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Author Topic:   Evolution Requires Reduction in Genetic Diversity
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 481 of 1034 (758021)
05-18-2015 3:31 PM
Reply to: Message 479 by Denisova
05-18-2015 2:45 PM


Re: Moderator Introduced Definitions
So you think that the original genetic diversity in the genomes of the species, created by God for the first time, is now lost due to deterioration as demonstrated by junk DNA?
"Junk DNA" was a very unfortunate term coined in the early days of genetic sequencing when it was thought that DNA --> Protein was the major player. It is now known that it is not anywhere near that simplistic. We now suspect that the majority of "non-coding" sequences actually have a function. Even spacer DNA that is 1000's of bases long serves an important function even though they don't "do" anything other than keep two segments seperated. The term "junk DNA" really needs to completely fall out of usage.
it should have been a lot of genes that turned into junk DNA, even when we know that not all non-functional DNA is pseudogenes. Because whatever definition you accept for "junk DNA", the proportion of pseudogenes in it must represent thousands of genes that were lost (according to your scenario).
Why do you think the proportion must represent thousands of genes? Are you thinking that each speciation event must mean a loss of one or more genes and there was thousands of speciation events (according to Faith's idea)? I think you would be hard pressed to get ANY creationist to speculate as to how many speciation events there has been since the flood, so that argument won't be much of a deterrent.
you claim the genetic bottleneck occurring during the Flood was the main cause for the loss of genetic diversity. I completely escapes me how a genetic bottleneck could cause a loss of genes. Of alleles that would make sense, but genes?
Good question! Apparently when all the alleles are lost, the gene dies. I don't know...
In this study Thewissen unravels how genetic mechanisms that cause the hind buds in cetacean embryos to start to develop, arrest and degenerate in 5th week of gestation. It turns out that cetaceans still have the genetic outline for developing hind limbs but one crucial Hox gene Sonic Hedgehog (Shh) has been disabled by mutations. It plays an essential role in the molecular cascade that controls limb development in vertebrae.
I suspect that most evolutionary change is due to regulatory changes rather than changes in protein coding sequences. Changes in proteins probably come after the gene regulation has been altered.
ALL of my core points have no[t] been addressed until now.
Just a little tip on your English usage here... "until now" implies that the points have now been addressed. It says they weren't addressed previously, but now they are. What you mean is "they have not been addressed yet."
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for... I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.
Ignorance is a most formidable opponent rivaled only by arrogance; but when the two join forces, one is all but invincible.

This message is a reply to:
 Message 479 by Denisova, posted 05-18-2015 2:45 PM Denisova has replied

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 Message 484 by Denisova, posted 05-18-2015 7:16 PM herebedragons has replied
 Message 486 by Faith, posted 05-18-2015 7:53 PM herebedragons has replied
 Message 492 by Taq, posted 05-18-2015 9:22 PM herebedragons has replied

  
Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 482 of 1034 (758023)
05-18-2015 3:49 PM
Reply to: Message 481 by herebedragons
05-18-2015 3:31 PM


Re: Moderator Introduced Definitions
"Junk DNA" was a very unfortunate term coined in the early days of genetic sequencing when it was thought that DNA --> Protein was the major player. It is now known that it is not anywhere near that simplistic. We now suspect that the majority of "non-coding" sequences actually have a function. Even spacer DNA that is 1000's of bases long serves an important function even though they don't "do" anything other than keep two segments seperated. The term "junk DNA" really needs to completely fall out of usage.
All based on "suspecting" that it has a function you want to throw out a concept that makes good sense in the Flood theory.

This message is a reply to:
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Dr Jack
Member
Posts: 3514
From: Immigrant in the land of Deutsch
Joined: 07-14-2003
Member Rating: 8.7


Message 483 of 1034 (758026)
05-18-2015 6:20 PM
Reply to: Message 481 by herebedragons
05-18-2015 3:31 PM


Re: Moderator Introduced Definitions
"Junk DNA" was a very unfortunate term coined in the early days of genetic sequencing when it was thought that DNA --> Protein was the major player. It is now known that it is not anywhere near that simplistic. We now suspect that the majority of "non-coding" sequences actually have a function. Even spacer DNA that is 1000's of bases long serves an important function even though they don't "do" anything other than keep two segments seperated. The term "junk DNA" really needs to completely fall out of usage.
This is an extremely minority view among actual working Geneticists. It essentially springs from the extreme overreach in the selling of the ENCODE project in which they absurdly equated 'transcribed' with 'has a function'. In fact, we know that a large chunk of DNA is junk because we know exactly what it is, and the majority of the rest is almost certainly junk. There are bits and pieces of signal among the noise but the majority of it has no function at all. The differential rates of mutation between Junk DNA and coding DNA across evolutionary time should be sufficient to convince you of that.

