I read the paper and found it easy enough to understand. I have corresponded enough with some others on these threads to get the impression that they wouldn't have much problem with it either.

You, on the other hand, have discounted every bit of evidence presented and have offered nothing in return but swarmy statements of how evolution couldn't be true because science is wrong. It is pretty obvious that you either didn't read the article above or were unable to comprehend it. It does, in fact and in great detail, explain almost every DNA growth scenario you have argued that can't happen. It gives species and timelines. It gives the mechanisms of gene reproduction and mutation.

Just like the telomere articles that you were so quick to discount, the information is so far over your head, you have great need to "make it go away" since you can't discuss it.

I never took a college biology course other than psychology but have studied in great depth ocean biology, ecosystems, global warming, and the like. After reviewing your posts, it would appear that you have not studied science and do not understand how such studies acquire knowledge.

Stating that BillyClub shouldn't post anything for any reason opens a window into your motivations and character. There are those who shouldn't post in a science thread because they don't understand science and their false statements and attempts to ridicule that which they don't understand tends to take on troll-like qualities of misinformation and distortion. You have reached that level. A ton of information has been offered to you in good faith and you appear incapable of absorbing any of it.

You should try to read the article. You might learn something.

How do you think we have learned to do this? Do you know what an ERV is? I will spell it out for you, Endogenous retrovirus. They occurred in nature long before we learned to make use of them for our own benefit.

The embarrassment in this thread is all yours, sadly I think you fail to even realize that.

BBC, I haven't finished the article, but the first half was awesome. Thank you for posting it.

ERV's are always recognisable as ERV's. They remain distinctive as additional insertions no matter how long they have been part of the genome. That is why for a couple of pages I was saying that evolution has to explain extra "non-viral" genes, it just becomes difficult for me to keep typing out "extra functional active beneficial non-viral protein coding genes" every time we are discussing these issues. Its not like the virus is ever absorbed into the genome in such a manner as to become indistinguishable from other coding genes, they are always recognised as separate insertions. If somehow they could adapt into normal genes they then could explain how humans came from bacteria.

I did read parts of the article and did find it a good read. I am always learning new information about the subject nearly every day.

It just isn't relevant to our "extra beneficial coding gene" debate as far as I can see, I haven't got the time to read everything posted unless the poster has the courtesy to point out the relevant section, then I will always read that detail. Because bbc did not highlight the relevant section and yet claims the article has some point, seems to indicate he is battling to find the relevance himself. He is welcome to point out the relevant section, but I doubt a debate about the usefulness of duplications will be relevant to adding an extra coding beneficial gene to the genome.(non-viral)

I said nothing like that, which shows your character :) You shouldn't get so nasty, its just a discussion :)

I said Billyclub shouldn't post something he does not understand. I feel that is logical and fair enough. If he does understand it, he could have the courtesy to point out where it contradicts my position. I feel it lacks manners to indicate that I must read this long article that supposedly disproves my position without even pointing out how or why. When I do point out how or why any links fail to disprove my position, I'm accused of ignoring science. I'm doing the opposite, I'm reading what is said, and it all shows that there is not one example of an extra beneficial (non-viral) coding gene created by nature.

I actually have no problem with the creation of new species (macro-evolution) through evolutionary processes. I just feel this cannot explain the increased complexity found in organs and limbs, brains etc, whereby bacteria can become humans. I am eagerly awaiting more genome sequencing studies, because I personally feel there will be some shockers for creationists who have a limited view of the ability for life to rapidly evolve. If you look at the diversity found in Australia and Madagascar, both countries I'm sure will reveal extreme diversity from common ancestors. There is some indication of "bottleneck" events of each species, yet they have not confirmed this between species yet. I believe in limited macro-evolution, but I do thoroughly believe in it.



Thanks for the compliment and the scientific approach, appreciated :)
There are not just a few remaining unknowns , molecular biology is a new field full of exciting truths to be discovered.

Let me summarise that article then:

Page 1 shows that scientists have identified that genome size increases. they found that this normally relates to NON-CODING genes (that's been my consistent point in this thread).

"Research into these differences soon revealed that in many organisms much of the DNA is noncoding and often repetitive. This provided a solution to the original paradox in that it showed that apparently simple organisms probably do have fewer ESSENTIAL genes than more complex organisms, even though they sometimes have larger genomes because of larger amounts of noncoding DNA."

The author then gives two common views on these duplicate non-coding genes:
A) they are Adaptive DNA, they assist and have a function even though they are non-active duplicates.
B) they are junk DNA with no value but accumulate too fast to de-select

The author proposes his view on page 2:
C) The extra DNA could have some value, but if it doesn't have value it normally will not be de-selected by nature because it causes little damage. Only when the accumulations of duplicated genes start to cause significant fitness damage will de-selection occur through the natural processes of natural selection. The author then advocates studying each case to see what selection pressures occurred in that particular case.

