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Author Topic:   How novel features evolve #2
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 375 of 402 (677621)
10-31-2012 8:57 AM
Reply to: Message 369 by Percy
10-30-2012 8:22 AM


Re: adding an extra functional gene
What you mean is that this is our chance to prove evolution to *you*. It's already been proven within science (in this context, "prove" means provide sufficiently convincing evidence that a strong consensus forms within the relevant scientific discipline). Since you refuse to accept even the most non-controversial and basic evidence, such as that for mutation rates (for a high level outline of what we think we know, see the Wikipedia article on Mutation Rates), I can't see how persuading you would ever be possible. If you can't see how two nearly identical genes must mean there was a recent duplication because any significant passage of time would have meant each would have accumulated a number of mutations absent in the other, then convincing you of something like the introduction of novelty that involves more subtle evidence is beyond well nigh impossible.
So that's all you can come up with to prove evolution?? I was expecting way better arguments than this.
Some try to prove evolution by assuming humans and apes had a common ancestor and working out mutation rates from the differences in the two genomes. This is extreme illogical thinking, trying to back up evolution using evolutionary assumptions as an argument.
The 50 mutations per generation is definitely something we can work with. You say I refuse to believe mutation rates, if they are calculated on the assumption that humans/apes evolved, well that is circular reasoning and I will not accept them. If they are based on observed fact without any assumptions, we can work with them. I will deal with this more in my reply to Taq.

This message is a reply to:
 Message 369 by Percy, posted 10-30-2012 8:22 AM Percy has replied

Replies to this message:
 Message 379 by Percy, posted 10-31-2012 9:59 AM mindspawn has replied

  
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 376 of 402 (677622)
10-31-2012 9:07 AM
Reply to: Message 374 by Taq
10-30-2012 4:26 PM


Re: adding an extra functional gene
Taq, I would love to get into a discussion about those predictions, but for the moment I want to stick to the topic regarding proof for novel genes. We seem to have suddenly created 6 more discussion topics before we have even finished the main one.

This message is a reply to:
 Message 374 by Taq, posted 10-30-2012 4:26 PM Taq has not replied

  
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 377 of 402 (677623)
10-31-2012 9:21 AM
Reply to: Message 372 by NoNukes
10-30-2012 12:22 PM


Re: Hopefull not too meta...
I think the latter argument has been dealt with effectively despite mindspaw's slowness in recognizing it. As for the significant amount of time, mindspawn relies strictly on his interpretation of the Bible as his reason for rejecting that man has been around for an enormous amount of time. MS absolutely rejects any kind of dating as is a YEC's wont. We aren't going to be able to deal with that portion in this thread.
It also appears that for mindspawn, "ID" is synonymous with God did it exactly as Genesis describes. I think we can commend him for not playing hide the frisbee.
Thanks NoNukes for trying to get to the bottom of my view. Unfortunately there's no clear label for it, and I don't know enough about the "genetic entropy" view to state clearly that is my view, but it certainly seem to be.
To clear up any confusion, I believe biological life was created on an old earth approximately 6000 years ago. I believe there has been some genetic entropy since. I believe nothing observed in current genome sequencing contradicts this, for example the ape was designed with its current chromosomal organization (bar some mutations), and the human as well. Because I believe in intelligent design, identical sequences with a few tweaks makes perfect sense to me , they are design differences to similar creations. An ape and human are similar, they will have many matching sequences unique to primates. As will mammals all have similarities, compared to reptiles.

