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Author Topic:   Evolution Requires Reduction in Genetic Diversity
Taq
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Posts: 9970
Joined: 03-06-2009
Member Rating: 5.6


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Message 496 of 1034 (758044)
05-18-2015 9:54 PM
Reply to: Message 495 by Faith
05-18-2015 9:50 PM


Re: Pseudogenes
Most creatures share design features in common, one creature happens to lose a gene to junk DNA that remains alive in another.
If that function were important, then the loss of that gene would reduce the fitness of that individual. Those with the mutation that knocked out the gene would be outcompeted by individuals with the functional allele. This would eliminate the pseudogene from the population.
It would seem to me that pseudogenes occur when there is a lack of negative selection against mutations in a gene, meaning that the function isn't needed in that gene.
Same evidence evolution has for its interpretation: None, or really, same facts, different interpretation. It's an interpretation.
How does your interpretation match up better with the evidence than the evolutionary interpretation?

This message is a reply to:
 Message 495 by Faith, posted 05-18-2015 9:50 PM Faith 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 497 of 1034 (758045)
05-18-2015 9:55 PM
Reply to: Message 493 by Taq
05-18-2015 9:37 PM


Re: Moderator Introduced Definitions
This makes sense overall.
These mutations will be selected against.
Is there evidence for this? It just sounds like another unevidenced evolutionist assumption.

This message is a reply to:
 Message 493 by Taq, posted 05-18-2015 9:37 PM Taq has replied

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


Message 498 of 1034 (758049)
05-18-2015 10:13 PM
Reply to: Message 497 by Faith
05-18-2015 9:55 PM


Re: Moderator Introduced Definitions
Is there evidence for this? It just sounds like another unevidenced evolutionist assumption.
Every time a child dies of hemophilia without passing on that defective gene, it is evidenced. Every time a person dies in their early 20's from Duchenne muscular dystrophy without passing on the gene, it is evidenced. There are tons of examples.

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


Message 499 of 1034 (758050)
05-18-2015 10:14 PM
Reply to: Message 496 by Taq
05-18-2015 9:54 PM


Re: Pseudogenes
Most creatures share design features in common, one creature happens to lose a gene to junk DNA that remains alive in another.
If that function were important, then the loss of that gene would reduce the fitness of that individual.
Well, I assume that any loss of a gene to junk DNA reduces the individual's fitness. I suppose most such losses aren't particularly important, since there are so many of them and we go on surviving. Like having a dysfunctional appendix. Some losses are surely important though, and the accumulated total loss definitely must have reduced the fitness of all species that possess so much junk DNA, but since we can't imagine a really fit healthy state it's hard to measure the loss.
Those with the mutation that knocked out the gene would be outcompeted by individuals with the functional allele.
Depends on what the allele is for. It may be for something that seems quite minor in the overall range of traits so its loss wouldn't make much difference, especially if other traits are possessed that are lost to others, which should also be the case. We notice people's different strengths and weaknesses anyway as just expressions of individuality.
This would eliminate the pseudogene from the population.
It would have to be positively lethal for that to happen, wouldn't it?
It would seem to me that pseudogenes occur when there is a lack of negative selection against mutations in a gene, meaning that the function isn't needed in that gene.
I'm sure that's what the ToE would suggest, but while living things seem to do OK without all those genes in junk DNA, the way we seem to do OK without a functioning appendix and without a gall bladder and tonsils too since they are easily dispensed with, my guess would be that we'd be a lot healthier and stronger if they were still functioning.
Same evidence evolution has for its interpretation: None, or really, same facts, different interpretation. It's an interpretation.
How does your interpretation match up better with the evidence than the evolutionary interpretation?
I think it makes more sense to assume nature wouldn't allow for so much death and disease in the normal course of things as the ToE takes for granted, so it has to be a degeneration from a formerly healthy state, but as I said there's really no actual evidence to put one interpretation above the other.
Edited by Faith, : No reason given.

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


Message 500 of 1034 (758061)
05-19-2015 5:41 AM
Reply to: Message 476 by Admin
05-18-2015 7:04 AM


Re: No 'new functions'
Percy,
Is it normal in this thread that you get no answers on the questions you pose?
I get posts by Faith in which she endlessly addresses unimportant details leaving the core and import unanswered.
I came here from Topix in the hope I would be spared from dodging and evading but it is not different here.

This message is a reply to:
 Message 476 by Admin, posted 05-18-2015 7:04 AM Admin has replied

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


Message 501 of 1034 (758062)
05-19-2015 5:44 AM
Reply to: Message 465 by Admin
05-17-2015 2:25 PM


Re: Moderator Introduced Definitions
To move discussion forward I'd like to introduce ....
The move the discussion forward it would also and particularly very helpful when Faith starts to answer questions and address the things we put forward. In the first place.

