Intelligent Design

In a pickle about Adam and Eve

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Professor Jerry Coyne can’t seem to leave the Adam and Eve question alone. In a recent post, Professor Coyne criticizes Bryan College in Dayton, Tennessee, for requiring its teaching professors to sign an updated “statement of belief” which, for the first time, explicitly affirms the existence of an historical Adam and Eve. Since Bryan College describes itself as “a nondenominational evangelical Christian college named after William Jennings Bryan: statesman, orator, and renowned prosecuting attorney in the famous Scopes Evolution Trial,” this requirement should hardly occasion surprise. What would be surprising is if the college didn’t require its professors to believe in a literal Adam and Eve.

In a related post published late last year, Coyne explains in detail why he is convinced that science has ruled out the existence of Adam and Eve:

The facts first. Sheehan et al., building on an earlier paper by Li and Durbin (references below), calculated that the minimum population size associated with the worldwide expansion of humans out of Africa about 60,000 years ago was 2,250 individuals, while the population that remained in Africa was no smaller than about 10,000 individuals. For population geneticists, this is the “effective population size,” invariably smaller than the census size, so these are minimum estimates, and ones derived from conservative assumptions. The population sizes are estimated by back-calculating (based on reasonable estimates of mutation rates and other parameters) how small an ancestral population could be and still give rise to the observed high level of genetic variation in our species.

Note: 2,500 is larger than two.

This means, of course, that Adam and Eve couldn’t have been the literal ancestors of all humanity.

Evidently math is not Professor Coyne’s forte.

Note: 2,500 isn’t the same as 2,250.

Note: 2,250 + 10,000 = 12,250.

The math lesson is over.

Coyne goes on to say that even these figures are under-estimates: they represent “the ‘effective population size,’ invariably smaller than the census size.”

I invite readers to have a look at the following article by Luke J. Harmon and Stanton Braude, of Princeton University:

Conservation of Small Populations: Effective Population Sizes, Inbreeding,
and the 50/500 Rule

I shall quote a brief extract:

There is no such thing as “the effective size” of a population. Different effective population sizes help us to estimate the impact of different forces. The effective size you estimate will depend on the scientific question you are trying to address (Box 12.1). Estimating the appropriate effective population size is crucial in biology; in most (but not all) cases, effective population size will be smaller than the actual number of organisms in the population. Think for a moment about why
this is so. A conservative rule of thumb used by some biologists is
that N_e [the effective population size – VJT] is usually about one-fifth of the total population size (Mace and Lande, 1991). Using such a rough estimate is risky because N_e can be larger than the census size of the population, depending on the history of the population and the particular N_e under consideration.

It’s rather embarrassing when a biology professor makes mistakes in his own field, isn’t it?

UPDATE: A final suggestion for Professor Coyne. Coyne claims that the effective population sizes he cites are “based on reasonable estimates of mutation rates.” Coyne is assuming here that the mutations are natural and undirected. If Coyne wants to refute the Adam and Eve hypothesis as entertained by believers in intelligently guided evolution, then the question he really should be asking himself is: what would the effective population size need to be, if the mutations that gave rise to the human line were artificial and directed?

127 Replies to “In a pickle about Adam and Eve

  1. 1
    nullasalus says:

    It’s rather embarrassing when a biology professor makes mistakes in his own field, isn’t it?

    Cut him some slack, he’s an evolutionary biologist. He’s far closer to a phrenologist than a physicist when you get right down to it.

  2. 2
    littlejohn says:

    Maybe if the good doctor understood that Adam and Eve were just two members of a larger population, he might accept the fact that Eve is the mother all living humans on the planet today. Genealogy 101.

  3. 3
    Querius says:

    Isn’t part of the issue the assumed genetic diversity of the mitochondrial Eve and Y-chromosomal Adam?

    -Q

  4. 4
    fryether says:

    Biologists, Please correct me if this would make no difference whatsoever, but to me if you want to concretely prove that Adam and Eve didn’t exist you can’t use existing population models. The bible has 3 variables that you’d have to consider. 1. Adam and Eve (1 human couple) 2. Adam and Eve were both supposedly perfect. 3. Subsequent generations of humans had near perfect DNA and lived to be much older than people today, the most famous being Methuselah living til the age of 969. If you are going to model a population and prove Adam and Eve didn’t exist wouldn’t you have to add in those factors?

  5. 5
    EvilSnack says:

    fryether:

    You have to remember that most secular “rebuttals” of Biblical claims consist of inserting a secular premise as quietly as possible into the mix of Biblical ideas, and then showing that the mix is self-contradictory.

    No straw man is safe!

  6. 6
    Robert Byers says:

    As a poster said here. man lived for hundreds of years before/after the flood and the females had maybe hundreds of children.
    An example are the Hebrews. From 70 at Joseph’s time they came in four hundred years to 3 million or so at the exodus,.
    We didn’t come out of africa. Were we black etc. did we lose african features.
    its so dumb speculative its embarrassing for their sake.

  7. 7
    Querius says:

    It’s my understanding that we all started out as brown. Mutations resulted in some people having less melanin, others more.

    I once saw a Smithsonian exhibit with tiles that matched all the shades of skin color in humans. There were hundreds of tiles ranging from coal black to an extreme white and everything in between.

    -Q

  8. 8
    Joe says:

    What evolutionists like Coyne and Joe Felsenstein fail to realize is that with Creation there would be an intial burst of rapid evolution to fill the niches as well as create diversity. With Creation there wasn’t any waiting for chance mutations, it was a prescibed evolution. And that means evolutionary methodology does NOT apply, yet they want to use it anyway.

    And that is why they will continue to fail.

  9. 9
    bornagain77 says:

    The following paper and video by Dr. Robert Carter totally dismantles the ‘minimum population size’ argument.

    The Non-Mythical Adam and Eve! – Refuting errors by Francis Collins and BioLogos
    http://creation.com/historical-adam-biologos

    CMI also has a excellent video of the preceding paper by Dr. Carter, that makes the technical aspects of the paper much easier to understand;

    The Non Mythical Adam and Eve (Dr Robert Carter) – video
    http://www.youtube.com/watch?v=8ftwf0owpzQ

    (Of note: although I don’t agree with the extreme 6000 year Young Earth model used as a starting presumption in the paper ans video for deriving the graphs, the model, none-the-less, can be amended quite comfortably to a longer time period. Which I, personally, think provides a much more ‘comfortable’ fit to the overall body of genetic evidence).

    As to large genetic diversity being harbored in two founding members of a species, Darwinists are always ‘surprised’ when an ancient lineage of a species is found to be more genetically robust than the younger lineages,,,

    Single male and female sheep maintain genetic diversity.
    A mouflon population (considered an ancient “parent” lineage of sheep), bred over dozens of generations from a single male and female pair transplanted to Haute Island from a Parisian zoo, has maintained the genetic diversity of its founding parents.This finding challenges the widely accepted theory of genetic drift, which states the genetic diversity of an inbred population will decrease over time. “What is amazing is that models of genetic drift predict the genetic diversity of these animals should have been lost over time, but we’ve found that it has been maintained,”
    Dr. David Coltman, an evolutionary geneticist at the University of Alberta

    Allozyme evidence for crane systematics and polymorphisms within populations of sandhill, sarus, Siberian and whooping cranes.
    “This is contrary to expectations of genetic loss due to a population bottleneck of some 15 individuals in the 1940s. The possibility should be explored that some mechanism exists for rapidly restoring genetic variability after population bottlenecks.”
    Molecular Phylogenetics and Evolution 1:279-288- Dessauer, H. C., G. F. Gee, and J. S. Rogers. 1992.

