Evolution Requires Reduction in Genetic Diversity

Dismissing requests for evidence, especially in this way, is very strongly discouraged. Bald declarations void of evidence should be eschewed.

Just to clarify one more time, I'm ruling out use of the the term "gene death" and all derivatives as too ambiguous and conflicted. If you want to refer to pseudogenes that have no function then you could use the phrase "functionless pseudogenes" or any meaningful variation.

AbE: I'm rewriting this first paragraph, which originally included the sentence, "I'm ruling off-topic any discussion about selection." What I meant was that this isn't a thread for discussing whether selection happens. Faith has made some side comments about selection not playing any significant role in evolution, that the resorting of alleles creates the traits, and organisms migrate to new regions where the traits are advantageous. But even Faith has argued for the power of selection when she talks about breeders adding and removing traits, and in any case, that's a discussion for another thread.Also off-topic is whether mutations can be selected against. For this thread it will be assumed that mutations can cause a decrease in fitness that will be selected against.More generally I'd like to request that participants try to move more aggressively toward concentrating on the central topic. I'm going to work hard to eliminate side issues and meaningless challenges.Edited by Admin, : AbE.

This is a bit of an over simplification. It is the overall fitness of an individual that gets tested, and even some hampering traits and loss of ability can get carried along for the ride because they don't hamper fitness sufficiently to be selected against because individual is fit enough based on other traits. And not all traits are tested in every environment.For example if humans once had some ability to detect magnetic fields that allowed them to migrate long distances and find their way home, we could do perfectly well without that sense now. Generally speaking, people who live within cities no longer need the ability to detect poisonous natural plants, run long distances at a stretch, endure extreme temperatures, or detect predators by smell. If some of those abilities were loss, there would be very little selection pressure as a result.And of course many traits that shorten life to something that is still well beyond child bearing/siring years are not selected against at all.Edited by NoNukes, : No reason given.

I have been following the thread and besides, I have heard it all before. I just don't have the time to be heavily involved in a debate with Faith, as you can see, it can be time consuming with not much productive feedback. Beside, I think you are handling it pretty well, so there is no need to overwhelm her.One thing I try to do is figure out what the core misunderstanding is and try to address that. In this case, what I see is Faith has latched on to this idea of there being so much "junk DNA" in the genome that it must be because there was more diversity in the past. I was trying to address this and point out that most "junk DNA" does not fit this idea at all. Perhaps it is overstating it to say that the majority has a function. Function implies a useful purpose or a necessary use to the organism and that is not really what I meant. What Faith is looking for specifically is pseudogenes - introns, SSRs, functional RNAs and centromere associated sequences, ect. don't qualify (perhaps she could make a case for LINEs, but they don't seem like good candidates to me).For example from Message 487She thinks "dead genes" constitute 95% of the genome. Very, very hard to do - trust me (cue accusations of misrepresenting her argument) but its all you can do with such limited hypotheses. Yea, no problem. I understand how speciation works. I was referring to how you were extrapolating her argument, and it wasn't meant to be critical. I don't think she would expect that humans have ever speciated, so, just wondering where the expectation of thousands of pseudogenes came from.HBD

I disagree that "junk DNA" is a perfect term. It is not specific enough. I will withdraw the statement that the majority has a "function," function has implications that I don't really mean, and which depends on what is meant by "function." For example, does spacer DNA have a function? Is it a "selectable function?" Maybe not, but could it just be clipped out? Probably not, separation of genes does affect expression and having two genes back to back may cause problems with transcription. Is that a function?I think it is more appropriate to refer to it as "non-coding DNA" and then to refer to specific types of non-coding DNA. You would never say "I sequenced a region of junk DNA..." Sure, but why haven't all species done that? If there wasn't some evolutionary constraint acting to preserve these non-coding sequences all genomes should be minimized. The tremendous amount of resources that must go into maintaining >50% of our genome that is simply disposable should experience significant negative selection. I just think it is too generalized and unspecific and gives a false impression of what it represents. Non-coding DNA is better. Reference to more specific types of non-coding sequences is even better.In the context of this discussion, there is not 95% of the human genome that is "dead genes." That is one example of how the term "junk DNA" is misleading.HBDEdited by herebedragons, : No reason given.