He then looks into different mutations, transposable elements (order change of base-pairs within a gene), deletions/insertions. The only relevant portion is insertions, but he lists these as pseudogenes or non-coding genes (inactive).

I found the whole article well written , informative, and confirming everything I have been saying. The number of beneficial coding genes does not increase. there can be a net decrease of these through deletions, but insertions are not protein-coding (they do not add useful genetic information to the complexity of the organism)

What this whole article has to do with extra beneficial (non-viral) coding genes is beyond me??

Perhaps you should have kept reading to the end. The Maize example had a 50% increase in genome size over the period given and the evolutionary benefits were discussed.

It would appear you missed the point of the whole article. Evolutionary pressures can cause loss or increase in genome size depending upon evolutionary pressures. Needed traits plays an important role in that if a trait is needed to fill a niche that required a longer gene sequence, a longer gene sequence is what will evolve.

Once again you play the role of "whatever is presented backs you up 100% and you understand science better than anyone else.

However, on one point you are absolutely correct. What this whole article has to do with extra beneficial (non-viral) coding genes is beyond you.

The whole point of the article discussing selection effects upon these gene additions would have been useless if they did not have the ability to be beneficial.

I do not have time to hand hold a dishonest person through the logical implications of such changes.

Your assertions are tired and worn out at this point.

http://forums.randi.org/showthread.php?t=237443 A fun thread that just started up at the JREF about single celled organism evolution.

I don't believe it indicates that at all. The pattern of BBC's posts suggest to me that he has lost interest in spending the time discussing the details of your argument. There are many possible reasons for this.





Oh!

I admit I have not read every single one of your posts with care, and if you said this already I missed it.

Again, I feel that defining evolution seems essential.

To me, evolution is not "a complete, definitive explanation for how and why all of life came to be on this planet". And while it is far more than 'the creation of new species', to me this is a significant sticking point for creationists.

Based on your quote above, and my concept of evolution, I would say, emphatically, that you believe in the theory of evolution. If you believe that new species can come into existence purely as a result of evolutionary processes, then you've got what matters.

It contributes to misunderstanding when we say we 'agree with the theory of evolution' or 'doubt the theory of evolution' without being very specific about which portions we are speaking of. It looks to me like you are: 'someone who believes in known evolutionary processes who doesn't think that what is know about evolution is adequate to fully explain the origin of complex life on this planet'.

Which is, also, my position. I just don't default to creationism in the face of the unknowns.

Perhaps you should have kept reading to the end. The Maize example had a 50% increase in genome size over the period given and the evolutionary benefits were discussed.

It would appear you missed the point of the whole article. Evolutionary pressures can cause loss or increase in genome size depending upon evolutionary pressures. Needed traits plays an important role in that if a trait is needed to fill a niche that required a longer gene sequence, a longer gene sequence is what will evolve.

Once again you play the role of "whatever is presented backs you up 100% and you understand science better than anyone else.

However, on one point you are absolutely correct. What this whole article has to do with extra beneficial (non-viral) coding genes is beyond you.


The maize did not have beneficial coding genes, merely beneficial duplications of non-coding genes, a concept I've been mentioning during this thread.

I understand your paraphrasing of my position and it is technically correct. Yet my consensus about an organism evolving into an ecological niche yet retaining the same genetic structure or having reduced complexity is completely different to evolutionist claims of evolution being the source of all complex life-forms. So you could say that I'm completely opposed to the main assumption of evolution, the evolving of complex life-forms. Observed evolution is micro-evolution and devolving into less complex life-forms (reduced gene functionality) to suit environmental ecological conditions. This flies in the face of the core claim of evolution of being the source for all complex life-forms.

All the examples listed of observed evolution in this thread do not support evolution's core assumption.

The word 'evolution' is being used in very different ways through this dialog.

When you use the verb 'evolve', it seems you treat the word as if its meaning assumes a certain kind of history or progression, whereas the word can correctly be used without that assumption.

So, in response to the bolded section, I would say that you do believe in the evolution of complex life forms, you just don't believe in the evolution of complex life forms from non-complex life forms. The phrase "from simpler life forms" is not implied by the word 'evolve', but for you it seems to be so implied. The heart of evolution, the process, from my POV, is speciation. Evolution is a process, not a history. There may be cases where its not wrong, exactly, to use the word evolution to imply a particular, assumed history, but this distinction is key and the two uses should not be confused.


Back to how you use the term - making the distinction using the terms 'micro-evolution' vs 'macro-evolution' is not sufficient to make your meaning clear to me. I've met many creationists who say "I believe in micro, but not macro" who explicitly disbelieve in any speciation of any kind. To them, the exclusion of speciation is implicit in their use of the word 'micro', and it is the main point or purpose behind their use of 'micro'. They only acknowledge a change of qualities within a species over time.

You are not like them - you acknowledge speciation - so your use of micro vs macro seems to be different to me.