    These following studies and video, on Cichlid fishes, are evidence of the ‘limited and rapid variation from a parent kind’ that would be expected in the ‘top down’ design model:

    African cichlid fish: a model system in adaptive radiation research:
    “The African cichlid fish radiations are the most diverse extant animal radiations and provide a unique system to test predictions of speciation and adaptive radiation theory(of evolution).—-(surprising implication of the study?)—- the propensity to radiate was significantly higher in lineages whose precursors emerged from more ancient adaptive radiations than in other lineages”
    http://www.pubmedcentral.nih.g.....d=16846905

    Multiple Genes Permit Closely Related Fish Species To Mix And Match Their Color Vision – Oct. 2005
    Excerpt: In the new work, the researchers performed physiological and molecular genetic analyses of color vision in cichlid fish from Lake Malawi and demonstrated that differences in color vision between closely related species arise from individual species’ using different subsets of distinct visual pigments.
    http://www.sciencedaily.com/re.....072648.htm

    Cichlid Fish – Evolution or Variation Within Kind? – Dr. Arthur Jones – video
    http://www.metacafe.com/watch/4036852

    “For all the diversity of species, I found the cichlids to be an unmistakably natural group, a created kind. The more I worked with these fish the clearer my recognition of “cichlidness” became and the more distinct they seemed from all the “similar” fishes I studied. Conversations at conferences and literature searches confirmed that this was the common experience of experts in every area of systematic biology. Distinct kinds really are there and the experts know it to be so. – On a wider canvas, fossils provided no comfort to evolutionists. All fish, living and fossil, belong to distinct kinds; “links” are decidedly missing.”
    Dr. Arthur Jones – did his Ph.D. thesis in biology on cichlids

    also of note:

    Children of the Corn: A Reader Objects – April 2012
    Excerpt: As John Doebley put the point in 2004, “The critical genetic variants involved in maize evolution were pre-existing in teosinte populations” (p. 46).
    – per Evolution News and Views

    Dogs, Dawkins infamous example of macroevolution,,,

    Richard Dawkins Tries to Refute Behe With Dog Breeding
    http://darwinianfundamentalism.....-behe.html

    are perhaps the best example of large genetic diversity being harbored in a few (very possibly two?) founding members of a species:

    Genome sequencing highlights the dynamic early history of Dogs – January 2014
    Excerpt Discussion: We provide several lines of evidence supporting a single origin for dogs, and disfavoring alternative models in which dog lineages arise separately from geographically distinct wolf populations (Figures 4–5, Table S10),,
    Our analysis suggests that none of the sampled wolf populations is more closely related to dogs than any of the others, and that dogs diverged from wolves at about the same time that the sampled wolf populations diverged from each other (Figures 5A, 5C).
    http://www.plosgenetics.org/ar.....en.1004016

    podcast – On this episode of ID the Future, Casey Luskin talks with geneticist Dr. Wolf-Ekkehard Lönnig about his recent article on the evolution of dogs. Casey and Dr. Lönnig evaluate the claim that dogs somehow demonstrate macroevolution.
    http://intelligentdesign.podom.....1_14-08_00
    Part 2: Dog Breeds: Proof of Macroevolution?
    http://intelligentdesign.podom.....7_07-08_00

  10. 10
    bornagain77 says:

    As well, a non-Darwinian process of epigenetic modification has now been implicated in the rapid domestication of chickens:

    Epigenetics: Swedish researchers say Darwinism is NOT the cause of wide variation in domestic chicken types
    Excerpt: Since methylation is a much faster process than random mutations, and may occur as a result of stress and other experiences, this may explain how variation within a species can increase so dramatically in just a short time.
    http://www.uncommondescent.com.....ken-types/

    More evidence for rapid radiations from a parent species can be found here:

    Biological Variation – Cornelius Hunter
    Excerpt: One hint that biology would not cooperate with Darwin’s theory came from the many examples of rapidly adapting populations. What evolutionists thought would require thousands or millions of years has been observed in laboratories and in the field, in an evolutionary blink of an eye.
    http://www.darwinspredictions......_variation

    Evolution of adaptive phenotypic traits without positive Darwinian selection – A L Hughes – November 2011
    Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity–relaxation–mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative environment and thus the permanent expression of one alternative phenotype. Once this specialization occurs, purifying selection on the molecular basis of other phenotypes is relaxed. Finally, mutations that permanently eliminate the pathways leading to alternative phenotypes can be fixed by genetic drift. Although the generality of the PRM mechanism is at present unknown, I discuss evidence for its widespread occurrence, including the prevalence of exaptations in evolution, evidence that phenotypic plasticity has preceded adaptation in a number of taxa and evidence that adaptive traits have resulted from loss of alternative developmental pathways. The PRM mechanism can easily explain cases of explosive adaptive radiation,
    http://www.nature.com/hdy/jour.....1197a.html

    No Positive Selection, No Darwin: A New Non-Darwinian Mechanism for the Origin of Adaptive Phenotypes – November 2011
    Excerpt: Hughes now proposes a model he refers to as the plasticity-relaxation-mutation (PRM) model. PRM suggests that adaptive phenotypes arise as follows: (1) there exists a phenotypically plastic trait (i.e., one that changes with the environment, such as sweating in the summer heat); (2) the environment becomes constant, such that the trait assumes only one of its states for a lengthened period of time; and (3) during that time, deleterious mutations accumulate in the unused state of the trait, such that its genetic basis is subsequently lost.
    ,,, But if most adaptations result from the loss of genetic specifications, how did the traits initially arise? One letter (Chevin & Beckerman 2011) of response to Hughes noted that the PRM “does not explain why the ancestral state should be phenotypically plastic, or why this plasticity should be adaptive in the first place.”
    http://www.evolutionnews.org/2.....52941.html

    A. L. Hughes’s New Non-Darwinian Mechanism of Adaption Was Discovered and Published in Detail by an ID Geneticist 25 Years Ago – Wolf-Ekkehard Lönnig – December 2011
    Excerpt: The original species had a greater genetic potential to adapt to all possible environments. In the course of time this broad capacity for adaptation has been steadily reduced in the respective habitats by the accumulation of slightly deleterious alleles (as well as total losses of genetic functions redundant for a habitat), with the exception, of course, of that part which was necessary for coping with a species’ particular environment….By mutative reduction of the genetic potential, modifications became “heritable”. — As strange as it may at first sound, however, this has nothing to do with the inheritance of acquired characteristics. For the characteristics were not acquired evolutionarily, but existed from the very beginning due to the greater adaptability. In many species only the genetic functions necessary for coping with the corresponding environment have been preserved from this adaptability potential. The “remainder” has been lost by mutations (accumulation of slightly disadvantageous alleles) — in the formation of secondary species.
    http://www.evolutionnews.org/2.....53881.html

    Perhaps the best evidence we have from the fossil record for this ‘top down’ loss of genetic diversity we would expect from the design perspective is seen from the study of trilobite fossils. Here is an article on the “surprising” loss of variation and diversity for trilobites over the 270 million year time span that trilobites were found in the fossil record, prior to their total extinction from the fossil record about 250 million years ago.

    The Cambrian’s Many Forms
    Excerpt: “It appears that organisms displayed “rampant” within-species variation “in the ‘warm afterglow’ of the Cambrian explosion,” Hughes said, but not later. “No one has shown this convincingly before, and that’s why this is so important.””From an evolutionary perspective, the more variable a species is, the more raw material natural selection has to operate on,”….(Yet Surprisingly)….”There’s hardly any variation in the post-Cambrian,” he said. “Even the presence or absence or the kind of ornamentation on the head shield varies within these Cambrian trilobites and doesn’t vary in the post-Cambrian trilobites.”
    University of Chicago paleontologist Mark Webster
    http://www.terradaily.com/repo.....s_999.html

    As well humans themselves are shown to be losing Genetic Diversity not gaining it even though they now have a large population size:

    “We found an enormous amount of diversity within and between the African populations, and we found much less diversity in non-African populations,” Tishkoff told attendees today (Jan. 22) at the annual meeting of the American Association for the Advancement of Science in Anaheim. “Only a small subset of the diversity in Africa is found in Europe and the Middle East, and an even narrower set is found in American Indians.” Tishkoff; Andrew Clark, Penn State; Kenneth Kidd, Yale University; Giovanni Destro-Bisol, University “La Sapienza,” Rome, and Himla Soodyall and Trefor Jenkins, WITS University, South Africa, looked at three locations on DNA samples from 13 to 18 populations in Africa and 30 to 45 populations in the remainder of the world.-

    Human Genome in Meltdown – January 11, 2013
    Excerpt: According to a study published Jan. 10 in Nature by geneticists from 4 universities including Harvard, “Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants.”,,,:
    “We estimate that approximately 73% of all protein-coding SNVs [single-nucleotide variants] and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000 -10,000 years. The average age of deleterious SNVs varied significantly across molecular pathways, and disease genes contained a significantly higher proportion of recently arisen deleterious SNVs than other genes.”,,,
    As for advantageous mutations, they provided NO examples,,,
    http://crev.info/2013/01/human-genome-in-meltdown/

    Daily thought: blue eyes and other gene mutations, April 25, 2013
    Excerpt: “Research on blue-eyes has led many scientist to further affirm that humans are truly mere variations of the same origin. About 8% of the world’s total population has blue eyes so blue eyes are fairly rare. In fact, blue eyes are actually a gene mutation that scientist have researched and found to have happened when the OCA2 gene “turned off the ability to produce brown eyes.”
    http://www.examiner.com/articl.....-mutations

    Dr. John Sanford “Genetic Entropy and the Mystery of the Genome” 1/2 – video
    http://www.youtube.com/watch?v=pJ-4umGkgos

  11. 11
    wd400 says:

    Apart from point-scoring (which Coyne does enough of too, but doesn’t interest me much) this doesn’t make a substantive difffernce to the studies.

