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Author Topic:   Evolution Requires Reduction in Genetic Diversity
Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 384 of 1034 (757612)
05-11-2015 1:33 PM
Reply to: Message 370 by Faith
05-19-2014 12:28 PM


Re: No 'new functions'
I don't believe mutations contribute anything at all to normal variation/microevolution, except possibly the very rare fluke when a mistake in replication happens to reproduce a sequence that revives a formerly lost function. But normal variation is the result of normal sexual recombination of built-in genetic possibilities. I know it's hard to think along these lines if you are used to thinking in terms of mutations, but this is the way it used to be understood and they were right.
Wow, I do hope that you just throw major parts of modern genetics into the litter box.
Anyway, it is not true as an abundance of experiments showed.
Let's take one of those: the long-term Lenski experiment on E. coli.
Sources:
- http://myxo.css.msu.edu/ecoli/, and:
- Just a moment...
Lenski took E. coli bacteria and bred them in 12 separate subpopulations (for reasons of proper experimental design). Some strains were exposed to deprivation of their normal energy source, glucose - almost to starvation. But they also were exposed to another energy source in the same time - citric acid. Normally E. coli bacteria cannot process citric acid in aerobic conditions.
Somewhere around the 30,000th generation, some strains were able to process citric acid in aerobic conditions. While Lenski's team kept a frozen sample of each generation - their "evolutionary history", they were able to trace back the exact differences in the genome.
Some 100 genes had changed their expression.
That means what is says: CHANGED.
Intermezzo:
But normal variation is the result of normal sexual recombination of built-in genetic possibilities. I know it's hard to think along these lines if you are used to thinking in terms of mutations, but this is the way it used to be understood and they were right.
I DO hope you know that bacteria don't reproduce sexually.
Hence: the changes in the gene expression in the E. coli bacteria in Lenski's experiment were entirely due to CHANGE in the base pair sequences. And that was exactly what Lenski observed and he also traced those mutations back to the exact loci and spelled out the exact altered base pair sequences on the CATG level.
Moreover, somewhere else you addressed the problem how a very small population of just 8 persons (after the Flood) could have produced the currently observed, pretty extensive genetic variance in humans by condoning that it came from the redundancy of junk DNA.
Let's take skin colour. Skin colour in humans in controlled by several genes. In order to obtain the current variation in skin colour out of 8 persons from the same genetic background, some junk DNA must have been CHANGED - well, according to *your* scenario. Because in that scenario non-functional DNA sequences allegedly became functional (coding for melatonin, pheomelanin or eumelanin.
But sexual reproduction DOES NOT change alleles.
In non-random mating they can change the frequency of alleles but it cannot introduce genetic CHANGE by altering junk DNA sequences into functional genes.
Already Mendel realized that.
Each allele in a heterozygote is EITHER from the mother OR from the father and is rendered UNCHANGED. So Mendelian genetics is not a matter of blending alleles but of segregated sorting. I thought we knew this for 150 years - the inheritance patterns of traits as observed make no sense in a blending model.

This message is a reply to:
 Message 370 by Faith, posted 05-19-2014 12:28 PM Faith has replied

Replies to this message:
 Message 385 by Faith, posted 05-11-2015 7:16 PM Denisova has replied
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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


(1)
Message 389 of 1034 (757705)
05-12-2015 10:27 AM
Reply to: Message 387 by Admin
05-12-2015 9:11 AM


Re: No 'new functions'
I DO hope you know that bacteria don't reproduce sexually.
True in a strict sense, but they do engage in sex, the technical term is conjugation.
I know but this is not the kind of sexual reproduction Faith was referring to nor is it relevant for his ideas about sexual recombination that allegedly lead to genetic change conceived by Faith.
I'm afraid when I would incorporate such details, post are getting very long and too detailed. Because there are constantly many more such points crossing my mind when writing my posts!
But sexual reproduction DOES NOT change alleles.
It depends upon how you define sexual reproduction. If it's defined as extending from the production of gametes through fertilization then since a mutation could occur during that process it must therefore be acknowledged that sexual reproduction can change alleles.
Yes but Faith was talking about the effects of Mendelian processes and excludes himself the possibility of mutations having any effect on a gain in genetic diversity.
Maybe I better had applied the term "sexual recombination" instead of "sexual reproduction" here.