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 Message 372 by NoNukes, posted 10-30-2012 12:22 PM NoNukes has replied

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mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 380 of 402 (677632)
10-31-2012 11:10 AM
Reply to: Message 371 by Taq
10-30-2012 11:09 AM


Re: adding an extra functional gene
If ID were science it would actually demonstrate that this was the case instead of just assuming it.
Lol! that's sweet coming from an evolutionist. Good one!
No, it isn't. It is a CONCLUSION drawn from evidence. We have the transitional fossils. We have the shared genetic markers such as shared ERV's and shared pseudogenes. We have different Ka/Ks ratios for coding regions and pseudogenes which evidences selection and random mutations. It is NOT assumed.
Well the fossil record is full of its own assumptions, and even transitional fossils are huge assumptions. get a lake with fish, amphibians/mudfish on the shoreline , and animals on the edge. Dry it up very slowly. Look at the fossils many years later. All this shows is that a watery environment became terrestrial. To assume the mudfish became an animal is not doing justice to the known fact that the landmass was originally small, and therefore most subsequent landmasses were originally ocean.
Now please tell me about shared pseudogenes and ERV's, and how they prove evolution?
Yes. It would appear that they filtered out the indels for that specific paper so, if I am reading the paper correctly, the 50 refers to base substitutions.
Now this is what I am REALLY interested, true observed evidence without any assumptions. Correct me if I'm wrong, this is a new field to me, but when there is genetic recombination in the next generation, the 50 mutations largely disappear due to the recombination process. But this cannot occur in the Y chromosome, recombination does not reduce Y chromosome mutations. Natural selection can eliminate the more damaging mutations, but we both agree the population has to collect mutations every generation. Given that the human Y chromosome has 1.67% of all base pairs (50 million of 3 billion), and the Y chromosome develops mutations at 4.8 times the normal rate of point mutations, the human Y chromosome should be collecting about 4 or 5 mutations each generation. Current studies show that there are approximately 28650 SNPs (old point mutations) in certain human Y chromosomes, but this figure could be vastly OVER-estimated. This is certainly pointing towards a recent beginning of mutations in the Y chromosome, rather than millions of years. Based at the current rate of 4 or 5 per generation.
So the only evidence you have given that is NOT already based on evolutionary assumptions, but is based on actual observed mutation rates , is pointing closer to creationist time frames, and not evolutionary time frames. Interesting stuff!
Runtime Error
Efforts to discover genome-wide sequence variation
have identified vast numbers of Y-specific single
nucleotide polymorphisms (SNPs): the Ensembl
database lists 28,650 at the time of writing, which
might seem enough to provide an extremely detailed
PHYLOGENETIC TREE of Y-chromosomal lineages. But how
many of these SNPs are real, and how many are artefacts
that are produced by unknowingly comparing
true Y-chromosomal sequences with similar sequences
(PARALOGUES) elsewhere on the same or other chromosomes2?
If the Y chromosome had been collecting mutations for millions of years, you would have literally millions of SNP's since the Y chromosome evolved, but we only observe thousands.

This message is a reply to:
 Message 371 by Taq, posted 10-30-2012 11:09 AM Taq has replied

Replies to this message:
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mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 382 of 402 (677638)
10-31-2012 11:36 AM
Reply to: Message 379 by Percy
10-31-2012 9:59 AM


Re: adding an extra functional gene
No one tries to calculate mutation rates this way. It would be impossible because we don't have the genome of the common ancestor. We do have the genome of chimpanzees (our closest evolutionary relative), but since humans are not descended from chimpanzees the number of mutational differences between us would not be a measure of the number of mutational differences between us and the common ancestor, which is what you really need. Even if we did have the common ancestor's genome, the time since the supposed split is only approximate.
I think I already provided a link to the Wikipedia article on mutation rates, but here it is again. It has a section on measurement. Measuring mutation rates by the impossible method you suggest some try to use is notably absent.
Evolutionary change at the DNA level is inevitable because the copying that takes places during cellular reproduction is imperfect. The error rate is very low (fortunately for life in general), but it occurs and it accumulates generation after generation with only natural selection to filter out the more deleterious changes. Without mutation adaptation to changing environments would be severely hampered.
That article says how varied the estimates are for the human mutation rate. They don't even try to give a figure. I preferred Taq's more definite figures of 50-100 per generation. The chances of these mutations actually showing in those two "duplicate" genes is very small due to genetic recombination. let's say 100 mutations are divided amongst 20000 genes, this means that each gene would show one single point mutation every 200 GENERATIONS. Through genetic re-combination the point mutation could be eliminated in the very next generation, and so if these two genes were created 6000 years ago, the fact that they show little variation from each other is absolutely consistent with creationist timeframes.
So going back to the original argument, an organism with two duplicate genes with better fitness when exposed to pesticides and with very few observed mutations in those two genes is absolutely consistent with both theories:
1) It is consistent with the theory of evolution that the duplication was recently created and increases fitness when exposed to pesticides.
2) It is consistent with the theory of creation that the duplicates were created alike, and the original population retained more fitness when exposed to pesticides rather than the subsequent mutated "gene deleted" population. And also consistent with a mutation rate of 100 per generation, at that rate not all gene's would experience continuously inherited mutations over a 6000 year time frame.
Edited by mindspawn, : grammar

