The End of Evolution By Means of Natural Selection

Hi Wounded King, Oh I am aware of the slippery eel there, however to claim that there is no evidence of beneficial mutations, when you have definite proof of beneficial mutations in bacteria, an analogous situations in other organisms, makes the argument that the higher forms do not have beneficial mutations rather weak.We also have the situation now where there is a lot of genetic information being gathered and documented, such as the study of children and their genetic inheritance. While a lot of these focus on finding deleterious mutations known to be in parents to see if they show up in the children (for early treatment) we are also likely to find mutations that counter them.Enjoy.

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Hi Percy, I'm aware of this, and that similar can happen around the ring, but I want Faith to derive it, and then be fixed by it, while we discuss the ramifications. I don't think the end result is what she thinks it is.Enjoy.Edited by RAZD, : clrty

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Hi Faith, Hold that thought and savor it. Dominance of a neutral allele is unrelated to it's selection (because it is neutral).Perhaps then we can relate this to your concept of hidden alleles that emerge in small populations ... presumably because other alleles that have kept it hidden are lost.Enjoy.

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Hi Faith Except that your supposed hidden alleles were never seen in previous populations, and this does not fit with the patterns above. In every 16 rabbits (if the alleles are evenly spread). If we assume that 50% of the Black alleles are knocked out of the population by some stochastic event, then there are twice as many of the other alleles than the black alleles (to keep the math relatively simple), and then we get:

	Black	Brown	Brown	Gray	Gray	Tan	Tan
Black	Black Black	Black Brown	Black Brown	Black Gray	Black Gray	Black Tan	Black Tan
Brown	Brown Black	Brown Brown	Brown Brown	Brown Gray	Brown Gray	Brown Tan	Brown Tan
Brown	Brown Black	Brown Brown	Brown Brown	Brown Gray	Brown Gray	Brown Tan	Brown Tan
Gray	Gray Black	Gray Brown	Gray Brown	Gray Gray	Gray Gray	Gray Tan	Gray Tan
Gray	Gray Black	Gray Brown	Gray Brown	Gray Gray	Gray Gray	Gray Tan	Gray Tan
Tan	Tan Black	Tan Brown	Tan Brown	Tan Gray	Tan Gray	Tan Tan	Tan Tan
Tan	Tan Black	Tan Brown	Tan Brown	Tan Gray	Tan Gray	Tan Tan	Tan Tan

So all the possible pairings give us 13 Black rabbits, 20 Brown rabbits, 12 Grey rabbits, and 4 Tan rabbits in every 49 rabbits (if the alleles are evenly spread). Not really a significant change in proportions for an impact of 50% of the Black alleles being removed. The population as a whole will still be predominantly Black, Brown and Gray in appearance, while the rare Tan rabbit goes from 6% to 8%.The allele that benefits (increases in appearance of the phenotype) the most from this change is the Brown one, the second most dominant allele in the original population, as essentially Black and Brown exchange places.Somehow I don't think this validates your claim.EnjoyEdited by RAZD, : added endEdited by RAZD, : added carriers

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Hi Faith, I mistakenly posted this on the other thread, and was advised by admin that it was deleted (as that is a great debate thread), so I am reposting it here: These are the mysterious "hidden alleles" that you claim I have misunderstood -- either (a) you have not explained your position very well at all or (2) you are caught out on your make-believe scenario. Sadly, what this shows is that (1) you have not done the math, and (b) that whenever someone makes a statement that counters what you have said that you change the rules.In the real world what you have said just went from improbable to extremely improbable (improbable x improbable). No. Do the math.Generation 1

Parent Alleles	BT Black	BT Tan
BT Black	Black Black	Tan Black
BT Tan	Black Tan	Tan Tan

Generation 2

Parent Alleles	BB Black	BB Black	BT Black	BT Tan	TB Black	TB Tan	TT Tan	TT Tan
BB Black	Black Black	Black Black	Black Black	Tan Black	Black Black	Tan Black	Tan Black	Tan Black
BB Black	Black Black	Black Black	Black Black	Tan Black	Black Black	Tan Black	Tan Black	Tan Black
BT Black	Black Black	Black Black	Black Black	Tan Black	Black Black	Tan Black	Tan Black	Tan Black
BT Tan	Black Tan	Black Tan	Black Tan	Tan Tan	Black Tan	Tan Tan	Tan Tan	Tan Tan
TB Black	Black Black	Black Black	Black Black	Tan Black	Black Black	Tan Black	Tan Black	Tan Black
TB Tan	Black Tan	Black Tan	Black Tan	Tan Tan	Black Tan	Tan Tan	Tan Tan	Tan Tan
TT Tan	Black Tan	Black Tan	Black Tan	Tan Tan	Black Tan	Tan Tan	Tan Tan	Tan Tan
TT Tan	Black Tan	Black Tan	Black Tan	Tan Tan	Black Tan	Tan Tan	Tan Tan	Tan Tan

