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If it were the case that psuedogenes are "useless/junk," then why wouldn't natural selection have weeded out the "left over" by now? I mean we're talking what, 70 - 80 Million years here with no function?

Surely natural selection would have eliminated them from it's tool box? It takes energy to replicate AND maintain genes, especially when they don't pick up any slack.  Why weren't those puppies just removed?

Why couldn't it be, that the fact that Puedogenes have any recognizable gene like structure AT ALL be suggestive of their importance? We just might not know it yet? I mean this science is still relatively young.

And to INSIST, at this point in our research, that they MUST point to Common Decent (by purely natural means) is a little premature, wouldn't you agree?  

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Oops, I forgot one: Why do you assume that just because a gene doesn't code for protein, that it must be useless?

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I'm going to respond Mark, but then I'm going to post my original questions for you to respond to in more depth.  

You said, "If it were the case that psuedogenes are "useless/junk," then why wouldn't natural selection have weeded out the "left over" by now? I mean we're talking what, 70 - 80 Million years here with no function? "

First, the timeline you are giving varies in every instance, and the human genes I mentioned are not on that scale (although the teeth gene is birds is).  I would expect some pseudogenes between species with a common ancestor 70-80 million years ago to have been eliminated, but its definitely possible some could survive this long.  The case of the teeth building gene in modern birds is a good example.    

The real answer to your question is actually simple.  There are no mechanisms for removing pseudogenes from genomes (or possibly as I mentioned above the process just takes a very long time).  Some bacteria and prokaryotes have mechanisms for removing 'junk dna', but this makes more sense since they would be much more likely to benefit from this sort of mechanism.  This is actually a really important lesson for those unfamiliar with how evolution often works.  Evolution isn't always going to be intelligent in its progress forward.  Refinements to inefficiencies like these may take a VERY long time, but if creationism were true we wouldn't expect to find them at all.


"Why couldn't it be, that the fact that Puedogenes have any recognizable gene like structure AT ALL be suggestive of their importance? We just might not know it yet? I mean this science is still relatively young."  

The science is not that young Mark, and this is something which has been studied in serious depth.  Also, we know many of the mechanisms which produce pseudogenes, so we can understand the biology well enough to draw conclusions.  Its not the least bit controversial to say most pseudogenes are 'junk dna' which is surviving in the genome.  

One final thought, it has been suggested that because pseudogenes undergo mutations at a faster rate(because mutations don't affect the organism), these pseudogenes provide a substrate for evolution to work on to possibly produce new functional genes.  I'm not sure how important this mechanism might be, but its an interesting possibility.  

"Why do you assume that just because a gene doesn't code for protein, that it must be useless?"

No Mark, you are misunderstanding the biology.  Pseudogenes do code for protein (might be some which code for functional RNAs or something, but mostly proteins).  I never said they didn't code for protein, I only said they aren't transcribed.  What happens in many pseudogenes is RNA polymerase doesn't transcribe the gene due to faulty regulatory regions associated with the gene.  If transcription does not occur, the protein coded for by the gene is never produced.  So if the purpose of a coding region is to produce a protein, and that protein is not produced... it is completely valid to say the gene is serving no purpose.  Also, as I mentioned in my previous post, we often know what jobs these proteins play in closely related species, so its just not likely at all that the gene could have been created to serve some other secret or unknown purpose.  Do you see my point?  This evidence is powerful, and I don't think you can dodge it.

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Why does the human genome contain genes like Wnt-3a and Cdx1 if creationism is true? More generally, I've mentioned before the vestigial genes in the whale genome which are associated with providing olfactory senses in other mammals, and I know a few posts here have discussed the existence of teeth in the genomes of many birds, so I would like a little bit of clarification from the creationist here on the topic. I could list a LOT more examples, but I'm more interested in a general response. No creationist can deny the evidence exist, so how do you logically dodge this bullet?

Would you agree that this sort of evidence is remarkably consistent with evolutionary theory, and remarkably inconsistent with creationism? If not, why?

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Originally Posted by David Norris:
I never said they didn't code for protein

What did you mean by this then:

Originally Posted by David Norris:
Also, most animal/plant genomes have 1000s of pseudogenes (genes which no longer code for proteins) and there is no doubt a SUBSTANTIAL portion of this DNA is worthless junk.

I have some more questions because this conversation is very fascinating to me...Dave you know your stuff!
  

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I did mislead you a bit with my simplified statement about pseudogenes "no longer coding for proteins", but trust I actually knew what I meant... So I'll take some of the blame for your misunderstanding there!

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Originally Posted by David Norris:
Why does the human genome contain genes like Wnt-3a and Cdx1 if creationism is true?

If I remember correctly, these are the genes for a tail?

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Let me ask a quick question here. By the way, as a side note, my decision as to how
we got to the level of complexity in life today is still up in the air. I do not categorize
myself as a strict 6 day creationist nor a staunch Evolutionist in the purely naturalistic
sense.

Personally, I like to look at the claims of evolution and creation in and of themselves
to determine their validity - not comparing them to each other to determine their
truthfulness. So when it comes to evolution, I like to leave "creationism" out of the
picture because sometimes I think it distracts from the conversation at hand.
On the other hand, to be fair, I like to leave evolution out of the picture when
determining the truthfulness of "Creationism."

I believe that both theories have "anomalies" that don't fit well within
their respective framework of interpretation.  And instead of throwing out
the interpretive paradigm all together, those anomalies are usually set aside
for a time until a plausible interpretation is presented. This is why I believe
the debate should be held in the arena of the philosophical assumptions of
the paradigms themselves - not just in the evidence used to support/debunk
those paradigms. Anyway, enough of the rant. I hope that sheds some light
on where I come from as to discussions of this nature.

Now back to my question: If one doesn't assume the Darwinian/NeoDarwinian/Unguided
Evolutionary paradigm is true, would it be ok to say that one doesn't know how to
interpret these examples yet? I mean I see how if one buys into those assumptions
then these examples will be interpreted as fitting quite nicely into that paradigm.
But if one doesn't, then holding off on an answer until future discovery wouldn't
be frowned upon would it?

I wanted to ask this question to you before I even attempt at offering an explanation
that doesn't match those of Evolutionary thought.

And I agree with you that the staunch creationist has to deal with these lines
of evidence head on and not dodge them...

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Originally Posted by Mark Deviny:

Now back to my question: If one doesn't assume the Darwinian/NeoDarwinian/Unguided
Evolutionary paradigm is true, would it be ok to say that one doesn't know how to
interpret these examples yet? I mean I see how if one buys into those assumptions
then these examples will be interpreted as fitting quite nicely into that paradigm.
But if one doesn't, then holding off on an answer until future discovery wouldn't
be frowned upon would it?

I don't think any assumptions are necessary to conclude this sort of evidence supports common descent through evolution.  If "one doesn't know how to interpret these examples yet", I would suggest they consider the prevailing scientific consensus and stop taking their skepticism to such extremes.  I've said before that I believe skepticism is healthy, but it needs to be constrained within limits or it becomes nonsensical.