This message is a reply to:
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mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 386 of 402 (677652)
10-31-2012 12:41 PM
Reply to: Message 381 by NoNukes
10-31-2012 11:11 AM


Re: Hopefull not too meta...
A lot of rationalizing about what a designer would do involves trying to understand the designer's thought process. We know that mammals have similarities, but one might ask why there are similar animals. Evolution comes with that explanation built in.
Or more specifically, one might ask why a designer would create life so that existing and distinct life forms a phylogenetic tree, particularly if the designer was omnipotent. I think this is a difficult thing for ID to answer, but Creationist simply deny everything that suggests natural reasons for extinctions other than a flood. But with evolution, such a tree is exactly what we would expect. Even more condemning is that Creationist attempts to explain the fossil record all border on the absolute ridiculous even after we reject dating.
The phylogenetic tree is just an evolutionist assumption. reality of the fossil record just shows that certain organisms proliferated when conditions were suitable. If there were low oxygen and low pressure conditions before the flood, we would have an early layer of mammals. You cant prove evolving from a logic succession of proliferation.
For example, if the bible is literally true, and radioactive dating is incorrect and if geology is accurate other than dating, then the terrestrial organisms would have been confined to a small landmass. Due to the long lifespans of humans and other animals compared to bacteria, we would have many many generations of dying and fossilized bacteria before the first trilobite dies. Now the ocean was anoxic, more suitable to trilobites than fish. So above the short lived bacteria, we would have a near worldwide layer of trilobites, reducing as the newly created vegetation oxygenated the atmosphere, creating fertilized conditions. As the world got colder, the ice caps caused the sea to recede, and therefore trilobite fossils are covered by a layer of semi aquatic and then terrestrial amphibian fossils in the low lying areas. Upper highlands would have the low oxygen and low air pressure conditions suitable to mammals. These are really rare during the carboniferous, much like Komodo dragons are rare now, in thousands of years you would have no chance of finding these rare Komodo fossils in the worldwide mammal layer of today. If you do find them it would be easy to incorrectly classify them because of their unique fauna /flora environment.
I could carry on and on about other possible scenarios, but the phylogenetic tree is just s theory. what is observed is different layers of huge numbers of animals suitable to the conditions of that period, and regular extinctions when the conditions change. numbers of species just dropping, and dropping all the time.
The essence of the fossil record is that evolutionists do not find all their relevant transitionary fossils, because those transitionary fossils were supposedly rare (rapid changes to environments). Creationists don't find mammals in the carboniferous because low oxygen highlands were rare. We both in the same boat, missing some fossils with good explanations for it.
Edited by mindspawn, : No reason given.

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Replies to this message:
 Message 388 by Taq, posted 10-31-2012 12:51 PM mindspawn has replied

  
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 389 of 402 (677663)
10-31-2012 1:08 PM
Reply to: Message 384 by PaulK
10-31-2012 11:53 AM