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


Message 502 of 1034 (758064)
05-19-2015 6:05 AM
Reply to: Message 488 by Faith
05-18-2015 8:09 PM


Re: Replaced from other thread to here
Denisova writes:
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.
All those pesky scientist doing science, how annoying isn't it.
A very miserable argument frankly.
So basically you are saying that the whole scientific community within the life and earth sciences are collectively biased towards an empirically unsubstantiated paradigm?
YOU MUST BE KIDDING.
Are we here on a scientific forum??????????
In other words THERE IS NO empirical evidence for a deteriorating genome.
I tell you a little secret: THERE IS NO SUCH THING.
As you may not recall, I dedicated a part of one of my post to the work of John Sanford who actually tried to substantiate the claim for a deteriorating genome. Due to distortion of the work of others, a lack of own empirical evidence and severe flaws, this is basically made minced meat.
A lack of evidence does not need evidence.
So, OFF goes your propositions. They not only lack evidence but the instance where it tried to substantiate empirically, it failed.
I picked it up here and there from internet sites. I'm sure you can find it without my help.
NOW I will come back to my old saying: DO YOUR HOMEWORK.
I will NOT fulfil YOUR obligations here.
Denisova writes:
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.
I WON'T spell out the evidence FOUR YOUR CASE.
Please DO YOUR HOMEWORK.
"Well on to the next dodge and evading".

This message is a reply to:
 Message 488 by Faith, posted 05-18-2015 8:09 PM Faith has not replied

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


Message 503 of 1034 (758065)
05-19-2015 6:14 AM
Reply to: Message 476 by Admin
05-18-2015 7:04 AM


Complaint
Percy,
I complain about the dishonest way Faith is debating here.
See her Message 488.
What may I expect from the scientific import of the debate here?
As I wrote, i moved here from Topix in order to find decent scientific debate. It's hardly there.
Edited by Denisova, : No reason given.

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


Message 504 of 1034 (758066)
05-19-2015 6:16 AM
Reply to: Message 482 by Faith
05-18-2015 3:49 PM


Re: Moderator Introduced Definitions
All based on "suspecting" that it has a function you want to throw out a concept that makes good sense in the Flood theory.
A lack of evidence does not need evidence.
WHERE is the empirical evidence for your concept?
No evidence?
NEXT.

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 Message 482 by Faith, posted 05-18-2015 3:49 PM Faith has not replied

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


Message 505 of 1034 (758067)
05-19-2015 6:41 AM
Reply to: Message 483 by Dr Jack
05-18-2015 6:20 PM


Re: Moderator Introduced Definitions
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.
The problem here is that in debate - even within the scientific realm - but certainly on sources like Wikipedia and else, the concepts used are highly blurring.
We have:
- junk DNA
- non-coding DNA
- non-functional DNA
and even more terms of use, all hopelessly muddled as mere mutual synonyms.
If you google "non-functional", you mainly get articles with "non-coding" and vice versa.
Purely on semantic grounds, non-functional DNA would be the best term.
Because much of the DNA that is non-coding, actually STILL is functional, including the transcriptional and translational regulation of protein-coding sequences, centromeres, telomeres, scaffold attachment regions (SARs), genes for functional RNAs, and many others.
So, if geneticists say 98% of the human is "non-coding" that DOESN'T say it is "junk" as well.
ENCODE claimed that 76% of the human genome's noncoding DNA sequences were transcribed and that nearly half of the genome was in some way accessible to genetic regulatory proteins such as transcription factors. And off went the common people in utter chaos. Because not every DNA sequence that is transcribed or accessible by transcription factors is FUNCTIONAL.
So, yes, we still can say that the very most of our genome is non-functional or, as the ENCODE team neatly admitted "the larger proportion of genome with reproducible but low biochemical signal strength and less evolutionary conservation is challenging to parse between specific functions and biological noise". And THAT part already is 70% of the documented transcribed coverage.
After all the noise in the aftermath of the ENCODE debates, the human genome, according to ENCODE, is left with 12-15% "under functional constraint".
In my language this reads that ENCODE implies 75-78% of the human genome to be non-functional. You may call it "junk".
ENCODE still contends that the 12-15% figure may still be an underestimate.
Nothing wrong with that prediction.
Just let's see what their or other research will bring.
Let the facts speak!
Edited by Denisova, : Typo...
Edited by Denisova, : No reason given.