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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 390 of 1034 (757709)
05-12-2015 11:00 AM
Reply to: Message 385 by Faith
05-11-2015 7:16 PM


Re: No 'new functions'
Sorry, I don't accept anything about bacterial genetics (your E. coli example) as applying in this discussion. You have to use examples from sexually reproducing creatures.
I thought we were discussing genetic and evolutionary PROCESSES here instead of the genetics of particular life forms.
Now I mentioned a case of clear genetic innovation in E. coli bacteria involving genetic mutations being sorted out by the process of natural selection and leading to the emergence of a new trait.
Do you think that the genomes of sexually reproducing species all of a sudden do not experience genetic mutations? And are sexually reproducing species not exposed to selective pressures due to natural selection anymore?
As I explained to you, EXACTLY because of a lack of Mendelian processes of sexual recombination in bacteria, they are a PERFECT example of gain in genetic diversity in the ABSENCE of such processes. Thus proving you wrong on your claim that genetic diversification is impossible to be caused by them.
Nothing "changed" in anything I said. I believe junk DNA is genes that died over the millennia as a result of the Fall, most as a result of the Flood which was a very severe bottleneck. If about 95% of the genome is junk DNA today, a rough guess would be that maybe about .0003% was junk DNA at the time of the Flood. So it just seems likely that there were even more genes governing skin color and every other variable trait as well.
Please, respond to the things I actually say.
Yes, I know that you think that genes died over the course of time and turned them into junk DNA.
But I was saying here that in order to account for a gain in alleles of the very same genes to account for a difference of 59 - 16 = 43 alleles between the maximum number possibly present in Noah's crew and the number in the extant human genome, you have 2 scenario's:
1. genetic mutation and natural selection leading to new alleles, or:
2. those new alleles emerging from junk DNA - which ALSO implies genetic mutations to accomplish that.
If you know any OTHER scenario, let me know.
Already Mendel realized that.
Each allele in a heterozygote is EITHER from the mother OR from the father and is rendered UNCHANGED. So Mendelian genetics is not a matter of blending alleles but of segregated sorting. I thought we knew this for 150 years - the inheritance patterns of traits as observed make no sense in a blending model.
Again I don't see what this has to do with anything I've said. But as far as blending goes, allleles don't blend but apparently the effect of so many genes for variations in skin color pretty much amounts to a blending of the traits themselves. You get degrees of lightness and darkness as well as combinations of shades of yellow, red and blue.
Well, to put it just quit and simple: according to Mendelian processes, sexual recombination per definition cannot lead to new alleles. In Mendelian processes, which govern sexual recombination, alleles are not added or changed or deleted. They are only - as the word says itself, recombined. They are reshuffled. A child may inherit one allele of the same gene from its mother and the other from its father or both alleles from its mother or from its father. No alleles are added or deleted or altered. the child NEVER inherit the same allele party from its father and the other part from its mother. It's the WHOLE allele from the father or the WHOLE allele from its mother. No "mixing" of alleles here.
believe junk DNA is genes that died over the millennia as a result of the Fall, most as a result of the Flood which was a very severe bottleneck. If about 95% of the genome is junk DNA today, a rough guess would be that maybe about .0003% was junk DNA at the time of the Flood.
...
The only thing I suggest is that genes died as a result of all those people and animals dying in the Flood, whose traits were lost to the species and therefore the alleles for those traits, so the genes just died and remain in the genome as corpses.
I think there was no such flood but that would be exceeding the scope of the actual thread so let's concentrate on genome again.
So you believe that the genome lost much of its genetic diversity.
Do you, again, also happen to have empirical evidence for that?
I already offered you some possible sources for that in another post to do the comparison.
Now the effect of a genetic bottleneck on the genome of a species (whether it is caused by the Biblical flood or not) is that a very small subpopulation out of the total gene pool is retained and the rest discarded.
Now explain please:
1. did the genome lost GENES or ALLELES by those being turned into junk DNA or BOTH?
2. if genes, which traits were lost than? Because your position implies that an astonishing number (accounting for at least a substantial part of the current 95% junk DNA) of different traits must have been lost.
3. if alleles, I shall have to remind that you already had severe difficulties explaining how Adam and Eve both could only have a maximum of 4 alleles and the Noah's crew a max. of 16, while in extant human populations, some genes can have as much as 59 alleles. So alleles were added since Adam and Eve or since the Deluge. And you are SUBTRACTING them from the initial genome.
Edited by Denisova, : Forgot something.
Edited by Denisova, : Correcting a wrong number.

This message is a reply to:
 Message 385 by Faith, posted 05-11-2015 7:16 PM Faith has replied

Replies to this message:
 Message 471 by Faith, posted 05-17-2015 6:58 PM Denisova has replied

  
Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 402 of 1034 (757761)
05-13-2015 4:56 AM
Reply to: Message 393 by Faith
05-12-2015 6:59 PM


Re: genetic diversity
As I've said a bazillion times, the PROCESSES of evolution REQUIRE the reduction of genetic diversity, doesn't matter how you get the diversity or when, IF YOU ARE GETTING NEW TRAITS you are also getting a reduction in genetic diversity WHERE THAT IS HAPPENING. Where it's not happening you can have lots of genetic diversity. It's either genetic diversity or microevolution, take your pick.
In that case you might bother to address the points I made on this in my previous 2-3 posts. Until now seen nothing yet.