Re: adding an extra functional gene
Well, no. You can only measure the number of mutations since the "Y-chromosome Adam", (who, in your view would probably be Noah, since in the Flood story the only male survivors are Noah and his sons). That isn't millions of years even in the mainstream scientific view.
And if mutations are really, really rare as you claim it seems a bit unlikely that thousands have accumulated in only about 5000 years in a small area of the genome..
For the sake of a lack of better figures given in this thread, I'm willing to accept a rate of 50-100 per generation as presented by Taq.
Now to apply this to evolution, you don't go back just to when man was seperately defined from the common ancestor with the ape. This common ancestor had the y-chromosome too. There is no mechanism that would have cleaned up the male Y chromosome just before the first human evolved. So this Y chromosome of humans would be accumulating mutations from the beginning of the evolving of the Y chromosome. We are talking 100s of millions of years. At a rate of 5 per generation in the Y chromosome, and an average generation of 20 years , we should have about 50 million point mutations in the 50 million base pairs of the human Y chromosome. The actual facts are not looking very good for the hypothesis of evolution at all. The truth is when we were just lizards etc the average generation was a lot shorter, so we should have even more mutations than than my approximation of 50 million.
50 million or 28000 mutations ? BIG difference.
Unless the human Y chromosome does not mutate much? But Wikipedia says it mutates at 4.8 times the normal rate, which Taq says is 50-100 base pairs per 3 billion base pairs per generation.
Wikipedia Y chromosome - Wikipedia
"The Y chromosome is one of the 2 sex-determining chromosomes in most mammals, including humans. In mammals, it contains the gene SRY, which triggers testis development if present. The human Y chromosome is composed of about 50 million base pairs."
Wikipedia Y chromosome - Wikipedia
"The human Y chromosome is particularly exposed to high mutation rates due to the environment in which it is housed. The Y chromosome is passed exclusively through sperm, which undergo multiple cell divisions during gametogenesis. Each cellular division provides further opportunity to accumulate base pair mutations. Additionally, sperm are stored in the highly oxidative environment of the testis, which encourages further mutation. These two conditions combined put the Y chromosome at a risk of mutation 4.8 times greater than the rest of the genome
So either way you argue the case it looks bad, argue that the mutations don't stick in the genome, and then you agreeing with me that that there are not a lot of carried mutations and your whole evolutionary process looks a bit slower. (and the duplicate gene example in this thread becomes weaker)
Or you suffer from a lack of evidence in current genomes of enough observable mutations to justify the theory that organisms accumulate many mutations.
Edited by mindspawn, : correcting quote
Edited by mindspawn, : spelling

This message is a reply to:
 Message 384 by PaulK, posted 10-31-2012 11:53 AM PaulK has replied

Replies to this message:
 Message 391 by NoNukes, posted 10-31-2012 1:29 PM mindspawn has replied
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mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 390 of 402 (677666)
10-31-2012 1:28 PM
Reply to: Message 388 by Taq
10-31-2012 12:51 PM


Re: Hopefull not too meta...
False. It is a CONCLUSION based on a comparison of morphology and DNA sequence. You seem to have a tough time differentiating between assumptions and conclusions. One is not the other
When an anoxic ocean recedes you get trilobite fossils below, then wetlands fossils, then terrestrial fossils. The evolutionists conclusion: They evolved??
Observable reality: the ocean receded! that's all. It was anoxic before thats why trilobites were first , then fish.
Extinctions dont prove evolution, they just prove extinctions. An excess of extinctions over new species seems to point to devolution.
There's nothing in DNA sequences that point to evolution. You have tried with the aphid example, but that fits in perfectly with creation and a subsequent gene deletion within the last 6000 years.
There was once an aphid population with two identical genes 6000 years ago. Some of the population then mutated a deleted gene. This was ok. Until sprayed one day with insecticide. Then the mutated ones died off.
there is no reason to assume the two genes would show any difference in mutation over 6000 years, at the low rate per base pair per generation that you indicated , very few genes would be much transformed over 6000 years. So where's your proof that evolution is a better theory than creation when even your base mechanism for the appearance of new beneficial novel coding genes is just one theory that fits the reality? Even your mechanism is unproven.
Edited by mindspawn, : No reason given.