    The only Nes that are likely to overestimate the census population size related to variance in offspring per individual (relevant to captive populations, but not really wild ones) and variance in population size. This latter one means the effective populatin size of a population right at the point of a bottle neck would be greater than it’s census size. Turned around, to explain a population growing from 2 to 6 billion in 10,000 years it would give us a modern effective population size of 400 or so. Many times lower than the observed.

    Of course, you can create some after-the-fact justification that keeps a literal Adam and Eve if you want (just like you can claim the world was created yesterday complete with memories), it’s just that there is no scientific support for that idea.

  12. 12
    littlejohn says:

    wd400
    The point is this- it is a plausible hypothesis that there was literally, one woman from which all humanity has descended, and that scenario is precisely what the Bible claims.

    The fun part is the tree thinking aspect, right? Interestingly, evolutionary biology is obsessed with tree building, and it just so happens, several models can be constructed that precisely fit natural history, as explained by secular science, and predicted by the holy scriptures.

  13. 13
    wd400 says:

    The point is this- it is a plausible hypothesis that there was literally, one woman from which all humanity has descended,

    Do you mean ‘mitochondrial Eve’? It’s an inevtiable consequence of finite population sizes that someone is the common ancestor of out matralines (and indeed, the same applies to all species). I’m not sure how that meets a prediction of the scriptures. Perhaps I’m not understanding your point?

  14. 14
    littlejohn says:

    There is significant congruence between the findings of secular science, and biblical predictions in the book of Genesis, and in particular, in regards to the time-line of human evolution.

    If you are interested in more information, Daniel Friedmann has written 2 short books on the subject, “The Genesis One Code”, and more recently, “The Broken Gift”.

    I believe Mr. Friedmann is on the right track, but also believe better and more precise models are coming soon, once the Biblical parable embedded in Genesis is unlocked.

  15. 15
    wd400 says:

    Without knowing what these apparent similarities are there is a little I can say about them. But it’s pretty clear that genetic data doesn’t support a literal Adam and Eve as co-founders of humanity, which was obstensibly the point of this thread?

  16. 16
    bornagain77 says:

    wd400 confidently claims that:

    But it’s pretty clear that genetic data doesn’t support a literal Adam and Eve as co-founders of humanity, which was obstensibly the point of this thread?

    And just what genetic evidence do you base such confidence on? The genetic similarity between chimps and Humans is turning out to be far less that what we were originally misled to believe by neo-Darwinists:

    Guy Walks Into a Bar and Thinks He’s a Chimpanzee: The Unbearable Lightness of Chimp-Human Genome Similarity – 2009
    Excerpt: One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. Relative differences: The myth of 1% Science 316: 1836.). ,,, In short, the figure of identity that one wants to use is dependent on various methodological factors.
    http://www.evolutionnews.org/2.....think.html

    Even ignoring the subjective bias of ‘various methodological factors’ that Darwinists introduce into these similarity studies, the first inkling, at least for me, that something was terribly amiss with the oft quoted 99% similarity figure was this,,,

    Humans and chimps have 95 percent DNA compatibility, not 98.5 percent, research shows – 2002
    Excerpt: Genetic studies for decades have estimated that humans and chimpanzees possess genomes that are about 98.5 percent similar. In other words, of the three billion base pairs along the DNA helix, nearly 99 of every 100 would be exactly identical.
    However, new work by one of the co-developers of the method used to analyze genetic similarities between species says the figure should be revised downward to 95 percent.
    http://www.caltech.edu/content.....arch-shows

    this had caught my eye in 2008,,,

    Chimpanzee?
    10-10-2008 – Dr Richard Buggs – research geneticist at the University of Florida
    …Therefore the total similarity of the genomes could be below 70%.
    http://www.idnet.com.au/files/pdf/Chimpanzee.pdf

    In late 2011 Jeffrey P. Tomkins, using an extremely conservative approach, reached the figure of 87% similarity:

    Genome-Wide DNA Alignment Similarity (Identity) for 40,000 Chimpanzee DNA Sequences Queried against the Human Genome is 86–89% – Jeffrey P. Tomkins – December 28, 2011
    Excerpt: A common claim that is propagated through obfuscated research publications and popular evolutionary science authors is that the DNA of chimpanzees or chimps (Pan troglodytes) and humans (Homo sapiens) is about 98–99% similar. A major problem with nearly all past human-chimp comparative DNA studies is that data often goes through several levels of pre-screening, filtering and selection before being aligned, summarized, and discussed. Non-alignable regions are typically omitted and gaps in alignments are often discarded or obfuscated.
    In an upcoming paper, Tomkins and Bergman (2012) discuss most of the key human-chimp DNA similarity research papers on a case-by-case basis and show that the inclusion of discarded data (when provided) actually suggests a DNA similarity for humans and chimps not greater than 80–87% and quite possibly even less.
    http://www.answersingenesis.or.....n1/blastin

    99%? 95%? 87%? 70%? How Similar is the Human Genome to the Chimpanzee Genome? – March 2010
    Excerpt: The nonsensical idea that human and chimp DNA are 99% similar comes from misinterpreting a 1975 paper by Mary-Claire King and A. C. Wilson.,,,
    Of course, the big question is: If 99% similarity was such strong evidence for a common ancestor between chimpanzees and humans, will 70% similarity be considered evidence against a common ancestor? Of course not! Evolution can use special pleading to accommodate any data. It does so with the fossil record, homology, etc. Why not do it with genome similarities as well?
    http://blog.drwile.com/?p=697

    Then last year, 2013, with better resolution of data, and still using an extremely conservative approach, Tomkins reached the figure of 70% genetic similarity between chimps and humans:

    Comprehensive Analysis of Chimpanzee and Human Chromosomes Reveals Average DNA Similarity of 70% – by Jeffrey P. Tomkins – February 20, 2013
    Excerpt: For the chimp autosomes, the amount of optimally aligned DNA sequence provided similarities between 66 and 76%, depending on the chromosome. In general, the smaller and more gene-dense the chromosomes, the higher the DNA similarity—although there were several notable exceptions defying this trend. Only 69% of the chimpanzee X chromosome was similar to human and only 43% of the Y chromosome. Genome-wide, only 70% of the chimpanzee DNA was similar to human under the most optimal sequence-slice conditions. While, chimpanzees and humans share many localized protein-coding regions of high similarity, the overall extreme discontinuity between the two genomes defies evolutionary timescales and dogmatic presuppositions about a common ancestor.
    http://www.answersingenesis.or.....chromosome

    Here a secular source comments on the Y chromosome:

    A False Trichotomy
    Excerpt: The common chimp (Pan troglodytes) and human Y chromosomes are “horrendously different from each other”, says David Page,,, “It looks like there’s been a dramatic renovation or reinvention of the Y chromosome in the chimpanzee and human lineages.”
    http://www.uncommondescent.com.....richotomy/