Worth pointing out in this context is that there is now considerable evidence of selection on non-coding DNA. As an example, see Positive and Negative Selection on non-coding DNA in Drosophilia simulans, chosen because it was one of the first relevant papers I found that was available as a free pdf rather than for any particular significance. Some non-coding DNA appears to be of adaptive signifcance, at least in fruit flies and humans, where this has been investigated in most depth.Edited by caffeine, : No reason given.Edited by caffeine, : tags

I think she's in big trouble there, see my post Message 506.
Basically: any instance of population bottlenecks can drastically diminish then number of alleles. But these alleles will these alleles will completely vanish from the species' genome. All the drowned people take their alleles with them in their inundated graves.Hence, the current junk DNA can't be explained out of allele diversity lost during the Fall or Flood.The same applies to eventually lost genes. The will also disappear into oblivion along with their owners dying in the Flood.
But Faith is assuming that 95% of the current genome is junk (the exact % isn't much of a deal here). And that most of the junk (she doesn't specify) are pseudogenes (disabled genes).As far as I know, a Flood cannot delete or disable genes. For that you need mutations. But during a few months lasting flood there can't be all of a sudden that much mutations to account for such a huge loss of genes.So the only escape Faith has is to assume all those genes becoming pseudogenes is by death of so many people. But dying people leave no silenced genes in the genome OF THE SURVIVORS. The survivors can't all of a sudden gather all disabled genes that were in the genomes of the dead.Hence, also genes that are lost due to mass extinction cannot contribute to junk DNA in the surviving population.Besides, when the population that died during the Flood would take away so much genes ("95%"), that would imply that thousands of genes (even when not all junk DNA turns out to be pseudogenes) apparently were in the extinct part of the population while the surviving part is only left with 5% of the original genetic diversity. That implies there was an unbelievable genetic variation in the original genome. That's by all means impossible for INTRASPECIES variation.In other words, junk DNA is not an argument for Faith's proposition whatsoever. Edited by Denisova, : No reason given.Edited by Denisova, : Corrected dBcodes.

Then let me try to clarify. I don't mean to be saying that the genes became junk DNA IN the bottleneck but as a result of it due to the loss of so many alleles for so many traits. This should have an effect on the genome over the generations afterward, not immediately. It's basically the same as my general argument in this thread. Severe bottlenecks today operate similarly except that they start from less genetic diversity. The bottlenecked population's genes aren't changed, it's only as they inbreed for a few generations that the loss of alleles becomes apparent and we find many fixed loci developing for lack of alternative alleles. This is the case for instance with the cheetah and with the elephant seal. Then in the formation of breeds and small subpopulations in the wild which we've been discussing, the reduced genetic diversity should also trend to an increase in fixed loci due to its loss of alleles that remain in the larger general population. In the case of domestic breeding the more fixed loci the more "pure" the breed. Even a reduction in alleles without a total loss would trend in this direction, and the fewest would eventually drop out of the population altogether.Apparently you wanted me to answer your comment, but it wasn't a question so I wouldn't have known that. Since you seemed to be saying that most junk DNA isn't really nonfunctioning genes I wanted to know what you think it is. I think I know now so it's no longer a question. All true. I'm not sure what point you are making here. I'm not expecting any difference in numbers of genes between individuals in a population. I have in mind that if enough alleles are lost in such a huge bottleneck then the genes themselves would eventually be compromised as well, but not immediately. Apparently I haven't been clear. I don't expect the effect on Noah's family to be immediate but something that would occur among his descendants in the following generations due to the reduction in genetic diversity, i.e., the great loss of alleles for many traits. Noah and his descendants would have all the same genes but those genes would have fewer alleles (still haven't worked out the question of new alleles forming or how many would have been in the reproducing pairs on the ark, the three human pairs.) Many genes would eventually be reduced to fixed loci and come to characterize the subpopulations that migrated to different parts of the planet.I did have in mind that simply the existence of many fixed loci could result eventually in the loss of function of many of those genes, but right now I'm thinking there is no real reason why that would be so: destructive mutations would have to occur for that to happen, and destructive mutations should have been on the rise after the Flood too. Not if you're thinking it would occur immediately, but down the generations as I've explained above it could, and especially, as I now think, if mutations are involved.[From Wikipedia: "Pseudogenes often result from the accumulation of multiple mutations within a gene whose product is not required for the survival of the organism."]It is enormous, for sure, but it does seem to be what happened. To my mind it speaks to the far more enormous original genetic diversity all species had. The loss is incalculable, but here we are. If some junk DNA isn't just disabled genes it would be much less of an effect but the vast majority do seem to be formerly functioning genes. Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.Edited by Faith, : No reason given.