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


Message 506 of 1034 (758068)
05-19-2015 7:21 AM
Reply to: Message 487 by Faith
05-18-2015 7:58 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.
In the first place your answer does no relate to the point I made. I was not talking about junk DNA in that particular point. I was saying that in a population bottleneck it is impossible for the number of genes to drop dramatically.
Now let's examine what happens when the vast majority of a population gets extinct by such an alleged event like the Flood. You imply that the great majority of the genes are silenced or just passed away along with their owners, leaving only the small subpopulation of Noah and his crew with their subset of genes and alleles.
Such an extinction event will delete many alleles from the original, common genome, without any doubt. They will be GONE because all the unfortunate ones that died throughout the flood took those alleles with them to their inundated graves.
That means that there will be NO REMNANTS of THOSE alleles in the genomes of Noah and his crew. Noah can't just take away with him the alleles of OTHER persons who just died. Not even in the junk parts of his genome.
Now what about the genes themselves?
Are there genes within individuals who belong to the very same species that may not exist in other members of that species? Without any doubt they will. But not much I think. Because too much of non-shared genes will imply interspecies rather than intraspecies differences.
When, as you imply, most of the original genes are silenced by an extinction event, it must be those ones that disappeared along with their deceased owners. In that case, again, Noah and his crew just can't "take over" those genes. When their owners died due to the Flood, those genes will be lost for eternity.
In other words, junk DNA in extant humans CANNOT be explained by extinction events by definition and sheer logic.
Moreover, when MOST of the genes ("95% junk DNA") are lost, the original human genome must have comprised thousands of genes more than today. BECAUSE all these genes originally were in the individuals that were killed during the Flood, there must have been an ENORMOUS genetic divergence between the unhappy mortals that died and the surviving Noah crew. I don't think that ANY definition of a biological species can be compatible with such an ENORMOUS genetic diversity within just the very same species.
Edited by Denisova, : No reason given.
Edited by Denisova, : No reason given.
Edited by Denisova, : Language issues.

This message is a reply to:
 Message 487 by Faith, posted 05-18-2015 7:58 PM Faith has replied

Replies to this message:
 Message 519 by Faith, posted 05-19-2015 7:33 PM Denisova has replied
 Message 520 by Faith, posted 05-20-2015 5:50 AM Denisova has replied

  
Admin
Director
Posts: 12995
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.3


Message 507 of 1034 (758070)
05-19-2015 8:16 AM
Reply to: Message 480 by Faith
05-18-2015 3:28 PM