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 Message 393 by Faith, posted 05-12-2015 6:59 PM Faith has not replied

  
Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 403 of 1034 (757762)
05-13-2015 5:24 AM
Reply to: Message 396 by Coyote
05-12-2015 10:00 PM


Re: genetic diversity
It does when you believe in a mythical Fall from a mythical perfect state some 6,000 years ago.
I highly doubt that as well!
The max. number of alleles of any gene in a population of 8 people of whom 3 individuals are sons of 2 other members is 10 (Noah, his wife, their 3 sons and those one's wives).
In extant human populations the number of alleles may as much as be 59 for particular genes.
In other words, since the Flood at least as much as 49 alleles must have been added to the human genome for such genes. and there are many genes with more than 10 alleles.
Hence, one would expect the genetic diversity to increase since the Flood. Also NEW alleles are to be explained.
But Faith contends the genetic diversity declined since the Flood.
Her problems are getting worse when you take Adam and Eve into account, whose genomes combined a maximum of 4 alleles for each gene.
A flood 4,500 years ago implies evolution at an outrageous rate.
Edited by Denisova, : Didn't know Faith was a she!

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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 415 of 1034 (757811)
05-14-2015 12:13 PM
Reply to: Message 410 by Dr Adequate
05-13-2015 6:48 PM


Re: genetic diversity
Interesting point. Now, looking at the great variety of domestic sheep
would we really say that O. aries has less diversity than O. orientalis?
Let's go back to the very core of evolution theory.
Basically, evolution needs a gain in biodiversity otherwise it can't explain the emergence of, say, multicellular life out of unicellular life or the vast diversification in all kingdoms of life into the taxes we see today or for that matter in any past era of the natural history of the earth.
This gain in biodiversity evidently also implies an increase in genetic diversification. The mere fact that there may be examples of speciation accompanied by a decrease in genetic diversity does not detract anything from this basic understanding.
Breeding by humans is just application of evolutionary mechanisms: selection acting on genetic variation. The most important difference between breeding and nature is the type of selective criteria - in breeding it's things like the looks, hunting traits or meatiness, in nature it's survival and/or reproduction chances.
Now O. aries indeed has more genetic diversity than O. orientalis. The variety in phenotype in your picture tells the story.
And sheep indeed perfectly show how it works: first more genetic diversity emerges, reflecting the selective criteria.
Of course there's also genetic drift which occurs irrespective of any selective pressure. Genetic drift can conduce to speciation by allowing the accumulation of non-adaptive mutations that can facilitate population subdivision. Genetic drift may contribute to speciation, if after a genetic bottleneck the resulting small group does survive.
That being said, I refocus on adaptive processes.
What your picture of the variety in O. aries shows is that the elementary requirement of evolution theory has been met: genetic diversity has been added. When one of the breeds would continue to diverge genetically from the other breeds or from O. orientalis to the extent genetic isolation occurs, we have speciation.
Of course the definition of "species" is multi-layered. I suggest that we THEREFORE should confine ourselves to the definition of genetic isolation. I don't think excluding other aspects or criteria for speciation does not jeopardize or blur the essence of the debate.
"It's only all about sexual recombination of existing traits since Adam and Eve"
Now here starts one of the major disagreements with Faith. She says that there is NO genetic INNOVATION occurring in sheep in the first place. Faith contends it's only all about reshuffling existing alleles through sexual recombination (thus basically Mendelian genetics) that were present from the very beginning (Adam and Eve). So, you can show her all kinds of pictures of sheep breeds - she just won't be much impressed.
Now to my opinion her flaws here are:
  • if you count the maximum number of alleles possible in Adam and Eve per gene, it would be 4. In that case, without any genetic innovation - and that's exactly Faith's position - there also would be no more than 4 alleles per genes maximally present in Noah's crew. And, as no genetic innovation is allowed in her scenario, today we would stuck with a maximum of 4 alleles per gene as well. But there is a bunch of genes in the current human genome having far more than 4 alleles.
  • So, plain observation learns that alleles must have been added since the days of Adam and Eve. The mere fact that some traits are related to more than one gene does not change anything to this simple observation.
  • In sexual recombination nothing not a single allele is altered. Alleles in sexual combination do not blend but are sorted out intact. In Faith's scenario the increase from 4 alleles per gene (Adam and Eve) up to 59 ones per some genes in the extant human genome cannot be explained in Faith's scenario.
  • I tried to investigate the possibility of those added alleles to emerge from junk DNA. But that's only possible when the DNA sequence of the pseudogenes is altered. Again that would imply mutations but that again is excluded from Faith's equations.
  • Faith says that mutations are only neutral or deleterious causing the initial genetic diversity to shrink to its current 5%. Which is an incorrect figure but even when it differs, there is still junk DNA and the exact figure needs not to be discussed here to discuss the principle points. Her contention implies that most of the genes and or alleles form the initial genome mus have been rendered into pseudogenes.
  • First of all, LESS genetic diversity is not what we observe as the number of alleles increased in many genes as indicated above. What we actually need is a gain in genetic diversity. But Faith is proclaiming an - enormous - LOSS instead.
  • When such a major parts of the genes and alleles had been lost and turned into junk DNA, I was wondering what all the traits were those genes were coding for.
  • Any claim needs to be backed up by empirical evidence. I offered some solutions to provide such evidence, like the genome sequences of ancient hominids that are known (H. Denisova, H. Neanderthalis, H. sapiens, H. Heidelbergensis). Those provide some means to compare among each other as well as with the extant human genome. Such comparisons have been performed, by Pbo and others. Until Faith does not come up with empirical evidence, to me only this counts: a lack of empirical evidence does not need evidence.
  • The impossibility for genetic mutations to produce genetic change that brings more fitness, is directly demonstrated by me by Lenski's E. coli experiment. As I understood, more examples are provided by others here. In other words: genetic innovation is proved in the lab. That also does not need further evidence.