You seem (?) to view 'evolution' as, first and foremost, 'a supposed explanation for how all of life came to be on this planet'. I'm constantly frustrated by people (from all camps! not just creationists) who view evolution through this lens.

There is a process that is occurring, which is very well evidenced. It is real. It is happening. Most creationists are in complete denial of this reality.

This process is called 'evolution', and your recent comments make clear that you fully acknowledge that this process is, in fact, occurring. It seems to me that you just don't see evidence supporting the notion that this process is the explanation for how complex life came to be, which to me is not intrinsic to the term evolution.

Also, it seems to me that you see a lack of evidence for the known processes to even allow for the development of complex species from simple species. My response is: Okay. So don't believe that notion. We have a lot to learn, as a species, about these two separate but entangled topics: the actual process of evolution, and the actual history of the development of life on this planet.

------

Just reread your post and want to respond; I'm sure I'm belaboring the point, but its really important to me:



This is true. Most people who, like you, believe in the process of evolution also (unlike you) believe that this process is the means by which we came to have so many complex life forms. So they make this additional, but separate, assertion.

I'm certain that they don't have the full story; and I suspect that it doesn't really matter. I predict that the gaps in knowledge are going to be filled with surprising discoveries such as in the mechanisms influencing gene movement and activation, rather than aliens or God. I could be wrong.

Again, belaboring the point, hahaha



In my view, this is not the core claim of evolution, no more than 'abiogenesis' (which is not even part of 'evolution') is the core claim.

Your view makes sense from a creationist perspective - creationists often see evolution and creationism as two competing theories to explain the same situation, and as such, project creation-like qualities onto 'evolution'.

God is a 'source', so creationists (and evolutionists from religious cultures!) often think of evolution in terms of it being a 'source'.

Evolution is not a 'source', evolution is a 'means by which'. You agree that its a means by which different species can come into existence, and you disagree that evolution is a means by which complex life can come from simple life.

Oh, damn, now that looks like I'm picking on your word choice, and jumping to conclusions based only on that one word. To be clear, I will refer to evolution as a 'source', because its easier to say and my audience knows what i really mean. And my (possibly wrong) view of how you map language to meaning is not based on that one word, its based on the whole of your statements..


Creationists have a 'complete story', and so they interpret evolution as a presumed 'complete story'.

I don't know how to respond to this except to say that you do seem to have a very accurate take on my position. I do see evolution as the explanation for the appearance of modern life-forms. This is how the word is used, and I understand your frustration with the narrow meaning, however this is really what the creation/evolution debate is about. Where did advanced life-forms come from, were they always there, or evolved from bacteria. (technically our common ancestor between humans/bacteria).

Semantically I've been finding it difficult to find the correct words. Who would have thought that the word "adding" a gene could be misunderstood, but it was misunderstood and I had to change it to "extra" genes. So I admit that semantically I have not used the best words to describe my position.

I suspect that both creationists and evolutionists are going to be shocked by the discoveries that are going to be revealed through genome sequencing, I'm especially interested in how the chromosomal patterns of Madagascan civets and lemurs relate and also Australian marsupials. There's a lot to be discovered and as you say they don't have the full story. In the meantime it's a bit irritating when you read a wikipedia article or watch National Geographic and they say this animal is a cousin to that animal and they have the common ancestor of xxxx fossil. All these assertions are guesswork based on the assumption of evolution and applying that assumption to closely matching DNA patterns, then this is adopted by the mainstream media and educational authorities as fact.

Anyway I'm just rambling, not making any particular point here, from an empirical view we seem to be in agreement, fortunately I have strong religious beliefs that give me an advantage when looking at these facts. hahahaha stirring!

Your right, how could anyone make us repeat ourselves over the course of several pages and still not get what this means?

Coding or non coding, its a gene addition, beneficial or non beneficial its a gene addition. A copy or not a copy is a gene addition.

Got it?

Many circumstances under which genes will be added, and they may or may not have an impact based on selection pressures. Even changes in genes are really new genes. Even though you end up with the same number of total genes. If I change my socks, just becuase I still only have one pair of socks, I have new socks. ie new genes. Both the total number and the uniqueness of genes changes, this has been shown definitively.

Get it?

We got it pages ago, in fact this was well known to me years ago. Massagetrade, I hope you look back a few pages and reread some of his posts. He is being weaselly in the extreme.

At first he said gene additions do not happen.
Then he said beneficial gene additions do not happen.
Then he said they happen, but not very often.

The goal posts have moved several times in this thread and each time evidence is presented to disprove a vague assertion it is then moved slightly.

What you mean is you are finding it harder and harder to find something to disagree with.

This wouldn't be a problem if you didn't move the goal posts and instead took some time to really read without bias what modern evolutionary biology really knows . . .

That is called bias, and it IS the hurdle that must be overcome in your understanding.