    Moreover, as if that was not devastating enough to the 99% similarity myth, a large percentage of completely unique orphan genes (10 to 30%,, no one really knows the exact percentage difference yet), with no sequence homology whatsoever, are now being found in each new genome that is sequenced, including humans and chimps:

    Genes from nowhere: Orphans with a surprising story – 16 January 2013 – Helen Pilcher
    Excerpt: When biologists began sequencing genomes they discovered up to a third of genes in each species seemed to have no parents or family of any kind. Nevertheless, some of these “orphan genes” are high achievers (are just as essential as ‘old’ genes),,,
    But where do they come from? With no obvious ancestry, it was as if these genes appeared out of nowhere, but that couldn’t be true. Everyone assumed that as we learned more, we would discover what had happened to their families. But we haven’t-quite the opposite, in fact.,,,
    The upshot is that the chances of random mutations turning a bit of junk DNA into a new gene seem infinitesmally small. As the French biologist Francois Jacob wrote 35 years ago, “the probability that a functional protein would appear de novo by random association of amino acids is practically zero”.,,,
    Orphan genes have since been found in every genome sequenced to date, from mosquito to man, roundworm to rat, and their numbers are still growing.
    http://ccsb.dfci.harvard.edu/w.....n_2013.pdf

    Proteins and Genes, Singletons and Species – Branko Kozuli? PhD. Biochemistry
    Excerpt: Horizontal gene transfer is common in prokaryotes but rare in eukaryotes [89-94], so HGT cannot account for (ORFan) singletons in eukaryotic genomes, including the human genome and the genomes of other mammals.,,,
    The trend towards higher numbers of (ORFan) singletons per genome seems to coincide with a higher proportion of the eukaryotic genomes sequenced. In other words, eukaryotes generally contain a larger number of singletons than eubacteria and archaea.,,,
    That hypothesis – that evolution strives to preserve a protein domain once it stumbles upon it contradicts the power law distribution of domains. The distribution graphs clearly show that unique domains are the most abundant of all domain groups [21, 66, 67, 70, 72, 79, 82, 86, 94, 95], contrary to their expected rarity.,,,
    Evolutionary biologists of earlier generations have not anticipated [164, 165] the challenge that (ORFan) singletons pose to contemporary biologists. By discovering millions of unique genes biologists have run into brick walls similar to those hit by physicists with the discovery of quantum phenomena. The predominant viewpoint in biology has become untenable: we are witnessing a scientific revolution of unprecedented proportions.
    http://vixra.org/pdf/1105.0025v1.pdf

  17. 17
    bornagain77 says:

    Moreover, genetic similarity is now known to be broadly similar across what are suppose to be widely divergent species,

    Kangaroo genes close to humans
    Excerpt: Australia’s kangaroos are genetically similar to humans,,, “There are a few differences, we have a few more of this, a few less of that, but they are the same genes and a lot of them are in the same order,” ,,,”We thought they’d be completely scrambled, but they’re not. There is great chunks of the human genome which is sitting right there in the kangaroo genome,”
    http://www.reuters.com/article.....P020081118

    First Decoded Marsupial Genome Reveals “Junk DNA” Surprise – 2007
    Excerpt: In particular, the study highlights the genetic differences between marsupials such as opossums and kangaroos and placental mammals like humans, mice, and dogs. ,,,
    The researchers were surprised to find that placental and marsupial mammals have largely the same set of genes for making proteins. Instead, much of the difference lies in the controls that turn genes on and off.
    http://news.nationalgeographic.....m-dna.html

    Family Ties: Completion of Zebrafish Reference Genome Yields Strong Comparisons With Human Genome – Apr. 17, 2013
    Excerpt: Researchers demonstrate today that 70 per cent of protein-coding human genes are related to genes found in the zebrafish,,,
    http://www.sciencedaily.com/re.....131725.htm

    Shark and human proteins “stunningly similar”; shark closer to human than to zebrafish – December 9, 2013
    Excerpt: “We were very surprised to find, that for many categories of proteins, sharks share more similarities with humans than zebrafish,” Stanhope said. “Although sharks and bony fishes are not closely related, they are nonetheless both fish … while mammals have very different anatomies and physiologies.
    http://www.uncommondescent.com.....zebrafish/

    Yet what accounts for such drastic differences in the species if the gene count is basically the same across widely divergent species (as well as supposedly closely related species)? Genomic regulatory systems do. For instance, alternative splicing, which is part of the extremely complex genomic regulatory system, is found to be species specific:

    Evolution by Splicing – Comparing gene transcripts from different species reveals surprising splicing diversity. – Ruth Williams – December 20, 2012
    Excerpt: A major question in vertebrate evolutionary biology is “how do physical and behavioral differences arise if we have a very similar set of genes to that of the mouse, chicken, or frog?”,,,
    A commonly discussed mechanism was variable levels of gene expression, but both Blencowe and Chris Burge,,, found that gene expression is relatively conserved among species.
    On the other hand, the papers show that most alternative splicing events differ widely between even closely related species. “The alternative splicing patterns are very different even between humans and chimpanzees,” said Blencowe.,,,
    http://www.the-scientist.com/?.....plicing%2F

    Yet variations to genomic regulatory systems are found to to catastrophic to (bottom up) neo-Darwinian scenarios because,,

    Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth (excellent update) – video
    Text from one of the Saddleback slides:
    1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
    2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
    3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
    Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.
    http://www.saddleback.com/mc/m/7ece8/

    verse and music:

    John 1:1-4
    In the beginning was the Word, and the Word was with God, and the Word was God. The same was in the beginning with God. All things were made by Him, and without Him was not anything made that was made. In Him was life, and that life was the Light of men.

    Lecrae Live at Passion 2013
    http://www.youtube.com/watch?v=gu59YLVTfV0

    Is evolution pseudoscience?
    Excerpt:,,, Thus, of the ten characteristics of pseudoscience listed in the Skeptic’s Dictionary, evolution meets nine. Few other pseudosciences – astrology, astral projection, alien abduction, crystal power, or whatever — would meet so many.
    http://creation.com/is-evolution-pseudoscience

    Darwinian Evolution is a Pseudo-Science – Part II
    https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/edit

  18. 18
    PaV says:

    Jerry Coyne as quoted in the Opening Post:

    The population sizes are estimated by back-calculating (based on reasonable estimates of mutation rates and other parameters) how small an ancestral population could be and still give rise to the observed high level of genetic variation in our species.

    Note: 2,500 is larger than two.

    This means, of course, that Adam and Eve couldn’t have been the literal ancestors of all humanity.

    This certainly is not an area of expertise on my part, but it looks like Dr. Coyne couldn’t have muddled it up any worse than he did.

    =======>

    From the version of the Sheehan paper that is available online, we know that she is employing a “coalescent method.”

    [From the abstract of the Sheehan paper of March 2013:]

    Here, we present a new coalescent-based method that can e?ciently infer population size changes from multiple genomes, providing access to a new store of information about the recent past.

    Now, what does Wikipedia tell us about such methods?

    [From Wikipedia:]

    Consider two distinct haploid organisms who differ at a single nucleotide. By tracing the ancestry of these two individuals backwards there will be a point in time when the MRCA is encountered and the two lineages will have coalesced. . . .

    At each successive preceding generation, the probability of coalescence is geometrically distributed — that is, it is the probability of noncoalescence at the t ? 1 preceding generations multiplied by the probability of coalescence at the generation of interest:

    P_c(t)=(1-1/2N_e)^(t-1)x(1/2N_e).

    For sufficiently large values of Ne, this distribution is well approximated by the continuously defined exponential distribution:

    P_c(t)=(1/2N_e)x exp(-[t-1]/2N_e)

    From these equations, it is quite clear that the “coalescent method” absolutely needs a number for the effective population size (= N_e). One can employ the method to sort of ‘back in’ to a number which works in known ways in other instances.

    So, effective population sizes are part and parcel of “coalescent methods.” Period. Nothing new here. Nothing important.