16 = Black-Black (25%)
16 = Black-Tan
16 = Tan-Black
16 = Tan-Tan (25%)After the second generation the pattern is the same, the frequency of alleles does not change (assuming every rabbit mates and produce more than one offspring etc etc as is assumed in the original population)Enjoy.Edited by RAZD, : added gridsEdited by RAZD, : found copy error mutation and removed

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Faith, Wikipedia is a volatile source, as any paragraph is subject to change. Several pages have experience change wars between people of different opinions.If the page has changed since your quote you can look at the history and pull up the version you quoted from, rather than accuse people of changing it just to embarrass you.The other thing you can do -- good practice for any reference from any internet site -- is not only cite the webpage, but when it was last accessed.Enjoy.

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Hi Faith, you accuse us of not understanding you, here you have a misunderstanding: New varieties are not new species, but subspecies, populations that are isolated, usually geographically, and that undergo different selection pressures can evolve to show visible differences.This may occur by your pet hypothesis of allele loss in both parent and offspring population, so that we can see different alleles in the majority of the populations.What you do not get is reproductive incompatibility. As long as you maintain all the alleles within either population that the ancestral population had, then there cannot be reproductive incomptibility, because they are the still the same species.ps -- I'm still waiting for you to work out the math on how your system works.Enjoy.

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Hi Percy, No, I meant alleles, as this is how you get variation in species, and varieties exhibit variation, but are still genetically compatible with other varieties. Varieties can - and frequently do - interbreed (see hybrid zones as one example).Varieties are cause by a shift in the frequency of alleles (hereditary traits) in populations in isolation from other populations, but can be reabsorbed into the parent population if conditions warrant.While this normally occurs, according to biological science and various field studies, with the modification of existing alleles by mutations, this is not necessary.The peppered moths (Peppered Moths and Natural Selection) are an excellent example of no genetic change, but a shift in the frequency distribution of alleles from one generation to the next, resulting in a shift between which variety of moth is most prevalent:

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Note first off that this article refers to the two varieties of the moth:

• Biston betularia typica (the light color version) and
• Biston betularia carbonaria (the dark color version)

In the scientific name structure (for those unfamiliar with it) we have family (Biston) species (betularia) and variety (typica or carbonaria) designations.

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An important distinction is made between 'species' and 'variety' and that is that 'varieties' can interbreed: when the genetic difference is great enough that no viable offspring are created then we would then have a different 'species' - this is the scientific distinction. As we are not talking about species differentiation at this point in this scenario, the speciation part of the theory of evolution is not tested, per se.

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From BIOLOGY by Miller & Levine, page 298:

"Kettlewell found that in unpolluted areas, more of his light-colored moths had survived. In soot-blacked areas, more of the dark-colored moths had survived. Thus Kettlewell showed that in each environment the moths that were better camoflaged had the higher survival rate. It was logical to conclude that when soot darkened the tree trunks in the area, natural selection caused the dark-colored moths to become more common. Today Kettlewell's work is considered to be a classic demonstration of natural selection in action."

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Sometimes classification is difficult if the populations are isolated. It is frustrating as a birder to see classifications change from different species to different varieties of the same species and back to different species, depending on the authorities and the latest cladistic information. I resolve this by tracking both species and variety when possible, in order to adjust as the new information comes out.Of course the bird species of special interest to me on this topic is the asian greenish warbler, Phylloscopus trochiloides, as noted in Message 260:

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The existence of the hybrid zones between each variety in the Greenish Warblers is evidence that hybrids only occur in these zones, AND that they can be (and are) identified as hybrids by having a mixture of traits\alleles present in one or the other neighboring variety population zone, but not common to both neighboring variety population zones. Instead we see:

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1. P.t.viridanus
   
2. a hybrid zone between P.t.viridanus & P.t.ludlowi
   
3. P.t.ludlowi
   
4. a hybrid zone between P.t.ludlowi & P.t.trochiloides
   
5. P.t.trochiloides
   
6. a hybrid zone between P.t.trochiloides & P.t.obscuratus
   
7. P.t.obscuratus
   
8. a hybrid zone between P.t.obscuratus & P.t.plumbeitarsus
   
9. P.t.plumbeitarsus

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This means we have a condition where there is sufficient reproductive isolation for the varieties to exist as independent populations, only mixing with other varieties through the hybrid zones, and that poorly at best.Of course evolution with natural selection, genetic drift AND mutation is fully capable of explaining these populations.It is Faiths hypothesis of allele loss with no new alleles that I have trouble with for explaining all the evidence.I have little doubt that once we get a formal formulation of the Faith Hypothesis, with an accurate description of how it operates within a population, a formulation succinct and explicit enough that predictions can be made, that there will be instances that fit the description. What I have trouble with is extending this to all populations all the time.Enjoy.