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 Message 410 by Dr Adequate, posted 05-13-2015 6:48 PM Dr Adequate has not replied

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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 416 of 1034 (757813)
05-14-2015 12:21 PM
Reply to: Message 408 by Faith
05-13-2015 12:08 PM


Replaced from other thread to here
The snark was because you didn't answer the reasonable questions and produced some 101 genetic information not asked for.
And yet, you STILL didn't answer the main questions.
THAN, not "then." [THAN the current genomes of extant humans."] This is a HORRIBLE grammatical error people are making these days.
Why this snark?
You are not my language teacher.
BTW. it is "diversity" and not "diversithy".
People are making a lot of awful spelling errors these days indeed.
Moreover, English is not my native language so now and then I will make some mistake. Get used to it.
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?
It's a reasoned guess that fits the biblical facts and also observations about both mutations and the loss of genetic diversity in evolutionary processes.
The bible does not comply to any criterion of scientific methodology and epistemology. You might as well had referred to the Rig Veda or any other random Bronze age mythology book. I asked you for empirical evidence. That is, observational evidence. We are on a scientific forum here.
Neither did I ask for your reasonable guesses but for observational, empirical evidence. Even reasonable guesses are just assertions.
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?
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.
Since you are bound to get the dates wrong there's really little point in arguing as you suggest above. And forget mitochondrial DNA if that's part of your argument.
Dates??????
WHERE did I mention dates??????
I neatly pointed you out to the all kinds of ancient genetic information we have in hominid specimens as possible sources for your evidence.
We are not discussing dating but your claim that genomes have lost genetic diversity. Stay tuned please.
And I didn't meant "do your homework" to denigrate you, I just asked "do your homework", which, as a non-native speaker of English, I thought it is also to be understood just as a saying "May I recommend that you cut to the chase and present your argument for this now" (which were YOUR words).
So, let's use your wording if that feels better: "May I recommend that you cut to the chase and present your evidence now"?
You've got all you're getting, my good reasoning. If you object then go argue with someone else.
I DO object your reasoning when I consider it to be incorrect, that's part of normal debating. In this case it makes no sense to start a new discussion line when the initial points are not resolved. It makes no sense to start to discuss causes of loss in genetic diversity when we do not even agree on WHETHER it occurred and HOW precisely.
AND I was not only asking for good reasoning but also for empirical evidence.

This message is a reply to:
 Message 408 by Faith, posted 05-13-2015 12:08 PM Faith has replied

Replies to this message:
 Message 488 by Faith, posted 05-18-2015 8:09 PM Denisova has replied

  
Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 417 of 1034 (757814)
05-14-2015 12:25 PM
Reply to: Message 408 by Faith
05-13-2015 12:08 PM


Replaced from other thread to here
The question can't possibly require more than a brief answer. If you just want to drive me off this thread with your attitude, say so and I'll go or just ignore your posts.
Now let me clarify.
The *topic* here was your claim that evolution theory requires a gain in genetic diversity and that subpopulations split into new species have less genetic diversity.
I answered this is a misinterpretation of evolution theory, which obliges me to shortly explain it.
Then you started to discuss the WHOLE of evolution theory in all its aspects. But the topic here is not the validity of evolution theory. The topic here is your claim. EVEN when you later manage to prove evolution theory to be incorrect on all those OTHER aspects, STILL you have to represent its contentions CORRECTLY in debate.
So it makes no sense to discuss the whole of evolution theory when ONLY your representation on genetic diversity is subject of this debate.
Otherwise the debate hives off in 100 directions and mostly this ends up in nothing.
That's all and that's why I wrote "I don't think I will go to explain the whole of biology and genetics to you. I don't think this suits the purpose of this forum here".
Which you utterly failed to demonstrate in your last post although you declared victory.
Well indeed it's the subject here!
what's wrong to emphasize one's assessment?
Just to be clear, does "variance" mean "diversity?"
Well I try to avoid repetitive use of the same words in the same sentence or paragraph. So yes they are used as synonyms here.
Sorry, I just proved that it is.
Not that I know.
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.
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.
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.
5. In other words, the evolutionary requirement for a gain in genetic diversity has been met. A POSSIBLE loss of genetic diversity in any of the sub-genomes AFTER the split is NOT an evolutionary requirement. 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.
The OBJECT of evolution theory is to explain speciation. When speciation occurs, there MUST be an initial gain in genetic diversity. >>>This requirement has been met<<<. 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.
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.
None of these points but #1. were addressed by you.
Edited by Denisova, : No reason given.