This message is a reply to:
 Message 388 by Taq, posted 10-31-2012 12:51 PM Taq has replied

Replies to this message:
 Message 396 by Taq, posted 10-31-2012 3:42 PM mindspawn has replied

  
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 393 of 402 (677673)
10-31-2012 1:49 PM
Reply to: Message 391 by NoNukes
10-31-2012 1:29 PM


Re: adding an extra functional gene
So how does the current Y chromosome compare to those of our ancestors one million years ago or to that of a lizard? Are you saying that there does not appear to be the correct amount of variation as predicted by the theory of evolution when we look at those things?
I don't believe you've shown any such thing. We don't have the DNA for any pre-human, ancestors and I don't think you can make the argument that human Y chromosomes look too much like modern lizard DNA to justify evolutionary thoery.
At least it is the case that neither of the quotations from Wikipedia seem to touch on the issue you are raising
Under the assumption of evolution the human Y chromosome isn't a recent development, but has been accumulating mutations for hundreds of millions of years. The alternative, that the common ancestor of mammals did not have a Y chromosome is a ridiculous thought. The current state of the Y chromosome is not reflecting enough mutations if evolutionary time frames are true.

This message is a reply to:
 Message 391 by NoNukes, posted 10-31-2012 1:29 PM NoNukes has replied

Replies to this message:
 Message 394 by NoNukes, posted 10-31-2012 2:31 PM mindspawn has replied
 Message 395 by New Cat's Eye, posted 10-31-2012 3:06 PM mindspawn has replied

  
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 397 of 402 (677706)
11-01-2012 2:31 AM
Reply to: Message 395 by New Cat's Eye
10-31-2012 3:06 PM


Re: adding an extra functional gene
Hundreds of millions of years ago, it would not have been a human Y chromosome. Humans weren't alive that long ago.
Exactly! thats what the others don't seem to get, if you assume evolution, there was not a single "Adam" moment when the ape-thing became a human. The Y-chromosome would reflect a continuous accumulation of mutations from long before humans appeared if evolution is true. that's not just 100 000 years. The principle of the Y chromosome collecting mutations would apply from the moment the Y chromosome evolved into a seperate chromosome representing the male. If you look at biology and the way common animals breed, and project a most likely point in evolution's so-called phylogenetic tree of the human, this point of the existence of the Y-chromosome in the human ancestor is millions of years ago. The alternative, that there were no male and female x and y chromosomes in the biology of the human ancestor 200 million years ago, is an illogical escape route if you would like to take that escape route. The Y chromosome is thought to have evolved 200 million years ago, I will be interested to see if you now start doubting mainstream evolutionary thought.
Edited by mindspawn, : No reason given.

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mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 398 of 402 (677708)
11-01-2012 2:54 AM
Reply to: Message 394 by NoNukes
10-31-2012 2:31 PM


Re: adding an extra functional gene
I'll be more direct. What is your baseline for comparison? Show me a Y chromosome from hundreds of millions of years ago, and then let's talk about the differences.
I'm not sure what you think I'm comparing? If the Y-chromosome has been accumulating mutations since it started 200 million years ago, then it should have more mutations than its currently showing. Scientists have come up with this 200 million date, not me:
Sex Drives Chromosome Evolution | The Scientist Magazine
The human X and Y chromosomes are thought to have originated from a matching pair of non-sex chromosomes, or autosomes, some 200 million years ago. And now, they are so different that they share just a tiny length of sequence. Indeed, the human X has about 1,000 genes, and the Y only has about 50, explained Doris Bachtrog of the University of California, Berkeley, who led the new study.
You do believe in evolution don't you? If so then the human did not suddenly appear, the human is a result of accumulated mutations, where are those?
Edited by mindspawn, : inserting link

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mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 399 of 402 (677709)
11-01-2012 3:03 AM
Reply to: Message 396 by Taq
10-31-2012 3:42 PM