    ==========>

    However, here’s what Sheehan, et. al. have to say in their paper:

    [From the Sheehan paper first submitted in March 2013:]

    As shown in Figure 10(b), our method inferred that CEU [n.b. this means European]and YRI [This means African] had very similar histories in the distant past up until about 117 kya; discrepancies up to this point are most likely due to few observed ancient coalescence events with the leave-one-out approach. We inferred that the European population underwent a severe (out-of-Africa) bottleneck starting about 117 kya, with the e?ective population size dropping by a factor of about 12 from ? 28,000 to ? 2,250. Furthermore, at the level of resolution provided by our time discretization, our results suggest that the Euro-pean population has recovered from the bottleneck to an average e?ective size of ? 12,500 for the past 16 thousand years.

    In contrast to previous ?ndings [e.g., Li and Durbin (2011)], our method did not infer a signi?cant drop in the YRI population size during the early out-of-Africa bottleneck phase in Europeans. Instead, the African e?ective population size seems to have decreased more gradually over time (possibly due to changes in structure) to an average e?ective size of ? 10,000 for the past 16 thousand years. We note that our results for real data are fairly robust to the choice of discretization, given that a su?cient number of coalescence events occur within each set of grouped intervals.

    From the bold-lettered sentences, one can infer that going back 117,000 years, the effective population size leading up to today’s Europeans shrank from N_e of 28,000 within the African lineage, to that of 2,250. Further back in time, both lineages would have been ‘coalesced,’ and one is free to assume that the effective population size as one goes further back in time would have been 28,000.

    Now, Dr. Coyne appears to have made three errors:
    (1) He supposes that the original population size of human ancestry was 2,250, instead of the 28,000 that the article implies;

    (2) He’s confused the “bottle-neck” that occurred in the “out of Africa” lineage 117,000 years ago, with that of the MCRA of ALL humans, which goes further back in time;

    and (3) He somehow thinks that what this particular modification of an earlier “coalescent method” has done is to give us the actual population size of humans, when, in fact, it is quite clear that the methodology employed by such “coalescent methods” cannot go back any farther than the MCRA, which only means that the genetics involved in leading up to the ‘original’ population is blind to this particular method, and so we don’t know how many generations were involved before the MCRA arose. Since homozygozity at a location is presumed by the method as a starting block, along with that of random drift, fixation of an allele via random drift takes, on average, 4N_e, or, in the case of 28,000 individuals, 112,000 generations!!! [BTW, 2^15=32,000 (approx.), so only 15 generations are needed to go from “Adam and Eve” to a population size of 28,000!]

    And, Jerry, 32,000 is greater than 28,000!

    ==========>

    One final note:

    This method uses a section of Chromosome #1 which is in a non-genic area, so that the “confounding” effects of “natural selection” can be discounted (i.e., as I said above, they assume random genetic drift). But we now know that even non-coding DNA is functional, and hence, should be preserved and affect by NS. So there is some dubious note to the method employed.

  19. 19
    wd400 says:

    The MRCA of humanity (or at least, of ‘contacted’ peoples, which can contribute to genetic studies) likely lived within the last 5,000 years. So these methods can certainly reach further back than the the last common ancestor of the population in question. Indeed the Li and Durbin papers goes back further than a million years without detecting a major bottleneck.

    I don’t know what the 2^15 business is meant to prove, but a population that grew like that would have an Ne of ~15

  20. 20
    bornagain77 says:

    wd400, I find it funny that you place enough confidence in the mathematics of population genetics, (with underlying Darwinian assumptions of course), to tell you that Adam and Eve could not have existed, but you don’t place any confidence in the mathematics of population genetics when the math tells you tells you that Darwinian evolution is effectively falsified:

    Using Numerical Simulation to Test the Validity of Neo-Darwinian Theory – 2008
    Abstract: Evolutionary genetic theory has a series of apparent “fatal flaws” which are well known to population geneticists, but which have not been effectively communicated to other scientists or the public. These fatal flaws have been recognized by leaders in the field for many decades—based upon logic and mathematical formulations. However population geneticists have generally been very reluctant to openly acknowledge these theoretical problems, and a cloud of confusion has come to surround each issue.
    Numerical simulation provides a definitive tool for empirically testing the reality of these fatal flaws and can resolve the confusion. The program Mendel’s Accountant (Mendel) was developed for this purpose, and it is the first biologically-realistic forward-time population genetics numerical simulation program. This new program is a powerful research and teaching tool. When any reasonable set of biological parameters are used, Mendel provides overwhelming empirical evidence that all of the “fatal flaws” inherent in evolutionary genetic theory are real. This leaves evolutionary genetic theory effectively falsified—with a degree of certainty which should satisfy any reasonable and open-minded person.
    http://www.icr.org/i/pdf/techn.....Theory.pdf

    Calling all Darwinists, where is your best population genetics simulation? – September 12, 2013
    Excerpt: So Darwinists, what is your software, and what are your results? I’d think if evolutionary theory is so scientific, it shouldn’t be the creationists making these simulations, but evolutionary biologists! So what is your software, what are your figures, and what are your parameters. And please don’t cite Nunney, who claims to have solved Haldane’s dilemma but refuses to let his software and assumptions and procedures be scrutinized in the public domain. At least Hey was more forthright, but unfortunately Hey’s software affirmed the results of Mendel’s accountant.
    http://www.uncommondescent.com.....imulation/

    Using Numerical Simulation to Better Understand Fixation Rates, and Establishment of a New Principle – “Haldane’s Ratchet” – Christopher L. Rupe and John C. Sanford – 2013
    Excerpt: We then perform large-scale experiments to examine the feasibility of the ape-to-man scenario over a six million year period. We analyze neutral and beneficial fixations separately (realistic rates of deleterious mutations could not be studied in deep time due to extinction). Using realistic parameter settings we only observe a few hundred selection-induced beneficial fixations after 300,000 generations (6 million years). Even when using highly optimal parameter settings (i.e., favorable for fixation of beneficials), we only see a few thousand selection-induced fixations. This is significant because the ape-to-man scenario requires tens of millions of selective nucleotide substitutions in the human lineage.
    Our empirically-determined rates of beneficial fixation are in general agreement with the fixation rate estimates derived by Haldane and ReMine using their mathematical analyses. We have therefore independently demonstrated that the findings of Haldane and ReMine are for the most part correct, and that the fundamental evolutionary problem historically known as “Haldane’s Dilemma” is very real.
    Previous analyses have focused exclusively on beneficial mutations. When deleterious mutations were included in our simulations, using a realistic ratio of beneficial to deleterious mutation rate, deleterious fixations vastly outnumbered beneficial fixations. Because of this, the net effect of mutation fixation should clearly create a ratchet-type mechanism which should cause continuous loss of information and decline in the size of the functional genome. We name this phenomenon “Haldane’s Ratchet”.
    http://media.wix.com/ugd/a704d.....fa9c20.pdf

    Why the inconsistency in how you weight the results from the mathematics of population genetics wd400? An unbiased observer might conclude that you are letting your personal philosophical bias dictate how you judge the mathematical evidence!

    Is evolution pseudoscience?
    Excerpt:,,, Thus, of the ten characteristics of pseudoscience listed in the Skeptic’s Dictionary, evolution meets nine. Few other pseudosciences – astrology, astral projection, alien abduction, crystal power, or whatever — would meet so many.
    http://creation.com/is-evolution-pseudoscience

    Darwinian Evolution is a Pseudo-Science – Part II
    https://docs.google.com/document/d/1oaPcK-KCppBztIJmXUBXTvZTZ5lHV4Qg_pnzmvVL2Qw/edit

  21. 21
    PaV says:

    WD400

    You misunderstood what I meant.

    Yes, of course, using the “coalescent method”, one travels from one ‘coalescent’ to another; or, from one ‘MCRA’ to the next. Wherever that process ends, you’re left with a ‘MCRA,’ and it is as far back as you can go. We then have no information of what happened before the establishment of that last ‘MCRA.’ Coyne’s attempt to extrapolate from that ‘effective population’ to the non-existence of “Adam and Eve” is still as wrong as ever.

    As to Li and Durbin, and their finding of no “bottleneck” even as far back as a million years, let’s remember this! Sheehan’s study is designed to overcome problems they perceived in the model used by Li and Durban. Again, this has no bearing whatsoever on Coyne’s errors.

    Lastly, you write:

    I don’t know what the 2^15 business is meant to prove, but a population that grew like that would have an Ne of ~15.