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Denisova
Member (Idle past 3216 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 484 of 1034 (758029)
05-18-2015 7:16 PM
Reply to: Message 481 by herebedragons
05-18-2015 3:31 PM


Re: Moderator Introduced Definitions
"Junk DNA" was a very unfortunate term coined in the early days of genetic sequencing when it was thought that DNA --> Protein was the major player. It is now known that it is not anywhere near that simplistic. We now suspect that the majority of "non-coding" sequences actually have a function. Even spacer DNA that is 1000's of bases long serves an important function even though they don't "do" anything other than keep two segments seperated. The term "junk DNA" really needs to completely fall out of usage.
I know and agree. Ask Faith, it's her vehicle and also read the thread first.
I also assume that at least a substantial part of the junk DNA are pseudogenes.
What proportion exactly is not very relevant here. I'm only driving Faith's assumptions to their logical consequences - that is, implding under its own weight.
Why do you think the proportion must represent thousands of genes? Are you thinking that each speciation event must mean a loss of one or more genes and there was thousands of speciation events (according to Faith's idea)? I think you would be hard pressed to get ANY creationist to speculate as to how many speciation events there has been since the flood, so that argument won't be much of a deterrent.
Ask Faith, it's here vehicle.
She is assuming that all the original genetic diversity was deteriorated or collapsed by the Flood or the Fall. I have no idea what proportions. Faith doesn't specify it. How could she because she has no empirical evidence to substantiate that or to calculate those proportions anyway. So I take her argument and bring it to its logical consequences and see what happens.
Speciation is not in Faith's vocabulary.
My opinion on speciation and its relationship to genetic diversity is spelled out numerous times in my previous posts, if you don't mind, i am not going to repeat that here again.
Good question! Apparently when all the alleles are lost, the gene dies. I don't know...
Every individual can carry a maximum of 2 alleles for each gene.
When there were a population bottleneck of the Flood proportions (only leaving 8 people alive, 3 of them being sons of 2 other ones), the maximum alleles per any gene cannot exceed a total of 10 (3 X 2 in the wives of the sons, max. 4 in Noah and his wife and therefore the same ones in their sons).
Hence, that number of 10 alleles would evidently have been much lower than the number in a much larger, pre-Flood population.
The number of alleles cannot drop to nil because there are 8 persons still surviving, thus this implies some alleles will always survive in such circumstance.
In the animals the situation is even worse because of many of them only two specimen, 1 male and 1 female, were taken on the Ark. So the maximum number of alleles for any gene in those genomes is 4.
But the number of genes cannot drop that much. Because all individuals in questions are of the same species. Species do not vary genetically much. Max. 1, 2 or 3% genetic diversity. Otherwise you would get a different species!
So the number of alleles after such severe population bottlenecks will drop dramatically but the number of genes only very slightly. Off go Faith's notions.
I suspect that most evolutionary change is due to regulatory changes rather than changes in protein coding sequences. Changes in proteins probably come after the gene regulation has been altered.
Well, if you compare species mutually, you will see that they share a lot of proteins. The more phylogenetically they resemble, the more proteins they share. But they do not share all proteins. So there must be at least some protein sequencing having occurred in the course of evolution. On the other hands, proteins are biochemically very redundant. Cytochrome C in algae may differ considerably in biochemical composition from the variant found in, say, bacteria or animals. But its functional part is biochemically spoken exactly the same among all known species. They even did transplant the cytochrome C from an alga (if I recall well) to an bacterium, two very distant life forms. Normally their cytochrome C differs considerably in chemical composition. But yet nothing happened with the bacterium. I could well do with the alga's cytochrome C.
So the picture is a bit complicated. But yes, much evolutionary change would be due to altered Hox genes and the like. But not all!

This message is a reply to:
 Message 481 by herebedragons, posted 05-18-2015 3:31 PM herebedragons has replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 485 of 1034 (758031)
05-18-2015 7:51 PM
Reply to: Message 483 by Dr Jack
05-18-2015 6:20 PM


Re: Moderator Introduced Definitions
.
There are bits and pieces of signal among the noise but the majority of it has no function at all. The differential rates of mutation between Junk DNA and coding DNA across evolutionary time should be sufficient to convince you of that.
And what are those differential rates of mutation?