Re: No 'new functions'
Hi Faith,
I'm trying to maintain a moderator stance in this thread, so I will concentrate on resolving side issues, clarifying ambiguities, and keeping discussion on topic. Necessarily that means there are large portions of your reply that I cannot address because that would force me to cross the boundary from moderation into participation.
Faith writes:
All bacteria have to do to adapt is generate one mutation that is then copied many times and becomes the characteristic of a new population. It's pretty specialized at that point though, having lost all its other genetic information, which doesn't sound like it's even particularly a good thing for bacteria. I'm sure this is way too simplistic but I'll have to come back to it later if it's too far out of the ballpark.
In sexually reproducing creatures a mutation has to occur in the right place at the right time with the right characteristics even to get passed on, and then you'll only have this one mutation that can only affect the phenotype if it's dominant; if it's recessive it has to continue to get passed on until it pairs up with another copy of itself in order to be expressed in the phenotype. I don't think there is really any valid comparison with bacteria and in fact I think even if beneficial mutations did occur the chances of their contributing anything to the organism is pretty iffy. Again I'm sure this is way too simplistic but I'll have to come back to it some other time.
As you yourself seem to be aware when you say (twice) that you'll have to come back to these issues, you may be drawing conclusions prematurely. You and Denisova should discuss your concerns about bacteria.
OK, I'll spell it out. Death started at the Fall, and all the disease processes, but we can tell from the fact that people normally lived hundreds of years up until the Flood that there was still a great deal of vitality in the genome of human beings; and most likely animals too since they were also taken onto the ark in very small numbers, from which all species since then descended, showing enormous genetic diversity and vitality compared to now.
This is a good statement of your hypothesis, but it must be followed by the evidence supporting it. Only some aspects of this hypothesis are relevant to this thread, so regarding the above for this discussion you only need evidence of:
  • "A great deal of vitality in the genome of human beings" prior to around 4500 years ago.
  • "Enormous genetic diversity and vitality compared to now" among animals prior to around 4500 years ago.
  • A decline in diversity and vitality between 6500 and 4500 years ago that is related to "gene death."
Also, you've introduced the term "gene death" but only provided a vague idea of what it means. Back in Message 467 you said:
I believe junk DNA is genes that died over the millennia as a result of the Fall,...
...
The only thing I suggest is that genes died as a result of all those people and animals dying in the Flood,...
But in this message you've provided this additional information:
But the Flood was a one-time catastrophic death of human beings and animals both. a massive fulfillment of the effects of the Fall which would have wiped out not only the creatures but their genetic information.
So it seems that you are defining gene death as occurring in two different ways. One way is when a gene becomes junk DNA, and another way is when a gene is removed from a population. I think you are both overloading and misdefining the term, so I'm ruling that the term "gene death" should no longer be used in this thread and that the discussion should use existing standard terms in this way:
  • "Non-coding DNA" will be the term this thread will use to refer to DNA that doesn't code for proteins, what used to be called "junk DNA".
  • "Gene loss" will be the term this thread will use to refer to what happens when a gene is no longer part of a species genome.
But I barely have the hypothesis worked out and where is the evidence going to come from?
In science hypotheses are formed around incomplete evidence and represent the starting point of a scientific process of evidence gathering to support the hypothesis. Creation science differs from science in the way it forms hypotheses, usually basing them upon the Bible instead of upon evidence. Here at EvC Forum forming hypothesis in this way is perfectly acceptable, but it doesn't relieve one of responsibility for the evidence gathering step that must inevitably follow hypothesis formation.
You ask where the evidence is going to come from. I can't answer that question for you, but I certainly can't let discussion continue indefinitely with no evidence.
I think the fact that it's a reasonable interpretation of junk DNA that fits the known facts ought to be treated as evidence.
No, absolutely not. A scenario consistent with all evidence is a working hypothesis, not evidence.
So where is the evidence for the evolutionist interpretation of the fossil record? It's all interpretation of facts that are open to other interpretations.
Science is a consensus activity. Theories become accepted because a significant proportion of the relevant scientific community becomes convinced by a body of interwoven evidence. It is perfectly legitimate to offer alternative theories, but if they ignore significant evidence (e.g., radiometric dating) or worse make no sense (e.g., fossil ordering) then their persuasive ability will be fatally handicapped.
In other words you are asking me for a kind of evidence that isn't even available for evolution.
If you think people are making arguments that are missing evidence then it is your responsibility to call them on it. One person's lack of evidence is not an excuse for everyone else to start pushing ideas without evidence.
But you personally don't get to decide what is evidence and what is not, which is the issue I originally responded to. If I let you simply dismiss Denisova's evidence then you could argue that Denisova has no evidence. But I'm ruling that participants don't have the right to decide which evidence they'll accept and which they'll reject. Participants must address all the evidence.
You're perfectly within your right to argue that evidence shouldn't be considered because it isn't relevant, which is what you're attempting to do with the Lenski bacterial evidence, but what comes across most in this attempt is that, as you said yourself, you may not have examined the issue closely enough yet.
Based on bogus dates but yes.
This is something you must establish through evidence, not simply declare.
So if you want to demand evidence of a kind I can't produce and a coherent statement of an alternative hypothesis and different system of interpretations isn't enough I'll have to leave.
Everyone is in the same boat. Everyone can argue their hypothesis using the evidence supporting it.

--Percy
EvC Forum Director

This message is a reply to:
 Message 480 by Faith, posted 05-18-2015 3:28 PM Faith has not replied

  
Admin
Director
Posts: 12995
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.3


Message 508 of 1034 (758071)
05-19-2015 8:25 AM
Reply to: Message 500 by Denisova
05-19-2015 5:41 AM


Re: No 'new functions'
Hi Denisova,
I understand and share your concerns and am trying to address them.

--Percy
EvC Forum Director

This message is a reply to:
 Message 500 by Denisova, posted 05-19-2015 5:41 AM Denisova has not replied

  
Admin
Director
Posts: 12995
From: EvC Forum
Joined: 06-14-2002
Member Rating: 2.3


Message 509 of 1034 (758072)
05-19-2015 8:39 AM
Reply to: Message 487 by Faith
05-18-2015 7:58 PM


Re: Moderator Introduced Definitions
Faith writes:
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 know you posted this before I issued my ruling in Message 507, but I just wanted to issue a reminder to everyone since that message was kind of long and it could have been missed.
I have ruled against using the term "gene death," and of course that means any related terms are also off limits, such as "dead genes." The term that should be used is "non-coding DNA," and any argument that some thousands of years ago species experienced a process of genes becoming non-coding DNA must be accompanied by evidence.

--Percy
EvC Forum Director

This message is a reply to:
 Message 487 by Faith, posted 05-18-2015 7:58 PM Faith has replied

Replies to this message:
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JonF
Member (Idle past 167 days)
Posts: 6174
Joined: 06-23-2003


(1)
Message 510 of 1034 (758073)
05-19-2015 8:40 AM
Reply to: Message 500 by Denisova
05-19-2015 5:41 AM


Re: No 'new functions'
Is it normal in this thread that you get no answers on the questions you pose?
It's extremely common in any online discussion between creationists and the reality-based community. Percy tries harder to fix the problem than most online moderators, but most of what he does has no effect.

This message is a reply to:
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