This message is a reply to:
 Message 408 by Faith, posted 05-13-2015 12:08 PM Faith has replied

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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 423 of 1034 (757850)
05-14-2015 3:39 PM
Reply to: Message 418 by Faith
05-14-2015 2:03 PM


Re: genetic diversity
Hope you're doing well again!
Because, again, my argument is that you only get new breeds or phenotypes by losing the genetic material for other breeds and phenotypes. I'd be SO happy if you actually GOT the argument and had a really GOOD objection to it instead of these typical straw man objections.
I think your argument is very well understood.
And you are wrong because you get new breeds NOT from losing genetic material for other breeds and phenotypes.
You get new breeds because of the OBSERVABLE GAIN in genetic diversity as shown by the picture of the O. aries variation which ALL comes from breeding the very same ancestor, O. orientalis.
That picture shows, all to see before our own eyes, that genetic diversity has INCREASED. Because:
1. ONCE you only had one phenotype, O. orientalis
2. NOW we have MANY phenotypes
3. more phenotype variation means more genetic diversity.
It is hardly imaginable how LOSING genetic material could cause MORE phenotype variation.
You are comparing one breed with the others.
WE are comparing the ancestral O. orientalis with its very low phenotype differences with the many breeds of O. aries, its descendants, with their GREATLY increased phenotype variation.
YOU compare descendant breeds mutually, WE compare the ancestor with its descendant(s). EVOLUTION is about how ancestral species produce descendant breeds that may eventually split up in separate species. This is even the very study object of evolution theory, the thing it tries to explain. Evolution theory is NOT about the relationships between breeds as such. It does so by contending that the genetic variation increases first (I leave the exceptions what they are for this moment) and then speciation occurs.
The mere fact that the breeds (or later daughter species) "take away" only a part of the total genetic diversity is NO problem for evolution theory, it was NOT excluded from its postulates. The gain in genetic diversity which is, with exceptions, crucial for evolution is assumed to occur BETWEEN ANCESTOR AND DESCENDANTS, not the distribution of the total genetic diversity among breeds and daughter species.
Edited by Denisova, : Fixed dbCodes.

This message is a reply to:
 Message 418 by Faith, posted 05-14-2015 2:03 PM Faith has replied

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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 424 of 1034 (757852)
05-14-2015 3:52 PM
Reply to: Message 422 by Faith
05-14-2015 2:42 PM


Re: genetic diversity
Your dating methods are highly suspect, and you really haven't "shown" me evidence. Go out and collect some ring species and read the DNA of the populations at different points around the ring. That's where I think the evidence should be.
First of all, the ring species cases do NOT need evidence from their DNA.
The mere fact that all subspecies are able to interbreed among each other but only two, suffices completely.
It is even, with out current understanding of genetics, not even possible to show genetic isolation by examining the DNA. As far as I know the BEST way to assess it is just observing if two subspecies are still interbreeding and/or produce valid offspring when they still were mating.
So, basically, this argument is a red herring.
Secondly, EVEN if your opponent was proven to fail to back up his own claims, does NOT dismiss you from your own obligations.

This message is a reply to:
 Message 422 by Faith, posted 05-14-2015 2:42 PM Faith has replied

Replies to this message:
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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 430 of 1034 (757870)
05-15-2015 3:59 AM
Reply to: Message 425 by Faith
05-14-2015 3:55 PM