    How, exactly, did you arrive at a number of approx 15 for Ne?

    Please stipulate. Numbers, please.

    As to what I meant to prove, simply this: from one man and one woman, a population is reached in a very short number of generations. If I had assumed, for example, that Adam and Eve gave birth to ten children, who themselves, paired up and had 10 children as well, one would then arrive at a population size of 28,000 is much less than 15 generations. So, very generously, 15 generations is really all that is needed to reach Sheehan’s last ‘MCRA’. 15 generations is not enough time for any one mutation to arise and spread through the population, and thus serve as a ‘coalescent.’ 112,000 generations, on average, would be needed. And, using Coyne’s logic, 112,000 >>> 15. So, no extrapolations from the last ‘MCRA’ can be made, and, obviously, there’s enough time in generations for a single man and a single woman to give rise to Ne of 28,000 without it being detected.

    Q.E.D.

  22. 22
    PaV says:

    Let me correct a number I’m using: I’ve used 1/4Ne as the probability of a mutation spreading via random genetic drift through a population. But this is for diploid populations. Since we’re considering haploid populations, this would then be 1/2Ne. So the above number of generations needed for a population of 28,000, that of 112,000, should be rather 58,000. The point I make is still every bit as evident.

  23. 23
    wd400 says:

    How, exactly, did you arrive at a number of approx 15 for Ne?

    It’s the harmonic mean of the census population sizes. In this case, as the number of generations (t) get’s large Ne approaches t as the numerator is the genometric series (approaching 1) and the denominator is t.

    If a population really did grow from 2 to 32 000 the Ne would not be 32000 or anythng like it.

  24. 24
    wd400 says:

    I should add, there are allels currently seggregating in human populations that coalesce deeper in time than the human-chimp speciation (http://www.sciencemag.org/cont.....1578.short). Very hard to see how you could include these w/ a literal adam and eve.

  25. 25
    bornagain77 says:

    Again wd400 I am amazed at the severe bias you place on these mathematical models that are jerry-rigged to support your Darwinian philosophy,,,

    Ann Gauger on genetic drift – August 2012
    Excerpt: The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival. (For a review go here.) According to this theory, actual genetic history is presumed not to matter. Our genomes are full of randomly accumulating neutral changes. When generating a genealogy for those changes, their order of appearance doesn’t matter. Trees can be drawn and mutations assigned to them without regard to an evolutionary sequence of genotypes, since genotypes don’t matter.
    http://www.uncommondescent.com.....tic-drift/

    and the total disregard you have towards any mathematics that show Darwinian evolution to be astronomically unlikely. You state:

    Very hard to see how you could include these w/ a literal adam and eve.

    Why wd400 are you not even more concerned with the fact that Darwinian evolution cannot account for the fixation of a single ‘coordinated mutation’:

    Thou Shalt Not Put Evolutionary Theory to a Test – Douglas Axe – July 18, 2012
    Excerpt: “For example, McBride criticizes me for not mentioning genetic drift in my discussion of human origins, apparently without realizing that the result of Durrett and Schmidt rules drift out. Each and every specific genetic change needed to produce humans from apes would have to have conferred a significant selective advantage in order for humans to have appeared in the available time (i.e. the mutations cannot be ‘neutral’). Any aspect of the transition that requires two or more mutations to act in combination in order to increase fitness would take way too long (>100 million years).
    My challenge to McBride, and everyone else who believes the evolutionary story of human origins, is not to provide the list of mutations that did the trick, but rather a list of mutations that can do it. Otherwise they’re in the position of insisting that something is a scientific fact without having the faintest idea how it even could be.” Doug Axe PhD.
    http://www.evolutionnews.org/2.....62351.html

    Douglas Axe co-author of Science & Human Origins – video
    http://www.youtube.com/watch?v=XxMmLakH2LQ

    Population Genetics and Adam & Eve? – The answer you get depends on several unknown a-priori assumptions – Dr. Ann Gauger, Pt. 2 – podcast
    http://intelligentdesign.podom.....9_04-07_00

  26. 26
    PaV says:

    wd400

    If a population really did grow from 2 to 32 000 the Ne would not be 32000 or anythng like it.

    Yes, that’s right. So, in the numerator you have: [1/2+1/4+1/8+1/16+….1/32,000 (approx)]/15.

    But what if we say the population stabilizes at 28,000 for an additional four generations. Then, for the last seven generations we’d have: [1/8,000 + 1/16,000 + 1/32,000 + 1/28,000 + 1/28,000 + 1/28,000 + 1/28,000]/7 = (approx) 24,000 = Ne.

    Your noting of the calculated Ne is a picayune detail and seems meant only to distract and to detract. Nothing more. We’re orders of magnitude away from any significance in terms of coalescence.

  27. 27
    PaV says:

    wd400:

    I should add, there are allels currently seggregating in human populations that coalesce deeper in time than the human-chimp speciation (http://www.sciencemag.org/cont…..1578.short). Very hard to see how you could include these w/ a literal adam and eve.

    Are you trying to change the subject?

    You’ll notice that in the abstract of the paper they speak of NS acting over time.

    The method of “coalescence” presumes “random genetic drift.” It turns off NS. So you’re trying to compare apples and oranges.

    Did anyone say that common inheritance didn’t apply to Adam and Eve?

    (BTW, I don’t believe in common descent for the simple reason that this presupposes that form A had to give birth to form A’ in some finely graded fashion, and not to some kind of new form B. Common inheritance simply says that transitions have as their basis what went before; i.e., A and B share commonalities of all sorts.)

  28. 28
    wd400 says:

    The harmonic mean is number of elements divided by the sum of their reciprocals. A population that went from 2 to 32,000 then stabalised for 100 generatoins would have an Ne of… 100. You can’t slice out the midle section without including the ealier ones.

    I’m certainly acting in bad faith – I honestly can’t understand how you think these calculations save a literal Adam and Eve.

    The point about the ancient coalescnces is that these genes for which the version I have might might be more closely related to the version a chimp has than the one you have. Polumorphisms that were present before the human chimp split are still polymorphic.

  29. 29
    wd400 says:

    (PaV’s confusion about the calculation of the harmonic mean is down to me – as I flipped the terms denominator and numerator while hasily editng my comment. The substantive point remains – rapidly growing populations have very low Ne which is dominated by the size of the bottleneck even if census population size later stabalises)

  30. 30
    bornagain77 says:

    And again wd400, I have a very hard understanding how you can put such confidence in such a shabby ‘coalescent theory’ you are currently supporting:

    The idea that evolution is driven by drift has led to a way of retrospectively estimating past genetic lineages. Called coalescent theory, it is based on one very simple assumption — that the vast majority of mutations are neutral and have no effect on an organism’s survival.
    Ann Gauger

    As far as I can tell wd400 this ‘coalescent theory’, in which you are basing your conclusions as to whether there was an Adam and Eve or not, This theory of ‘genetic drift’, in which most mutations are assumed to be neutral, and, as PaV stated, Natural Selection is ‘turned off’, is nothing more than mathematical fantasy. In fact, Dr. Berlinski retorted to this ad hoc theory that you seem to place so much confidence in:

    Majestic Ascent: Berlinski on Darwin on Trial – David Berlinski – November 2011
    Excerpt: The publication in 1983 of Motoo Kimura’s The Neutral Theory of Molecular Evolution consolidated ideas that Kimura had introduced in the late 1960s. On the molecular level, evolution is entirely stochastic, and if it proceeds at all, it proceeds by drift along a leaves-and-current model. Kimura’s theories left the emergence of complex biological structures an enigma, but they played an important role in the local economy of belief. They allowed biologists to affirm that they welcomed responsible criticism. “A critique of neo-Darwinism,” the Dutch biologist Gert Korthof boasted, “can be incorporated into neo-Darwinism if there is evidence and a good theory, which contributes to the progress of science.”
    By this standard, if the Archangel Gabriel were to accept personal responsibility for the Cambrian explosion, his views would be widely described as neo-Darwinian.
    http://www.evolutionnews.org/2.....53171.html

