yet the same Pseudogene is found in different species (only 6 differences between human and chimp in the whole sequence!).

Why are they there? Maybe there is some sort of function. The problem is that function has been sought by many for a number of years. Nothing yet has surfaced. Of course this is an open ended search. Jim Gibson by the way, wrote an article supporting the idea that there must be some purpose that is yet undiscovered. His article is on the internet in the Geoscience web pages.

The other possibility is that there is no function. That the sequence is what it looks like, defective. Many say that the presence of the b-hemoglobin Pseudogene is very strong evidence for a common ancestor. Human, Chimp, Gorilla, Monkeys (both new and old world), Baboon, etc., all have virtually the same Pseudogene. (However as more species are compared, the differences also increase as well)

In my yet unpublished work, (don't spread my research around yet) I see evidence for the existence of either viral or enzymatic activity that creates mutations.

So I think there is a mechanistic process that has produced many of the Pseudogenes that we have, rather than a random process. If the Pseudogene is truly defective and if the mutations are truly found in patterns (not random), then the idea that it's a common mechanism is possible. Viruses have enzymes that, under the same conditions, do repeatable reactions.

If the DNA in Humans, Chimps, Monkeys, etc., are very similar, then if they are all infected by the same virus, would we expect the virus to do the same thing in the different species? I think so.

The "dreaded endogenous retroviral sequence common to both chimp and human DNA" is probably the major example of Common Mechanism. Viral enzymes (proteins) react with specific DNA sequences. If both chimp and human DNA have the same active sites, I would expect the viral proteins to react in the same exact way to both human and chimp.

Common descent or common Ancestor is not the only answer.

Yours in Christ

Mike

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Copyright 1998 - 2014 by Michael Brown all rights reserved
Officially posted June 19, 1998
last revised January 31, 2014