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 486 of 1034 (758032)
05-18-2015 7:53 PM
Reply to: Message 481 by herebedragons
05-18-2015 3:31 PM


Re: Moderator Introduced Definitions
I suspect that most evolutionary change is due to regulatory changes rather than changes in protein coding sequences. Changes in proteins probably come after the gene regulation has been altered.
I didn't know what you meant by this at first; now I gather it's another way of talking about junk DNA. Right? All those "regions" that affect diversity but don't code for proteins are what is usually called Junk DNA, right? Leaving that 2% you said do code for proteins.
Edited by Faith, : No reason given.
Edited by Faith, : No reason given.

This message is a reply to:
 Message 481 by herebedragons, posted 05-18-2015 3:31 PM herebedragons has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 487 of 1034 (758034)
05-18-2015 7:58 PM
Reply to: Message 484 by Denisova
05-18-2015 7:16 PM


Re: Moderator Introduced Definitions
But the number of genes cannot drop that much. Because all individuals in questions are of the same species. Species do not vary genetically much. Max. 1, 2 or 3% genetic diversity. Otherwise you would get a different species!
So in your view what are all those dead genes in the genomes of so many species? 95% or more. If you said in your post, I didn't get it.
I'm intending to get to all your neglected posts next.

This message is a reply to:
 Message 484 by Denisova, posted 05-18-2015 7:16 PM Denisova has replied

Replies to this message:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 488 of 1034 (758035)
05-18-2015 8:09 PM
Reply to: Message 416 by Denisova
05-14-2015 12:21 PM


Re: Replaced from other thread to here
OK, yes, that is what I meant. I think the original genome could have had more genes per trait, meaning five or six where now there are three or four. Yes I believe there has been a great loss of genes and genetic diversithy in human AND ANIMAL genomes since Adam and Eve, but more since the huge bottleneck of the Flood that wiped out most living creatures, which I suggest is most likely the source of junk DNA. And more genes per trait is one way the earlier genome was probably fuller than it is now.
Very well then, so may I have the empirical evidence for it?
Where in the scientific literature can we find evidence for the claim that the original genomes had more genetic diversity than today?
No, because the scientific literature is in thrall to the evolutionist paradigm and assumes the opposite. Assumes I say, it is not evidenced, it's an interpretation imposed on all the data.
So, that leaves only this part of your contention intact:
....and also observations about both mutations and the loss of genetic diversity in evolutionary processes.
Yes, that's exactly what I asked for.
Now, where may we find those observations in the genetic literature?
I picked it up here and there from internet sites. I'm sure you can find it without my help.
And you will not find this answer by explaining how skin colour in extant humans (of whom we know the genome) is related to 4 genes.
We do not have the gene sequence of Adam and Eve.
But we DO have the gene sequence of Homo Neanderthalis, Homo Denisovia and Homo Heidelbergensis. And the genome sequence of many specimens of archaic Homo sapiens as well.
Or we may retrieve information from DNA of old human remains and compare them to modern human DNA. Or just look for genetic evidence in the extant human genome by smart comparison.
It's all there.
In that case you really need to spell it all out here.
I just realized there wasn't much point in answering this post. Well, on to the next one.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 489 of 1034 (758037)
05-18-2015 8:41 PM
Reply to: Message 417 by Denisova
05-14-2015 12:25 PM