Re: genetic diversity
I'm arguing that new phenotypes require the loss of GENETIC diversity. There may still be lots of "biodiversity" possible, if you mean by that phenotypic diversity, but each new breed or race formed from it requires a reduction of genetic diversity. Evolution NEEDS a gain in genetic diversity, that's why if in fact its own processes that lead to new breeds and races require a reduction instead, evolution is not possible.
This is well addressed by me in other posts of which I an still awaiting your answer.
Depends on what you mean by "diversification." If what you mean is that you are getting new combinations of genes/alleles from new gene/allele frequencies in new subpopulations, this is true, but that's not the same thing as genetic diversity, which is what I've been talking about. Genetic diversity is basically the genetic variability /diversity within a population, and this is what gets reduced when a new subpopulation forms from relatively few individuals.
The only possible source of an increase in genetic diversity, apart from the remixing of formerly separated populations, is mutation, which the ToE requires as the source of all genetic material, which I'm of course disputing.
Indeed.
Genetic innovation by mutations, acted upon by natural selection, has been observed and an example of it has been provided by me. I a still awaiting your answer on that.
And as I also keep arguing, even if mutation really did accomplish this, any subpopulation that develops new traits or phenotypes can only do it with the reduction of genetic variability in its own collective genome. Whatever the source of the original diversity the formation of new breeds or races requires the elimination from that subpopulation of whatever doesn't contribute to the new breed or race.
This is well addressed by me in other posts of which I an still awaiting your answer.
"First more genetic diversity emerges." From where would it come? What would produce it?
Read your own answer above on it - and my response. I am still awaiting your answer on that.
And what do you mean "reflecting the selective criteria?" Can't be. First some number of sheep get separated from the original wild population, in this case by human selection. There's nothing different in their general appearance at first, but over time as they inbreed among themselves apart from the original population new traits will begin to emerge, and this is because of the new set of gene frequencies they possess in contrast with those of the original population. (Depending on how big a proportion of sheep were separated out of the original population, that original population could also undergo the development of new traits over time because of its own changed gene frequencies as a result of the split.) The new gene frequencies, which means more of some alleles, fewer of others by comparison with the original population, and even the complete absence of some (which nevertheless remain in the other population) bring out a new set of traits in the subpopulation, which over some time of inbreeding among the individuals get merged into a new breed with a new overall appearance. (Domestic breeds traditionally started with many fewer individuals but the principles are the same).
Your mantra again.
This is well addressed by me in other posts of which I am still awaiting your answer.
The rest of your answers are addressing details which are not essential to the points made by me.
Edited by Denisova, : No reason given.

This message is a reply to:
 Message 425 by Faith, posted 05-14-2015 3:55 PM Faith has replied

Replies to this message:
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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


(1)
Message 431 of 1034 (757872)
05-15-2015 5:23 AM
Reply to: Message 428 by Faith
05-14-2015 7:44 PM


Re: genetic diversity -- rest of Denisova
Apparently you think the many different breeds of domestic sheep show that "genetic diversity has been added." But as usual this is confusing phenotypic with genetic diversity. Lots of new breeds (phenotypes) yes, but no evidence whatever of increased genetic diversity, which, as I've been arguing forever, is not how you get new breeds / phenotypes. That takes reducing genetic diversity. So all those breeds of sheep each has its own genome with LESS genetic diversity in it than the original population or the other breeds combined. Of necessity.
The evidence of genetic innovation has been provided. By others here. They all complain you won't address it. But let's confine myself to the evidence I brought in myself - the Lenski experiment. You just conveniently discarded it. Without any sound argument. But STILL it is neatly demonstrating how mutations bring more genetic variance, which is sorted out by natural selection, ending up in new genetic traits and a different phenotype. Same DNA (biochemically spoken), same kind of mutations (radiation, chemical mutagens, haphazard copying errors), same selective pressure (food sources changing, food deprivation).
Until you provide sound arguments why this example should be discarded within the context of the ongoing debate, I will continue to bring it up - and abide your answers.
Note, important, that Lenski started with a monoclonal population.
The most important changes (in the phenotype) in Lenski's E. coli bacteria were:
  • larger cell volume
  • lower population density
  • in first instance they got specialised in glucose
  • later metabolism of citric acid in aerobic conditions emerged.
Now, Lenski performed a genomic analysis on the Cit+ population (the one that managed to evolve metabolism of citric acid). See Blount ZD, Barrick JE, Davidson CJ, Lenski RE (2012-09-27). "Genomic analysis of a key innovation in an experimental Escherichia coli population". Nature 489 (7417): 513—518.
Lenski's team sequenced the entire genomes of 29 clones isolated and stored from various time points in the subpopulation that eventually gave rise to Cit+, using them to reconstruct the phylogenetic history of the subpopulation.
He writes: "The evolution of the Cit+ trait involved three successive processes: potentiation, actualization, and refinement." he elaborates on the actualisation step. He observed that a gene duplication had occurred that amplified citrate transport. One reason that E. coli cannot grow aerobically on citrate is its inability to transport citrate.
Lenski then continues: "Amplification mutations can alter the spatial relationship between structural genes and regulatory elements, potentially causing altered regulation and novel traits" - as observed in other studies. But that's is not enough to conclude this also happened here. so he tested it experimentally. And indeed it was confirmed.
Then he proceeded with the Cit+ refinement stage in the same manner.
In this study, Lenki painstakingly identifies and analyses and enumerates the different genes that changed expression, he described the gene that was duplicated and exactly depicts the observed changes in its arrangement:
Just plain genetic innovation, introduced by mutations and fixed into the genome by natural selection.
And NOTE that bacteria do not reproduce sexually. So no allowance for your allele mixing and frequency changes in a deteriorating genome scenario.
Now Percy mentioned bacterial conjugation as a way bacteria exchange genetic material. But this is not relevant here because Lenski started with a monoclonal population. Those bacteria may conjugate as much as they like - but basically they only will exchange the same, unchanged DNA chunks (unless that DNA DID change - and that's only possible by mutations in their case).
And I am still awaiting your evidence of the super genome of Adam and Eve. Or evidence for a loss in genetic evidence in the last 6,500 years (Adam and Eve) or the last 4,500 years (the Deluge).
A lack of evidence does not need further evidence.
Denisova writes:
2. So, plain observation learns that alleles must have been added since the days of Adam and Eve. The mere fact that some traits are related to more than one gene does not change anything to this simple observation.
I agree, but it does depend on the quality of the extra "alleles" as Isaid.
Alleles being added means a gain in genetic diversity.
There's no way around this.
The "quality" thing is only relevant when you have empirical evidence for it. Until then, it will be just ignored by me as an argument.
Edited by Denisova, : No reason given.
Edited by Denisova, : No reason given.