Taking another look at this. I think I really don't get what you're trying to say. The reason I asked about junk DNA was that you seem to be implying that junk DNA can't have many nonfunctioning genes because there's only a few percent genetic diversity in a species anyway. I really don't know what you are saying and I should have asked. More than that and you'd "get a different species?" This really makes no sense. This too is hard to decipher. I didn't say genes dropped at all in the bottleneck. So again the only relevance is my claim that junk DNA was a result of the Flood, but that didn't happen immediately so that's why I answered as I did above. Loss of genes to junk DNA would have happened due to new combinations that lead to fixed loci through generations, and mutations that wipe out those alleles.I think the rest of my post addresses the topic.

Hi Faith,I didn't understand much of your next to last paragraph. I think it likely that others will experience the same difficulty, so I have a couple questions. Would a correct interpretation be that the Flood marked the beginning of gradual process of genes becoming pseudogenes (genes that no longer produce proteins), where pseudogenes are what you mean when you referred to "junk DNA" just above? If not then it would really be helpful if what was meant could be explained, without using the term "gene death" or any related terms.Also, you said the same thing about the Fall, that it caused a gradual process of genes becoming pseudogenes. Since this was already happening when the Flood occurred, how could the flood be said to have caused this process? I'm not sure why you say that new allele combinations lead to fixation, so that point needs clarification.

And NOW reality as observed in nature:

1. in a population bottleneck many alleles will be lost but almost no genes
2. new alleles are formed due to genetic mutations in conjunction with natural selection
3. the forming of new alleles is observed in the human genome that possesses an abundant number of alleles for all kinds of genes. Apparently since the Flood many alleles have been added: some genes have as much as 59 alleles
4. there is no other way to explain such a gain in alleles
5. among dozens of other reasons from geology and by sheer logic, this BTW refutes such mass extinction events like the biblical Flood to have happened: such increase in alleles ending up in as much as 59 alleles for a single gene implies an astonishing, I even would say a baffling rate of evolution allowed in the time frame of the Flood (4,500 years ago). Such rates of evolution are by all means impossible
6. the particular way genetic mutations and natural selection indeed leading to new alleles of existing genes but even to the emerging of new genes, is observed in different experiments: E. coli long term experiment of Lenski but other ones on prokaryotes and eukaryotes (beetles, yeast, fruit flies and dog breeds like dachshunds) as well. I pointed you out to those
7. there is no evidence provided for deteriorating genomes, although Sanford tried to substantiate it empirically. He failed altogether and utterly
8. non-functional DNA is quite well explained. It tells the story of evolution like the abundance of pseudogenes silenced in all kinds of animals due to changing and innovating genomes under selective pressure. I have provided many examples of these.

In reality the alleles that were lost in bottlenecks will gradually be replenished by new ones added to the genome. This is evidently proven by the fact that Adam & Eve had a combined genome with a maximum of 4 alleles for each gene. Now we have genes with up to 59 alleles. The evolutionary mechanisms are well known and proven to actually work by the many experiments on both prokaryotes and eukaryotes (mentioned above). No gene will be compromised.
Even in your fictional Flood story there are 8 persons left and within that population each gene will have 2 alleles. These are passed to the next generation and will stay within the genome of that population until it is selected out due to chance by genetic drift or selective pressure. The bigger the population grows, the greater the number of individuals with the same allele and, thus, the lesser the odds that genetic drift will delete alleles by pure chance. Moreover, alleles are replenished by genetic innovation, see above.So, as I explained, the total genetic diversity of the population has not declined, that is a flaw by you, but is DISPERSED among the breeds. Each breeds carries a subset of the original combined genome and all subsets tallied up over all breeds will equal the diversity of the original genome. ONLY when one of those breeds will split of into a new species, some proportion of the original genetic diversity will be lost to the ancestral genome. But the diluted genetic diversity due to the emergence of breeds is constantly replenished by genetic innovation. No it didn't happen.
Junk DNA CAN NOT be explained by al loss of alleles, as explained.
A mass extinction will kill off many alleles but those alleles will be gone with the individuals who died who take them with them in their graves. the same applies to eventual genes that were unique for the ones that died in the flood.Those alleles that were left over in the surviving population will just be passed over to the next generations and only vanish due to genetic drift and most likely when the population still is small and more prone to random chance.Alleles are NOT very likely to disappear due to deleterious mutations. THAT would imply that in the very same generation ALL individuals owning the same allele would have been struck collectively by a harmful mutation hitting that particular allele. That would be extremely rare event. Because as soon as one individual (out of a growing number due to population growth) survives with that allele intact, it is still within the population and will spread in next generations.There are only two mechanisms known in genetics to account for a loss of alleles:

1. natural selection. When the environmental pressures do not favour a particular trait anymore, individuals hit by mutations that jeopardize the alleles and genes responsible for that trait, will not experience lower survival and/or reproduction chances by those mutations. Because in the new environmental setting those traits are not essential anymore. Once deleterious mutations now became neutral ones.
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   ONLY THEN mutations will "turn" alleles and whole genes for that matter as well, into pseudogenes and junk DNA. And by definition this kind of mutations ARE NOT deleterious. they are neutral (with respect to fitness and related to the whole genome).
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   AS LONG as genes and alleles represent useful and functional traits that are under selective pressure, that is, contributing to the fitness of the individual in terms of survival and/or reproduction chances, any mutation that silences an allele or gene will bring lower survival and/or reproduction chances to its owner and thus have lower odds to be passed to the next generation - THUS tend to be weeded out of the species' genome. ONLY then those mutations are called deleterious.
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2. genetic drift. Alleles can be deleted by random chance. Genetic drift describes random fluctuations in the numbers of gene variants in a population. Genetic drift takes place when the occurrence of variant forms of a gene, called alleles, increases and decreases by chance over time. These variations in the presence of alleles are measured as changes in allele frequencies.
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   Typically, genetic drift occurs in small populations, where infrequently occurring alleles face a greater chance of being lost. Once it begins, genetic drift will continue until the involved allele is either lost by a population or until it is the only allele present in a population at a particular locus. Both possibilities decrease the genetic diversity of a population. Genetic drift is common after population bottlenecks, which are events that drastically decrease the size of a population. In these cases, genetic drift can result in the loss of rare alleles and decrease the gene pool. Genetic drift can cause a new population to be genetically distinct from its original population, which has led to the hypothesis that genetic drift plays a role in the evolution of new species.

Edited by Denisova, : No reason given.

No I do believe that much of the human genome is non-functional.
And that much of the non-functional part consists of pseudogenes.
Even after the excellent job done by the ENCODE team, which reduced the proportion of functional DNA to 12% - but unfortunately with flawed conclusions drawn - even 88% of non-functional DNA remained. So your 95% is too high but the exact figure is not essential to the discussion here. Even 88% will do for your argumentation.But it is a major flaw to imply that all those non-functional DNA parts are due to a genetic bottleneck. It is well explained by me in post Message 518.

No not at all. Gene regulation is a complex and multi-leveled process. It involves proteins, histone modifications, cis-regulatory elements (on the same strand of DNA), ssRNA, miRNA, cAMP, etc. These all work together to determine where and when genes get expressed. Changing the amino acid sequence of a protein can be detrimental to the organism if a non-functional protein is produced. However, changes in regulation can modify where and when the gene is expressed and produce significant phenotypic changes - without modification of the protein itself.A good example of this is found in three-spine sticklebacksHBD

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Then let me try to clarify. I don't mean to be saying that the genes became junk DNA IN the bottleneck but as a result of it due to the loss of so many alleles for so many traits. This should have an effect on the genome over the generations afterward, not immediately.

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So what you are saying is that humans had many times more genes than they do now. But all those extra genes became useless because they were only useful with particular combinations of alleles which were no longer possible.Why would that even be the case ? Why would there be so many genes that are only conditionally useful ? More importantly why do you think that was the case ?Come to that, why even assume that even most junk DNA is pseudogenes ? Only a small proportion is identifiable as such, and I don't think that mutation rates aren't high enough to obliterate that many genes in a few thousand years.