Re: Replaced from other thread to here
I am still awaiting your response on the points I made:
1. there is no overall loss in genetic diversity, it's only parcelled out in two isolated genomes - the evolutionary requirement for initial gain in genetic diversity is met.
Assertion without evidence. Don't demand evidence of me if you aren't giving any of your own.
However, being "parceled out in two isolated genomes" doesn't provide a gain at all, where do you get that? The two together retain the original genetic diversity though, at least until the new gene frequencies have been worked through them. But my contention is that EACH new subpopulation is where we see the reduction in genetic diversity-- the alleles remain in the other population. The idea is that these populations are actively evolving because of their new gene frequencies and that's where reduced genetic diversity occurs.
2. the fact that after the split into two genetically isolated genomes, both of those sub-genomes take away only a subset of the original, total genome DOES NOT detract ANYTHING of the simple fact that there was an initial gain in genetic diversity BEFORE the split, which is what evolution theory ACTUALLY requires.
You have yet to show this actually happens, and there is certainly no reason why it should happen. What could possibly bring about this "initial gain? Mutations see the split coming and jump on the bandwagon?
3. evolution theory DOES NOT require each of the subset genomes AFTER the split to retain all the initial genetic diversity at the moment of the split. As a matter of fact, evolution theory predicts those two sub-genomes to be SPECIALISED due to different environmental conditions. And specialization implies the reinforcement of some traits, mostly at the expense of other ones. If you think otherwise, show me the papers by evolutionists who say so. So your rendition of evolution theory on this is flawed.
This actually sounds like what I'm saying happens, in different words, so I don't "think otherwise." I THINK I know what you mean by "specialized" but I could be wrong. In my system it wouldn't apply to the subpopulations at the split but after a period of inbreeding in which the new gene frequencies get worked through the whole population. That changes combinations sometimes drastically enough all by itself to prevent the reintroduction of gene flow between the two populations.
|
However, I haven't found discussions anywhere of how genetic diversity is lost in these splits so if you know where to find them please provide links. But I see by your next point that I must be misreading you anyway.
5. In other words, the evolutionary requirement for a gain in genetic diversity has been met.
By what where? You haven't said one thing to show where this would come from, you just keep saying it.
A POSSIBLE loss of genetic diversity in any of the sub-genomes AFTER the split is NOT an evolutionary requirement.
It depends on the numbers that form the new subpopulations whether there will be an apparent loss in genetic diversity or not, though that will always be the trend; but one thing there won't be is an increase. I guess you think you are dealing with this by insisting on it as a done deal before the split occurs but again there's no reason to think this occurs and you haven't offered any.
MORE THAN THAT, it is the thing for evolution theory TO EXPLAIN ("speciation", which is a split into two genetically isolated sub-genomes). Hence, it is the CONSEQUENCE of the evolutionary processes as conceived. And you CAN'T take the consequence of a process as its own requirement.
So you keep saying but in this case you have to have reduced genetic diversity, which is, yes, also a consequence of splitting the populations, in order to get the new traits brought about by the new gene frequencies. You can't have new traits without this trend to reduction, though it doesn't have to be a big reduction at first; so it IS a requirement as well as a consequence.
The OBJECT of evolution theory is to explain speciation. When speciation occurs, there MUST be an initial gain in genetic diversity.
Nope. Speciation is really only the formation of a subpopulation that has lost its ability to interbreed with the former population. This requires no increase and must very often result from the decrease which soon renders it a genetic mismatch with the former population. Are "new species" tested for genetic diversity? I didn't think so. At the end of a series of subspecies one that speciates must have lost so much diversity there's little left for any further formation of subpopulations.
>>>This requirement has been met<<<.
Again, I ask, by what? How?
There also MIGHT be a SUBSEQUENT loss in genetic diversity in any of the diverted sub-genomes AFTER THE SPLIT but that's a CONSEQUENCE of and the THING TO BE EXPLAINED by evolution theory.
I hope you acknowledge that you cannot take THE THING TO BE EXPLAINED as a REQUIREMENT for a scientific theory. That would be circular reasoning.
See above.
6. MOREOVER, I EVEN hardly doubt any of the resulting sub-genomes after the split ACTUALLY to have smaller genetic diversity than the original overall genome before the split, as I tried to explain in the elaborated example in my post #163.
Perhaps I missed it. Will check.
ABE: You did not write post 163 on this thread. /abe
None of these points but #1. were addressed by you.
Hope they now are.
Edited by Faith, : No reason given.

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 490 of 1034 (758038)
05-18-2015 8:49 PM
Reply to: Message 430 by Denisova
05-15-2015 3:59 AM


Re: genetic diversity
All you are doing in this post is saying I haven't addressed your posts. I just addressed two so if that isn't enough you'll have to provide links to any others that exist.

This message is a reply to:
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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 491 of 1034 (758039)
05-18-2015 9:03 PM
Reply to: Message 473 by PaulK
05-18-2015 2:00 AM


Pseudogenes
PaulK writes:
. How do genes "die" ? They certainly can't be "killed" just by a bottleneck. How does this hypothesis explain the quantity of junk DNA ? What evidence is there that all junk DNA is "dead" genes ?
The Wikipedia article on Pseudogenes describes very well what I have in mind except for the parts about how it may have a function, which I doubt:
Pseudogenes are dysfunctional relatives of genes that have lost their protein-coding ability or are otherwise no longer expressed in the cell.[1] Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism. ...
Because pseudogenes are generally thought of as the last stop for genomic material that is to be removed from the genome,[5] they are often labeled as junk DNA. We can define a pseudogene operationally as a fragment of nucleotide sequence that resembles a known protein's domains but with stop codons or frameshifts mid-domain. Nonetheless, pseudogenes contain fascinating biological and evolutionary histories within their sequences. This is due to a pseudogene's shared ancestry with a functional gene:...
And here it goes into evolutionist interpretations I don't share. But otherwise the description and analysis are very much what I have in mind.
Edited by Faith, : No reason given.