This message is a reply to:
 Message 428 by Faith, posted 05-14-2015 7:44 PM Faith has not replied

Replies to this message:
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Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 447 of 1034 (757913)
05-16-2015 7:18 AM
Reply to: Message 438 by Faith
05-15-2015 6:11 PM


Re: genetic diversity
But it does. The fact that you don't see how this happens shows you continue not to get it. I've said my argument is counterintuitive and it is.
For purpose of feedback I shall shortly represent your position as I conceive it:
  • no genetic innovation is possible but genetic deterioration is happening all the time instead, that's why we see junk DNA today - all old rubble from old worn and torn genes
  • when we see phenotype diversification occurring, this is therefore not caused by genetic innovations but by activating genetic diversity that's still left in the genomes by selective processes
  • as no genetic innovation is possible, every split into different breeds or subspecies causes genetic depletion among those, every single breed or subspecies only taking away a subset of the original genome.
You can't get a breed or new subspecies by adding genetic diversity but even if you could, where is your increase in diversity going to come from? As I say above mutation is the only possible source and it's completely insufficient for the job, too slow and with too many negative results.
Where is the increase in diversity coming from?
Explained numerous times by now and not addressed by you.
See the E. coli experiment which plainly demonstrates how:
  • mutations ARE bringing genetic diversity, completely unravelled by Lenski how on the molecular and gene level
  • it took about 31,000 generations and some 19 years to accomplish that. Not very slow I think
  • negative results do not matter. they are weeded out by natural selection.
Yes we can get a breed or new subspecies by adding genetic diversity. Because such genetic change due to mutations (plus natural selection) as observed in Lenski's experiment, will cumulate when further environmental changes occur. When those changes accumulate beyond the species' boundaries, that is, when reproductive and genetic isolation occurs, speciation takes place.
And that's what we exactly observe in the fossil record.
Now, I know you have problems with radiometric dating, so let's only take the fossil record as it pops up as it is. Even then you observe the distinct geological formations and strata to differ enormously in the particular fossil record they contain. Sheer logic says that lower strata found beneath those ones more aloft are older.
In other words, the geological formations show that life changed throughout the course of the natural history of life. Moreover, this change does not attest any loss in complexity.
For instance, in the Early Cambrian the following life forms were completely absent:
- fish
- amphibians
- reptiles
- dinosaurs
- mammals
- birds
- all land plants.
See the listing of the subsequent, geological strata of the Grand Canyon as depicted on the website of the Old Earth Ministries: Creation Science Rebuttals, Stratigraphy and the Young Earth Global Flood Model, Part 1. There you see the Early Cambrian is situated below a pile of ~880 metres of strata.
There is no way you can explain the forming of completely new animal and plant groups without genetic innovation. We are talking here about taxonomic phyla, clades, classes and the like, not about breeds. And note again, I didn't need any dating technique. I only draw the only logical conclusion from layered superposition of geological strata: a sedimentary rock layer in a tectonically undisturbed sequence is younger than the one beneath it and older than the one above it.
In the lowest strata of the Grand Canyon, the ones below the Early Cambrian, only contain trace fossils and stromatolites. That is, only unicellular life.
In other words, not only the geological strata are stratified, but the fossil record itself as well.
No, I am speaking of what it takes to form a breed from an original larger population. I'm not comparing the breeds with each other, I'm comparing each with the original population from which they formed from a smaller pool of gene frequencies.
This point is well understood by me and others here - as far as I can see - and addressed accordingly. I am still awaiting your answers on:
  • We see a gain in the number of alleles per gene by all means maximal possible in Adam & Eve or Noah's crew, compared with the number per gene we observe in extant human genomes today
  • we do not see a loss in genetic diversity of the original ancestral genome but it being distributed among the breeds
  • genetic innovation has experimentally demonstrated.
The mere fact that the breeds (or later daughter species) "take away" only a part of the total genetic diversity is NO problem for evolution theory, it was NOT excluded from its postulates. The gain in genetic diversity which is, with exceptions, crucial for evolution is assumed to occur BETWEEN ANCESTOR AND DESCENDANTS, not the distribution of the total genetic diversity among breeds and daughter species.
First, there's no possible way it could happen, as discussed above, and second, it isn't needed. An ancestral species with high genetic diversity, which was obviously the case with O. orientalis, can bear many population splits forming new subspecies with their attendant loss of diversity. Even many breeds developing from those breeds may be possible if the original genetic diversity was quite high.
Yes there is a way it can happen, see the Lenski experiment example.
Also, I MUST happen because otherwise we can't explain the vast transitions in life's history as observed in the fossil record. We NEED it to explain the observed stratigraphy of the fossil record.
The empirical evidence for such genetic innovation as provided, the Lenski experiment, is YET to be addressed by you.
The higher genetic diversity in ancestral genomes is YET to be backed by you through observational, empirical evidence.
The supposed loss in genetic diversity in species' genomes is YET to be backed by you through observational, empirical evidence. There are examples of ancient genomes of H. Neanderthalis, H. Heidelbergensis, H. Denisova and archaic H. sapiens as well, all sequenced by now, which could provide the material needed for that.

