Pseudogene function: regulation of gene expression

Gup20 · Jul 13, 2005

Full Article here

Article Summery:
The discovery of a functional nitric oxide synthase (NOS) pseudogene compels us to understand pseudogenes in a new light. It confirms earlier clues suggesting that seemingly nonfunctional pseudogenes can regulate the expression of paralogous genes by producing antisense RNA. Moreover, only a partial sequence complementarity between sense and antisense segments of the gene and pseudogene is compatible with this function. This confutes the common evolutionary belief that major differences in sequence between paralogous genes and pseudogenes imply that the latter is necessarily a nonfunctional gene copy in a state of mutational drift. A second pseudogene may regulate the NOS gene by producing a truncated protein that can bind with the normal protein to produce an inactive heterodimer. Finally, the world of noncoding RNA, whether sense or antisense, offers further large-scale possibilities for undiscovered pseudogene function.

Full Article here

UTEOTW · Jul 13, 2005

Wow! You find an example of a pseudogene that has a function and you think you have overturned the whole logic of the shared pseudogenes as a marker of shared descent.

Let's take a look at why this logic is wrong.

This discussion always comes back to vitamin C. Here we have a case where four different genes code for different enzymes to make a single product. We know that in all primates that one particular gene of the group is broken and in the same manner. We also can compare the accumulated mutations since the disabling one for phylogeny and compare this tree with others from independent means. It is the classic case of a psuedogene and is well documented. Does my one example trump yours?

But let's move on. There is a second reason why remnant function in a pseudogene is not surprising. The human genome is very complex. Many sections of DNA code for more than one protein. The are complex interaction with RNA produced from some sections of DNA that regulate other functions. A mutation may knock out a DNA section that makes part of a protein, turning it into a psuedogene, without altering some of the other functions that bits of the DNA may perform.

There is another logical reason that I can come up with. Probably the most important source of new genetic variety is the duplication and subsequent mutation of sections of DNA. These old genes can become something new. In a not dissimilar manner, why is it hard to imagine that a pseudogene through further mutation might become useful in some new role?

Another problem for you is that there have been studies where large sections of DNA believed to be noncoding have been removed with no ill effects. There must not have been any improtant regulatory fnctions in those sections.

Finally, you ignore a very important way to identify the junk. DNA is divided into three "letter" codons that code for amino acids and starts and stops and so on. Mutation does not equally affect all three positions of each codon, however. Changes to the first two positions will usually result in significant change to the resulting protein. However, changes to the third position will generally result in either the same amino acid or a very similar one. These changes are often reffered to as silent. In coding DNA, the changes tend to be more preserved in the third position becuase other changes will normally destroy the function of the protein and will be selected against. In noncoding DNA, mutations can happen to all three positions and should not favor the silent mutations only.

So you have a much higher mountain to climb to disprove the implications of pseudogenes than finding use for one or a couple.

Gup20 · Jul 14, 2005

Wow! You find an example of a pseudogene that has a function and you think you have overturned the whole logic of the shared pseudogenes as a marker of shared descent.
Click to expand...

Evolutionists have touted for years that there is this large store of "junk" in our DNA that it champions as evidence leftover from our mutational evolution. Daily, more and more usefulness is being discovered in what used to be considered junk DNA. Like the appendix, once thought a vestigial leftover from evolution, this only serves to diminish to so-called evidence for evolution. As this pool of "evidence" shrinks, I will have been glad to have stuck with my creationist views that line up with scripture. Eventually science will have no choice but to abandon the concept of vestigial organs and junk DNA. Because my views are not weighed down by evolutionary dogma, I am free to watch science get closer and closer to the truth revealed in scripture, and farther and farther away from evolution. This will be yet another item in a long list of abandon "evidences" for evolution. It's interesting to see the multitude of evidences which have been abandon, yet see the faith in evolution remain the same as it has ever been. Truly, evolution is more faith than fact.

UTEOTW · Jul 15, 2005

"Evolutionists have touted for years that there is this large store of "junk" in our DNA that it champions as evidence leftover from our mutational evolution. Daily, more and more usefulness is being discovered in what used to be considered junk DNA."