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Replies to this message:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 492 of 1034 (758040)
05-18-2015 9:22 PM
Reply to: Message 481 by herebedragons
05-18-2015 3:31 PM


Re: Moderator Introduced Definitions
"Junk DNA" was a very unfortunate term coined in the early days of genetic sequencing when it was thought that DNA --> Protein was the major player. It is now known that it is not anywhere near that simplistic. We now suspect that the majority of "non-coding" sequences actually have a function.
Junk DNA is a perfect term. It is disposable DNA. It is DNA we can throw out.
We now suspect that less than 10% of the human genome has selectable function. The problem is that the ENCODE group tried to make their data look more important than it was by conflating function with "does something". Those aren't the same thing. This is where it all comes full circle. The trash in your kitchen trash can does something. It releases odor molecules into the air in your kitche. It is still trash, even though it does something. What it doesn't do is perform a function that is important to your kitchen. Junk DNA is like the boxes of old stuff we have jammed in our garage that we have accumulated over the years but no longer have a use for.
In fact, some species have chucked a majority of their junk DNA. In the case of the bladderwort, it is probably due to the lack of phosphates in the environment.
"Here we report the sequence of the 82-megabase genome of the carnivorous bladderwort plant Utricularia gibba. Despite its tiny size, the U. gibba genome accommodates a typical number of genes for a plant, with the main difference from other plant genomes arising from a drastic reduction in non-genic DNA. "
Architecture and evolution of a minute plant genome | Nature
82 million bases, that's it. And it has a genome with the normal number of genes for a plant. The onion, for comparison, has a 100 billion base genome. Billion, with a B.
In the end, I think junk DNA is a perfect term.
I suspect that most evolutionary change is due to regulatory changes rather than changes in protein coding sequences.
Those are not mutually exclusive. Changes in the protein coding sequence of a regulator protein can change the expression of other genes.

This message is a reply to:
 Message 481 by herebedragons, posted 05-18-2015 3:31 PM herebedragons has replied

Replies to this message:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 493 of 1034 (758041)
05-18-2015 9:37 PM
Reply to: Message 485 by Faith
05-18-2015 7:51 PM


Re: Moderator Introduced Definitions
And what are those differential rates of mutation?
The rates of mutation should be equal across the genome. What differs is whether those mutations accumulate in a given section of DNA. If a section of DNA has function, then there has to be a chance of a deleterious mutation happening in that stretch of DNA. These mutations will be selected against. When we compare genomes, these regions will show up as having more bases in common than in junk DNA where there is no function so no possibility of deleterious mutations.

This message is a reply to:
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Taq
Member
Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


Message 494 of 1034 (758042)
05-18-2015 9:40 PM
Reply to: Message 491 by Faith
05-18-2015 9:03 PM


Re: Pseudogenes
The Wikipedia article on Pseudogenes describes very well what I have in mind except for the parts about how it may have a function, which I doubt:
What you would need to explain is why psuedogenes share sequence homology with functional genes in other species.
And here it goes into evolutionist interpretations I don't share.
What evidence do you have that would refute that interpretation?

This message is a reply to:
 Message 491 by Faith, posted 05-18-2015 9:03 PM Faith has replied

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Faith 
Suspended Member (Idle past 1444 days)
Posts: 35298
From: Nevada, USA
Joined: 10-06-2001


Message 495 of 1034 (758043)
05-18-2015 9:50 PM
Reply to: Message 494 by Taq
05-18-2015 9:40 PM


Re: Pseudogenes
What you would need to explain is why psuedogenes share sequence homology with functional genes in other species.
Most creatures have similar design features, one creature happens to lose a gene to junk DNA that remains alive in another.
And here it goes into evolutionist interpretations I don't share.
What evidence do you have that would refute that interpretation?
Same evidence evolution has for its interpretation: None, or really, same facts, different interpretation. It's an interpretation.
Edited by Faith, : No reason given.

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