This message is a reply to:
 Message 438 by Faith, posted 05-15-2015 6:11 PM Faith has not replied

  
Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 448 of 1034 (757914)
05-16-2015 7:35 AM
Reply to: Message 446 by Tangle
05-16-2015 3:35 AM


Re: dating methods and consilience of evidence
The modern idea of ring species is that they don't exist. In fact some people said that many years ago when I was learning about evolution but now there's genetic evidence that shows that they all seem to have had a geographic isolation event at some or at several points in their evolution. See
https://whyevolutionistrue.wordpress.com/...-no-ring-species
It's still proof of evolution, just not the neat story we'd like it to be. Shame, I was very fond of the gull ring.
It is still a neat story in its latest rendition.
Only the mechanism - previously only a continuous gene flow scenario but now it seems also geographical isolation instances involved - is shown to be different than previously thought. But both mechanisms are evolutionary and therefore it is still a very strong evidence for evolution. Even the name "ring species" satisfies still.

This message is a reply to:
 Message 446 by Tangle, posted 05-16-2015 3:35 AM Tangle has not replied

  
Denisova
Member (Idle past 3329 days)
Posts: 96
From: The Earth Clod....
Joined: 05-10-2015


Message 453 of 1034 (757937)
05-16-2015 2:03 PM
Reply to: Message 441 by Faith
05-15-2015 6:52 PM


Re: genetic diversity
But my argument goes against the very assumptions that lead you to say that, which is why DNA evidence is required. Ability to interbreed is an artificial category invented for the ToE. In reality this inability occurs WITHIN a species and is no marker of forming a new species at all, especially since if you did test the DNA they should show a very evident loss of genetic diversity from previous populations, most likely in the form of more fixed loci.
Also, you get reduced genetic diversity even without so-called "speciation" which is a misnomer anyway as I just said. The point of DNA analysis would be to look for evidence of this reduction from population to population, probably mostly concentrating on the formation of fixed loci for the most characteristic traits of a population, or if possible, the reduction in number of alleles for those traits from the previous population from which it developed. Hybrid zones may make the investigation difficult but those are usually identifiable.
With all respects but I can't make any sense out of this.
Interbreeding an artificial category?????
Nothing to add here.
.... the reduction in number of alleles for those traits from the previous population from which it developed....
Until now we only see a GAIN in the number of alleles for those traits.
The max. number of ANY gene in the Adam & Eve population is just 4.
Nowadays we observe genes that count as much as 59 alleles. The human gene with the most alleles is HLA-DRB1. It is one of the genes in the human leukocyte antigen complex. It plays a central role in the immune system so it's a very crucial gene.
The point is to look for evidence of this reduction from population to population? Well DO IT then and show us the empirical results.
I am STILL awaiting it 4 to 5 posts in a row.
Deisova writes:
It is even, with out current understanding of genetics, not even possible to show genetic isolation by examining the DNA.
Faith writes:
The only marker I have in mind is the number of fixed loci from population to population, showing that a population has been reduced to one allele for a given trait. This should be possible to identify, shouldn't it? A general reduction in alleles for the characteristic traits could also be shown, couldn't it?
To me it suffices that all subpopulations of a ring species are able to interbreed while two of them won't. It would be nice to identify such instance by genetic DNA analysis but it is only a bonus.
Rng species give evidence for evolution. there is no way around that.

This message is a reply to:
 Message 441 by Faith, posted 05-15-2015 6:52 PM Faith has not replied

  
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