    Dr. Hunter with a bit more restraint, and with a bit more clarity as to the shell game Darwinists are playing with the evidence, stated this in regards to this ‘coalescent theory’ in which most mutations are considered neutral:

    Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
    Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
    Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
    Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.
    http://darwins-god.blogspot.co.....ay-of.html

    wd400, even the assumption that mutations are neutral was not derived from empirical evidence, but was an assumption that was forced upon Darwinists by the math:

    Haldane’s Dilemma
    Excerpt: Haldane was the first to recognize there was a cost to selection which limited what it realistically could be expected to do. He did not fully realize that his thinking would create major problems for evolutionary theory. He calculated that in man it would take 6 million years to fix just 1,000 mutations (assuming 20 years per generation).,,, Man and chimp differ by at least 150 million nucleotides representing at least 40 million hypothetical mutations (Britten, 2002). So if man evolved from a chimp-like creature, then during that process there were at least 20 million mutations fixed within the human lineage (40 million divided by 2), yet natural selection could only have selected for 1,000 of those. All the rest would have had to been fixed by random drift – creating millions of nearly-neutral deleterious mutations. This would not just have made us inferior to our chimp-like ancestors – it surely would have killed us. Since Haldane’s dilemma there have been a number of efforts to sweep the problem under the rug, but the problem is still exactly the same. ReMine (1993, 2005) has extensively reviewed the problem, and has analyzed it using an entirely different mathematical formulation – but has obtained identical results.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 159-160

    Kimura’s Quandary
    Excerpt: Kimura realized that Haldane was correct,,, He developed his neutral theory in responce to this overwhelming evolutionary problem. Paradoxically, his theory led him to believe that most mutations are unselectable, and therefore,,, most ‘evolution’ must be independent of selection! Because he was totally committed to the primary axiom (neo-Darwinism), Kimura apparently never considered his cost arguments could most rationally be used to argue against the Axiom’s (neo-Darwinism’s) very validity.
    John Sanford PhD. – “Genetic Entropy and The Mystery of the Genome” – pg. 161 – 162

    A graph featuring ‘Kimura’s Distribution’ being correctly used is shown in the following video:

    Evolution Vs Genetic Entropy – Andy McIntosh – video
    http://www.metacafe.com/watch/4028086

    Thus wd400, I certainly see no empirical warrant for the confidence you place in your assumption that most mutations are neutral (i.e. the confidence you place in ‘genetic drift’). Especially considering the fact that common sense, and empirical evidence itself, contradicts your unwarranted assumption that most mutations are neutral:

    “Moreover, there is strong theoretical reasons for believing there is no truly neutral nucleotide positions. By its very existence, a nucleotide position takes up space, affects spacing between other sites, and affects such things as regional nucleotide composition, DNA folding, and nucleosome building. If a nucleotide carries absolutely no (useful) information, it is, by definition, slightly deleterious, as it slows cell replication and wastes energy.,, Therefore, there is no way to change any given site without some biological effect, no matter how subtle.”
    – John Sanford – Genetic Entropy and The Mystery of The Genome – pg. 21 – Inventor of the ‘Gene Gun’

    Unexpectedly small effects of mutations in bacteria bring new perspectives – November 2010
    Excerpt: Most mutations in the genes of the Salmonella bacterium have a surprisingly small negative impact on bacterial fitness. And this is the case regardless whether they lead to changes in the bacterial proteins or not.,,, using extremely sensitive growth measurements, doctoral candidate Peter Lind showed that most mutations reduced the rate of growth of bacteria by only 0.500 percent. No mutations completely disabled the function of the proteins, and very few had no impact at all. Even more surprising was the fact that mutations that do not change the protein sequence had negative effects similar to those of mutations that led to substitution of amino acids. A possible explanation is that most mutations may have their negative effect by altering mRNA structure, not proteins, as is commonly assumed.
    http://www.physorg.com/news/20.....teria.html

    Experimental evolution of gene duplicates in a bacterial plasmid model.- 2007
    The fate of gene duplicates subjected to diversifying selection was tested experimentally in a bacterial system.,,,
    In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow.,,,
    http://www.ncbi.nlm.nih.gov/pubmed/17211548

    Thus wd400, without empirical warrant, in fact with empirical evidence contradicting your ‘neutral’ assumption, I find the mathematical model you place so much confidence in so as to inform you about man’s ancestry, to be nothing but an exercise in mathematical wish fulfillment! ,,, i.e. You have left the bounds of true empirical science and are practicing nothing more than pseudo-science!

  31. 31
    Querius says:

    ba77 concludes the following:

    Thus wd400, without empirical warrant, in fact with empirical evidence contradicting your ‘neutral’ assumption, I find the mathematical model you place so much confidence in so as to inform you about man’s ancestry, to be nothing but an exercise in mathematical wish fulfillment!

    So, continuing in this vein, my question is why WD400 would continue to cling to Darwinism when the facts and the math have turned decisively against the idea?

    There are several possibilities:

    A. Strong desire to remain scientifically orthodox.

    B. Reasonable scientific scepticism.

    C. Fear of ridicule, ostracism, and career damage.

    D. Aversion to the moral and philosophical consequences.

    A. I would rule out A as a primary motivator. While it might be present to some degree, WD400’s posts are not consistent with the defensive nature of this position.

    B. Similarly, I think we can also rule out B on the grounds that a reasonable person would admit the challenges posed by emerging genetic, epigenetic, and mathematical data. Still, an argument can be made that WD400 is simply presenting all the counter–arguments in preparation to a dramatic shift in outlook. A stronger argument can be made that WD400 is steeped in 19th century Darwinism, and, as a result, all facts are tainted by the Darwinistic paradigm.

    C. This is certainly a valid and very real concern considering the professional carnage suffered by people who demonstrate even a neutral, unbiased treatment of people who agree with the Intelligent Design paradigm. Nevertheless, this motivator, like A is primarily defensive, and isn’t consistent with WD400’s posts.

    D. This would explain the posts and strict, religious adherence to a theory from the age colonialism and the industrial revolution. But we’re still somewhat lacking in the vituperation department, so I don’t know . . .

    Any ideas, ba77?

    -Q

  32. 32
    littlejohn says:

    wd400
    Was UCA an individual, or a population? And how can you know when? Maybe UCA is a trillion years old from another universe, eh?

    But in all seriousness, I think you probably truly have genuine faith in naturalistic science, and perhaps love your science. Therefore, I vote for none of the above.

  33. 33
    littlejohn says:

    Opps, I guess it could be B?

  34. 34
    bornagain77 says:

    “Any ideas, ba77?”

    None really that I would hazard a guess on. It is not as if wd400 is too dense to understand that Darwinism is bankrupt. Thus I cannot fathom his primary motivation for refusing to be honest. The underlying motives of a man’s heart is, many times, a mystery that would make the deepest mysteries in Quantum Mechanics seem like child’s play by comparison

  35. 35
    bornagain77 says:

    Querius, Thankfully there is One who does understand the human heart and is able to reach its deepest recesses.

    Proverbs 15:11
    Death and Destruction lie open before the LORD– how much more do human hearts!

    Music:

    Evanescence – My Heart Is Broken
    http://www.vevo.com/watch/evan.....WV41100052

  36. 36
    Querius says:

    ba77,

    The part I like the best is God’s promise of giving us a new heart that lets go of pride and selfish ambition and instead finds pure delight, amazement, appreciation, and reverence in discovering the designs hidden in nature—if only we are willing!

    -Q

  37. 37
    PaV says:

    wd400:

    If a population is steadily increasing, and then reaches some stabalized level, then please explain how you can then speak of a “bottle-neck.” How can something be constrained when it is steadily increasing to some greater level? Should the population shrink to some reduced level at some later time, then, yes, you can talk about a “bottle-neck.”

    I study quantum mechanics. Do you think something as simple as an harmonic mean is going to through me for a loop? Please.

    Where you go wrong is that you think these equations give us actual truth when, in fact, their educated guesses that involve making assumptions about a number of things. They’re just little tools—more like toys—that population geneticists use. To say that these types of equations constitute disproof of Adam and Eve is just silliness. Science isn’t God.