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Hi Percy,The first paragraph was your answer, the rest is just explanation for it.Essentially, I see no reason that some cases exist where separate varieties become isolated with different sets of alleles through loss.The problem is that they were interfertile before and that if they have no had any mutations, changes to the genetics, that there is no reason for interfertility to be lost. The only possibility is graded fertility originally, possibly hidden due to the number of other mating possibilities, as Wounded King suggests, however the lack of evidence for\against this as a pre-existing condition in original populations is a problem either way.PaulK has his finger on another problem with the Faith Hypothesis: it is not possible for a single organism to carry all the alleles in existence today, they can only carry two at a time. You need an original population to carry all the alleles.Enjoy.

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Hi Faith, Mutations don't have to change genes or cause sufficient difference to lead to incompatibility. The probability is that most small mutations will have small effects that accumulate to provide sufficient difference after many generation.There are, however, some mutations that can cause significant change in the phenotype.The point, however, is that you cannot have gene change without change - mutation - to the gene, and you need gene change for speciation.You have a gene for hair production. Hair can be blond, brown, red and black, curly, wavy and straight. These are the effects of alleles on the gene for hair production. To turn hair into something else (spines? quills?) you need to change the gene that produces hair. And which you would need a mutation to move to the active part of the DNA or a mutation to shut down one area and active another area. All you have done is invoked mutations by another name.Junk DNA could have some sections that would be historical genes\alleles, but you can't recover them without mutations. Which is essentially the problem PaulK et al have pointed out - you don't have enough carriers, so you are forced into making up other ways to carry genes and alleles that don't currently exist, and for which there is no evidence. Then to get from your super-pac animals to normal ones you still need mutations to move these genes and alleles around into the places they currently reside (a totally unnecessary step for creation, especially as the magic super-pac animals didn't need such arrangement), so that you can match the current evidence, and curiously end up mimicking evolution mutation and selection in the process. Which is known as the post hoc ergo propter hoc logical fallacy. Making up stuff after the evidence is provided that shows your hypothesis to be unable to provide the answers.Of course, you're still going to claim that it happened. Without mutations. Which still does not produce new genes nor new alleles, it is a mutation that duplicates whole genes. Which still does not produce new genes nor new alleles. The point is that you have to make stuff up to shoe-horn cram fit the evidence to the story. If the story is true it should be apparent in the evidence. It starts from knowing nothing about how genetics actually works. Only except that it shows how incompatable your argument is with reality. And curiously, you still have not provided a coherent concept that shows how speciation can occur. Assertion doesn't cut it. Wounded King suggested that it was theoretically possible, but that he knew of no examples.Curiously this too would be an extremely rare occurrence, if indeed it ever occurs.Every system you have tried to explain your hypothesis relies on a rare to non-existent mechanism occurring every time. Life don't work that way.Enjoy.Edited by RAZD, : mid#

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Actually Iblis ... Two of the chromosomes in horses are fused to make a single chromosome in donkeys. It is possible to match up the two parts to the one for reproduction - that is how you get mules.Similar between Chimps and Humans - we have a fused pair that they (and other apes) have as individual chromosomes.The genes on the chronomosomes are still comparable when you line them up.Chimpanzee genome project - Wikipedia
Chromosome fusionEnjoy.

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Hi Wounded Knee, Of course, for they can always claim that it was a deleterious or disease mutation that caused the breakup of the super-pac ark animals.Enjoy.

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Faith, And it is an average value. That means that for every 10 people there will be 6 new mutations. They may be in 6 individuals, or less if some have multiple mutations.Enjoy.

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No problem, Faith, ...... just making sure that we are all talking apples and apples. Glad to see you are finally getting around to doing the math.Of course, in order to know what happens, you also need to know what the rate of allele loss is.I would also like some clarification on the difference between "gene" and "allele" to be discussed, so we know we are talking about the same thing here as well.Allele Definition & Meaning | Dictionary.com

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allele (ə-lēl') n.
One member of a pair or series of genes that occupy a specific position on a specific chromosome.
The American Heritage Dictionary of the English Language, Fourth Edition Copyright 2009 by Houghton Mifflin Company.