Re: Hopefull not too meta...
Radiometric dating would place them all from the same geologic period, so no they would not assume that they evolved from one to the other. We also have many examples of very recent anoxic lakes that sit above much older terrestrial sediments.
Huh? If the ocean recedes, why would they all be dated simultaneous? Obviously the fish were in that area before the ocean receded and only then you find land fossils. You not being logical here. Radiometric dating and ocean receding would show the same sequence. To assume evolution instead of animals walking onto new landscapes that used to be seabeds, isn't the most logical conclusion at all. If nearly everywhere around the world you find trilobites first, but there are one or two places where you do not find trilobites first, this fits in with isolated terrestrial animals taking a walk after oceans receded.
and of course if ocean fossils were there first, then terrestrial, this proves the ocean came first. Evolved seems to be the most illogical projection of the fossil sequence.
The entire scientific community disagrees with you, as does 60 years of research done on DNA. Sorry, but you are extremely wrong about this.
As just one example of thousands, there is this paper on endogenous retroviruses:
Just a moment...
In this paper they state:
"Given the size of vertebrate genomes (>1 10^9 bp) and the random nature of retroviral integration (22, 23), multiple integrations (and subsequent fixation) of ERV loci at precisely the same location are highly unlikely (24). Therefore, an ERV locus shared by two or more species is descended from a single integration event and is proof that the species share a common ancestor into whose germ line the original integration took place (14)."
Guess what? We share thousands and thousands of retroviral integrations with other apes, including chimps. Common ancestry is proven way beyond a reasonable doubt.
What is the rate of ERV insertion between two parents and a child? You gave me a mutaton rate of point mutations, have they proved that some of these inheritable ERV's are found in offspring but not in parents. They have proved this with point mutations as you so correctly pointed out, what about ERV's?
(my argument here is that ERV's could all have a precise function in the genome, and be created 6000 years ago, what evidence have you got they are insertions)
Creationism is not a theory. No scientist is using creationism to explain anything as part of a scientific research program. Scientists ARE using evolution, and it works. That is why evolution is a better theory: it works.
Darwin wrote a well-written book. Since then evolution has been prematurely accepted by science. but there is no more actual evidence for evolution than for creation. The ONLY evidence you have brought forward is the point mutation rate that points more towards creationist time frames than evolutionist time frames.
The assumption for the aphid so-called duplication event has no proof to back it up. It is no more logical than an aphid created with two identical genes that subsequently undergoes a gene deletion. The only reason to reject the creationist view on the aphid, is a biased propensity to believe in the miraculous process of evolution rather than the miraculous process of creation.
Edited by mindspawn, : No reason given.
Edited by mindspawn, : No reason given.

This message is a reply to:
 Message 396 by Taq, posted 10-31-2012 3:42 PM Taq has not replied

  
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 400 of 402 (677712)
11-01-2012 3:33 AM
Reply to: Message 396 by Taq
10-31-2012 3:42 PM


Re: Hopefull not too meta...
Why is there any reason to assume that they would have had exactly the same sequence when they were created?
this is the nature of design. Think of a car with four cylinders, four pistons, four flickers, two rear doors, two front doors, if the best design requires a duplication then it works. the results are there to see, the duplication had more hardiness under attack (pesticides) so I would say the duplication added strength to that area.

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 Message 396 by Taq, posted 10-31-2012 3:42 PM Taq has not replied

  
mindspawn
Member (Idle past 2660 days)
Posts: 1015
Joined: 10-22-2012


Message 402 of 402 (678081)
11-05-2012 3:00 AM


I haven't participated in the full thread, but I've really enjoyed the discussions I've been involved in. I'm more interested in novel genes than novel features per se. I am really keen to see if there are any ways that additional coding genes with novel functions that actually benefit fitness can evolve. Unfortunately the aphid example was not convincing enough because of the possibility that this was a deleted gene and not an evolved gene.
There were interesting side issues that were raised concerning mutation rates and ERV's, but these side issues were still core to the debate regarding if we should observe any divergence in the two identical genes of the aphid. True science would look at the respective so-called mutations from the view of an impartial observer, to see if there is evidence of mutations, or if these genetic sequences have always been there. There is definitely evidence of some mutations, unfortunately for evolutionists the mutation rates point more towards creationist time frames than evolutionist time frames, some seemed to battle to grasp this point.

  
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