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Author Topic:   How novel features evolve #2
mindspawn
Member (Idle past 610 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 yet responded

  
mindspawn
Member (Idle past 610 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.


This message is a reply to:
 Message 372 by NoNukes, posted 10-30-2012 12:22 PM NoNukes has responded

Replies to this message:
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Tangle
Member
Posts: 6238
From: UK
Joined: 10-07-2011
Member Rating: 2.4


(1)
Message 378 of 402 (677624)
10-31-2012 9:51 AM
Reply to: Message 377 by mindspawn
10-31-2012 9:21 AM


Re: Hopefull not too meta...
mondspawn writes:

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.

er, but we know that life on earth is older than 6,000 - you know, we have proof of it, real evidence. But anyhow - it's off topic.


Life, don't talk to me about life - Marvin the Paranoid Android

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Percy
Member
Posts: 17873
From: New Hampshire
Joined: 12-23-2000
Member Rating: 2.3


(1)
Message 379 of 402 (677626)
10-31-2012 9:59 AM
Reply to: Message 375 by mindspawn
10-31-2012 8:57 AM


Re: adding an extra functional gene
mindspawn writes:

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.

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.

So that's all you can come up with to prove evolution?? I was expecting way better arguments than this.

So was I.

--Percy


This message is a reply to:
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Replies to this message:
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mindspawn
Member (Idle past 610 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!

https://www.familytreedna.com/pdf/nrg1124_fs.pdf

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 responded

Replies to this message:
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NoNukes
Inactive Member


(1)
Message 381 of 402 (677634)
10-31-2012 11:11 AM
Reply to: Message 377 by mindspawn
10-31-2012 9:21 AM


Re: Hopefull not too meta...
Because I believe in intelligent design, identical sequences with a few tweaks makes perfect sense to me

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.

don't know enough about the "genetic entropy" view to state clearly that is my view

What do you know about entropy in general?

Edited by NoNukes, : No reason given.


Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846)

The apathy of the people is enough to make every statue leap from its pedestal and hasten the resurrection of the dead. William Lloyd Garrison.

If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass


This message is a reply to:
 Message 377 by mindspawn, posted 10-31-2012 9:21 AM mindspawn has responded

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mindspawn
Member (Idle past 610 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


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Taq
Member
Posts: 7594
Joined: 03-06-2009
Member Rating: 3.4


(1)
Message 383 of 402 (677639)
10-31-2012 11:38 AM
Reply to: Message 380 by mindspawn
10-31-2012 11:10 AM


Re: adding an extra functional gene
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.

That's not quite accurate. Each mutation will occur on just one chromosome in any given pair. This means that each new mutation will have a 50/50 chance of being passed on since just half of one's chromsomes are used to create eggs and sperm. So, on average, 25 of the 50 mutations that a person is born with will be passed on to the next generation, along with a set of brand new mutations that is specific to them.

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.

I would need to see the study you are citing. From first glance the numbers you are citing may be the variation within just the human population. This would be a collection of mutations that have occurred over just the last 50,000 years as measured by the coalescence time for the human Y-chromsome most recent common ancestor.


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PaulK
Member
Posts: 14488
Joined: 01-10-2003
Member Rating: 1.6


(1)
Message 384 of 402 (677642)
10-31-2012 11:53 AM
Reply to: Message 380 by mindspawn
10-31-2012 11:10 AM


Re: adding an extra functional gene
quote:

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.

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...


This message is a reply to:
 Message 380 by mindspawn, posted 10-31-2012 11:10 AM mindspawn has responded

Replies to this message:
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Taq
Member
Posts: 7594
Joined: 03-06-2009
Member Rating: 3.4


(1)
Message 385 of 402 (677645)
10-31-2012 12:17 PM
Reply to: Message 382 by mindspawn
10-31-2012 11:36 AM


Re: adding an extra functional gene
That article says how varied the estimates are for the human mutation rate.

Those estimates are based on the sequence differences between orthologous pseudogenes in chimps and humans using probabilities based on neutral drift. What those estimates are really modelling is the mutation rate needed to produce the observed amount of divergence over the last 5 to 7 million years. They use pseudogenes and neutral drift because DNA sequence under selection can diverge at unpredictable rates. However, neutral mutations accumulate at a much more predictable rate, and become fixed at a rate dependent on population size.

As it turns out, the actual observed mutation rate is not that far off from the estimated rate needed to produce the observed amount of divergence.

Through genetic re-combination the point mutation could be eliminated in the very next generation,

No it wouldn't.

2) It is consistent with the theory of creation that the duplicates were created like like,

Anything is consistent with magic. That's the problem. If the genes were different you would still claim that they were created that way. Creationism makes no predictions as to the divergence seen in duplicated genes.


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 Message 382 by mindspawn, posted 10-31-2012 11:36 AM mindspawn has not yet responded

  
mindspawn
Member (Idle past 610 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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Tempe 12ft Chicken
Member (Idle past 57 days)
Posts: 436
From: Tempe, Az.
Joined: 10-25-2012


(1)
Message 387 of 402 (677656)
10-31-2012 12:49 PM
Reply to: Message 382 by mindspawn
10-31-2012 11:36 AM


Re: adding an extra functional gene
mindspawn writes:

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.

So, if you are stating that it is consistent with both ideas (which as Taq said anything is consistent with magic) then why should we add what could only be considered a needless entity, i.e.-God, into the equation. I see no reason to add God into the mix when evolution is enough of an answer, as you have just said. Especially considering the lack of evidence for any sort of God outside of the human imagination. Plus add in all of the other evidence that you would have to throw out from other fields, nuclear decay, all of cosmology, etc., and your solution requiring 6,000 years seems far more unlikely than the simple solution of a recent mutation increasing fitness, through the process of evolution.

...I mean, after all, you agreed the evidence is consistent with evolution as well.


The theory of evolution by cumulative natural selection is the only theory we know of that is in principle capable of explaining the existence of organized complexity. -Richard Dawkins
Creationists make it sound as though a 'theory' is something you dreamt up after being drunk all night. -Issac Asimov
If you removed all the arteries, veins, & capillaries from a person’s body, and tied them end-to-end…the person will die. -Neil Degrasse Tyson

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Taq
Member
Posts: 7594
Joined: 03-06-2009
Member Rating: 3.4


(1)
Message 388 of 402 (677657)
10-31-2012 12:51 PM
Reply to: Message 386 by mindspawn
10-31-2012 12:41 PM


Re: Hopefull not too meta...
The phylogenetic tree is just an evolutionist assumption.

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.

reality of the fossil record just shows that certain organisms proliferated when conditions were suitable.

The reality of the fossil record is that species fall into a nested hierarchy as predicted by the theory of evolution. A nested hierarchy is simply inexplicable in a creationist model. There is absolutely no reason that a creator would be confined to a nested hierarchy. For example, there would be nothing stopping such a creator from producing a species with teats and feathers.

The reality is that the theory of evolution is able to make very precise and testable predictions, and those predictions continue to pass every test we put in front of them. On the other hand, creationism makes no testable predictions. Creationism can not even explain the most fundamental observation in biology, that life falls into a nested hierarchy.


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Replies to this message:
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mindspawn
Member (Idle past 610 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 http://en.wikipedia.org/wiki/Y_chromosome
"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 http://en.wikipedia.org/wiki/Y_chromosome
"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:
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mindspawn
Member (Idle past 610 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.


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