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An allele is not something that is attached to a gene (or genes), like a tag as it were, rather it is a variation of the gene/s, a different form.Allele - Wikipedia

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An allele (pronounced /ˈliːl/ (UK), /əˈliːl/ (US); from the Greek αλληλος allelos, meaning each other) is one of a series of different forms of a genetic locus.[1] The word is a short form of allelomorph ('other form'), which was used in the early days of genetics to describe variant forms of a gene detected as different phenotypes. Alleles are now understood to be alternative DNA sequences at the same physical locus, which may or may not result in different phenotypic traits. In any particular diploid organism, with two copies of each chromosome, the genotype for each gene comprises the pair of alleles present at that locus, which are the same in homozygotes and different in heterozygotes. A population or species of organisms typically includes multiple alleles at each locus among various individuals. Allelic variation at a locus is measurable as the number of alleles (polymorphism) present, or the proportion of heterozygotes (heterozygosity) in the population.

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For example, at the gene locus for ABO blood type proteins in humans,[2] classical genetics recognizes three alleles, IA, IB, and IO, that determines compatibility of blood transfusions. Any individual has one of six possible genotypes (AA, AO, BB, BO, AB, and OO) that produce one of four possible phenotypes: "A" (produced by AA homozygous and AO heterozygous genotypes), "B" (produced by BB homozygous and BO heterozygous genotypes), "AB" heterozygotes, and "O" homozygotes. It is now appreciated that each of the A, B, and O alleles is actually a class of multiple alleles with different DNA sequences that produce proteins with identical properties: more than 70 alleles are known at the ABO locus.[3] An individual with "Type A" blood may be a AO heterozygote, an AA homozygote, or an A'A heterozygote with two different 'A' alleles.

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Again, a variation in the form of the gene, the DNA that comprises the gene is not the same in the different allele variations.Now in "evo-speak" this means that some mutations of the ABO locus are minor and do not affect the phenotype of the individual more nor less than the basic A, B, and O alleles. In "Faith-speak" these alternatives could be the long sought "hidden" alleles ... the ones that can form new species in isolated conditions ...... except that they do not affect the phenotype of the individual more nor less than the basic A, B, and O alleles.Enjoy.

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Nothing Faith, Just making sure we are working on the same page, so that when we get to the math it isn't muddled.The wiki article also has this part:Allele - Wikipedia

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Allele and genotype frequencies

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The frequency of alleles in a population can be used to predict the frequencies of the corresponding genotypes (see Hardy-Weinberg principle). For a simple model, with two alleles:

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p + q=1,

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p^{^2} + 2pq + q^{^2}=1,

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where p is the frequency of one allele and q is the frequency of the alternative allele, which necessarily sum to unity. Then, p^{^2} is the fraction of the population homozygous for the first allele, 2pq is the fraction of heterozygotes, and q^{^2} is the fraction homozygous for the alternative allele. If the first allele is dominant to the second, then the fraction of the population that will show the dominant phenotype is p^{^2} + 2pq, and the fraction with the recessive phenotype is q^{^2}.

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With three alleles:

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p + q + r = 1, and

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p^{^2} + 2pq + 2pr + q^{^2} + 2qr + r^{^2} = 1,

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**Note that I have edited this section for clarity in the last equation.**This allows you to calculate the relative frequency distribution of the alleles in a population in the different homozygous and heterozygous proportions. Note that if you know the proportions of the various phenotypes and the dominance\recessive relationships, that you can derive the proportions of the individual alleles by reversing the maths.If we look at Zen_Monkey's rabbits:Bl(black) + Br(brown) + Gr(gray) + Tn(Tan) = 1

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and

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Bl^{^2} + 2BlBr + 2BlGr + 2 BlTn + Br^{^2} + 2BrGr + 2 BrTn + Gr^{^2} + 2 GrTn + Tn^{^2} = 1and

• Bl^{^2} + 2BlBr + 2BlGr + 2 BlTn + Br^{^2} + 2BrGr + 2 BrTn = Black appearing
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• Br^{^2} + 2BrGr + 2 BrTn = Brown appearing
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• Gr^{^2} + 2 GrTn = Gray appearing
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• Tn^{^2} = Tan appearing

This works for different proportions of the alleles within the population. This is the same as box grid system (with frequency applied to the alleles, rather than assuming an equal distribution), but this is a lot easier to manage once you get the hang of the math.Enjoy.

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