You did nothing to dispel the reasons I gave above for identifying some DNA as genuine junk just as you have no answer for the implications of this junk.

Sorry to spam one of my posts from another topic, but it seems relevant.

The question to be asked is what interpretation best explains the evidence that we observe. As new information comes in, it will either support your interpretation or contradict it. Support tells you that you are on the right track. Contradiction tells you that you need to rethink your theory.

The first observation that gets discussed is morphology. Now if we look at the animals that are alive today and the animals that the fossil record tells us were alive in the past, we see that the form a nested heirarchy. All by itself this could mean that all of these animals were produced by common descent or by common designer. (As a note, I am not trying to set up a false dilemma here. I recognize that there may be other explanations that could be put forward but I am purposely restricting the discussion to the two possibilities under discussion.) So you have to go to the next observation.

The next most obvious observation is genetic. If you examine all the different types of genetic material that has been tested and use it to construct phylogenic trees, you find that you get much the same pattern as you do when you arrange the fossils by morphology. Let's see how these observations stack up.

One easy test is to look at just the functional genes. These can again be used to support common descent or a common designer. Both will claim that creatures that are the most similar should have the most similar DNA.

But you can start to untangle the two by looking into further types of genetic material that is not related to the functional part of DNA. One example would be to look at retroviral inserts. These happen when a virus inserts part of its genome into its host. If this happens in a reproductive cell, then the genome of the virus can be passed on to the offspring. Since this has nothing to do with the functional part of the genome, it can shed light on the situation for us. For example, if common descent were true, then you would expect the retroviral DNA to show the same pattern as the other lines of observation. If a common designer were the true explanation, then you would expect a random distribution of the retroviral inserts when compared between the species. In fact, you see that the pattern follws that which wbe expected of common descent. The common designer option cannot explain this pattern.

If you take the retroviral discussion and repeat it with things like paralogs, pseudogenes, retrotransposons and such you will find the same result. One pattern would be predicted by common descent and another by a common designer but the patterns only fit that of common descent. For example, whales have a complete set of psuedogenes identical to what land based animals possess for their sence of smell. If whales evolved from land based ancestors, this is easily explained. But if they were recently created as is, there is no reason for them to possess such useless genes. A common designer advocate is forced into giving an arbitrary, ad-hoc explanation for this observation.

From here let's move on to other topics. Let's first loook at atavisms. We have brought a few into discussion already. Atavistic legs on whales. Two extra toes on horses. Unfused leg bones in horses. Atavistic tails on humans. The observation is that these atavisms ONLY manifest themselves in a pattern consistent with the phylogenic trees generated from the other lines of evidence. The atavisms only make parts that were possessed by their ancestors in the common descent interpretation. You never see atavisms that fail to follow this pattern. Common descent offers a simple explanation. The common designer option gives no reason why we should expect whales to have genes for making legs of humans to have genes for making tails. They are again forced into capricious explanations.

Development tells a similar story.This has the potential to get rather complicated, so I'll stick with an example already in play. We observe that whales go through a developmental stage in which they possess rear legs. Again, this shared developmental trait follows the same pattern as the other lines of evidence. Common descent offers a simple reason for this to be the case. A common designer has no logical reason to send whales through a stage with legs which must later be reabsorbed.

This can keep going for a long time. If you look at other areas of evidence, you keep coming back to the observation that all the bits always fit the tree that you get from morphology and genetics. This is true for parahomlogy. This is true for vestiges. This is true for the chronology of the fossils. Every observation that you make brings you back to these same trees.

So the question is which interpretation of the data fits the observations. The answer is that common descent offers a simple and compelling answer for each one. A common designer can be hypothesized for some of the observations but for many of the observations, the evidence is the opposite of what would be expected. The only recourse for YEers is to ignore these contradictions. BUt you really must worry about someone's ideas when they must ignore so much.
Click to expand...

Pseudogene function: regulation of gene expression

Gup20 Active Member

UTEOTW New Member

Gup20 Active Member

UTEOTW New Member

Useful Searches

Pseudogene function: regulation of gene expression

Gup20 Active Member

UTEOTW New Member

Gup20 Active Member

UTEOTW New Member