    And, again, should I point out to you that this method involves RGD which, as you should know, prescinds NS; so think about what you’re saying: human populations arose through completely random methods. This is an absurd scientific statement on its face. And, where, exactly, should we be looking for Darwinism here?

    Darwinists are wonderful. When it suits their purpose, they abandon their theory, and then tell others who dispute the theory that they don’t know what they’re talking about.

  38. 38
    wd400 says:

    If a population is steadily increasing, and then reaches some stabalized level, then please explain how you can then speak of a “bottle-neck.”

    The bottleneck is the very small starting size. That means the population will have much less diversity that one that has been at the present stable size for a very long time.

    I study quantum mechanics. Do you think something as simple as an harmonic mean is going to through me for a loop? Please.

    Well, you got it wrong…

    To say that these types of equations constitute disproof of Adam and Eve is just silliness. Science isn’t God.

    It’s not sillyness, and you yourself started by trying to use the tools to save the literal Adam and Eve. Of course someone cen beliefe in a lieteral Adam and Eve, but you can’t pretend the genetic evidence supports such a couple.

    And, again, should I point out to you that this method involves RGD which, as you should know, prescinds NS; so think about what you’re saying: human populations arose through completely random methods. This is an absurd scientific statement on its face. And, where, exactly, should we be looking for Darwinism here?

    Ok, what do you think would happen to an esimtate of population size if natural selection was operatin (which it is not, in most of the genome). Selection means fewer members of population contribute to the next generation than would otherwise be the case, so selection (positive or negative) makes Ne lower with repsect to the census population. In fact – scans of lowered Ne are one of means by which we can estimate historical selection.

    Darwinists are wonderful. When it suits their purpose, they abandon their theory, and then tell others who dispute the theory that they don’t know what they’re talking about.

    “Darwinists” are largely the invention of creationists. Evlutoinary biologists undertand that much of the variation in our genome can be best explained by neutral theory, other parts by selection. If someone can’t understand that modern evolutioary biology includes more than just natural selecton then they certainly don’t know what they’re talking about.

  39. 39
    bornagain77 says:

    You just don’t understand evolution wd400! 🙂

  40. 40
    PaV says:

    wd400:

    The bottleneck is the very small starting size. That means the population will have much less diversity that one that has been at the present stable size for a very long time.

    You didn’t answer the question. A “bottle-neck” OCCURS when a population’s size changes drastically shrinks from one generation to the next, or if it fluctuates wildly over time. You simply want to call the small starting size a “bottle-neck,” and no more. Remember, the coalescent method they employ can’t look beyond the ‘last’ effective popoulation size. It’s uncharted territory. You simply want to make the claim that this constitutes a ‘bottle-neck.’ You don’t get to make things up. If you look at the formula for Ne, it’s a summation. It doesn’t show a sum of minus infinity to plus infinity, or even zero to positive infinity. You have a starting population size, and an ending population size. That’s it. If you’re doing an experiment in the wild, or in the lab, you can keep track of all of this. But when they want to use molecular biology to go back in time, they simply back into these numbers.

    Ignorance cannot be replaced with exact equations—which is what you’re trying to do. Sorry.

    Well, you got it wrong…

    It’s one thing not to understand an equation, and quite another to make an algebra mistake, especially when you do it in a hurry so as not to waste any more time than is necessary.

    But, in the end, who really got it wrong? You come up with an answer of roughly the inverse of 1/6, 15, and then say this is the effective population size. Does that number make much sense? No. Isn’t the true Ne closer to 32,000 than it is to 15? No common sense employed. Just plug in the formulas. Follow the recipe. Recite the dictionary words.

    Here’s an example. Imagine 9,990 generations of population size 28,000, then followed by 10 generations of population size 100. Now think of 1 generation of population size 100, which then increases to 400 in the next generation, which then increases to 1,600 the next, and then increases to 6,400 in the fourth, 12,800 in the fifth, and 28,000 in the sixth and all the following up until the ten-thousandth generation.

    Per the FORMULA, the second lineage would have a higher Ne, but both would be about the same. Now tell me, WHERE did the “bottle-neck” take place? You have no idea mathematically, and if you ventured to say the bottleneck occurred in the first generation, you’d be off by almost 10,000 generations! Do I make myself clear?

    It’s not sillyness, and you yourself started by trying to use the tools to save the literal Adam and Eve.

    I used the tools so as to point out their limitations, something you don’t want to accept.

    Ok, what do you think would happen to an esimtate of population size if natural selection was operating (which it is not, in most of the genome). Selection means fewer members of population contribute to the next generation than would otherwise be the case, so selection (positive or negative) makes Ne lower with repsect to the census population. In fact – scans of lowered Ne are one of means by which we can estimate historical selection.

    How does this respond to my statement. I’m sure population geneticists have plenty of toys. Look, face it, the methods employed are for the vast majority of the time are educated guesses and nothing more. Before gel-phoresis methods, Darwinists were sure that there would be very few sites where SNPs would be found. Wrong. Very Wrong. And they were using the very same logic you applied in the paragraph above. But why should that slow down a Darwinist?

    “Darwinists” are largely the invention of creationists.

    A Darwinist is someone who believes in DARWIN’S theory of evolution. Do you believe in that theory, or not?

    A “creationist” is largely the invention of Darwinists. I stopped telling people I wasn’t a “Creationist” but got tired of having to do it over and over. “Creationist”, with a small letter, is nothing more than the attempt by Darwinists to lump anyone who disagrees with Darwin’s theory into the same camp as those who take the first six days of ‘Creation’ to mean six literal solar days. When it is objected that the person doesn’t believe that, then the Darwinist simply switches from ‘upper case’ Creationist to ‘lower case’ creationist. Now I believe that God created the world. I’m sure that Ken Miller also believes that God created the world. He simply believes that God used NS and such in bringing the full diversity of life into being. But I’m not afforded such leeway. Why? Because, whereas Ken Miller accepts Darwin’s theory, I do not. So that doesn’t make him a ‘creationist’ while it does me.

    So, the basic meaning of ‘creationist’ has really nothing at all to do with what one “believes” religiously, but, rather, whether or not one “believes” in Darwinism. IOW, you ERR in calling me a creationist—along with many others. But I DON’T ERR in calling you a Darwinist—-unless, of course, you want to tell everyone here and elsewhere that you really don’t believe in Darwin’s theory.

    If someone can’t understand that modern evolutioary biology includes more than just natural selecton then they certainly don’t know what they’re talking about.

    Many attempts have been made to understand genetics, some employ NS and some genetic drift, which has long been recognized as playing some role. But if you eliminate NS ENTIRELY, then Darwin is dead, and, guess what, then there is no longer any THEORY. What other theory of evolution has been proposed, exactly (not just some mechanism, but a full-blown theory. The only one I’m aware of is Margolis’ and now that of Shapiro)

    Let me ask you a question, did Mendel believe in Darwinism, or not? Did Mendel believe in God, or not? Did he believe that God created the world, or not? Was Mendel a ‘creationist’? IOW, it was a religious person who was behind all of what you want to promote as sensible science.

    Here is the ruination of population genetics. The genome of a moth: is it the genome of a moth, or of a butterfly?

    Just mull that one over a bit. Two hugely different phenotypes and the EXACT SAME genotype. If it is genetically the same, identical in fact, than how in the world do you explain the huge phenotypic differences? I await a wonderful answer here.

  41. 41
    bornagain77 says:

    PaV, while I read with your whole article with interest, and was pleased, it was the last part of your article that really caught my attention, namely:

    Here is the ruination of population genetics. The genome of a moth: is it the genome of a moth, or of a butterfly?

    Just mull that one over a bit. Two hugely different phenotypes and the EXACT SAME genotype. If it is genetically the same, identical in fact, than how in the world do you explain the huge phenotypic differences? I await a wonderful answer here.

    I would certainly like to have a solid reference for that if you have it handy! 🙂

  42. 42
    wd400 says:

    Remember, the coalescent method they employ can’t look beyond the ‘last’ effective popoulation size.

    Kind of… but it’s effective population size at the last coalescence that matters. And that size reflects the history of that population as well.

    You have a starting population size, and an ending population size. That’s it. If you’re doing an experiment in the wild, or in the lab, you can keep track of all of this. But when they want to use molecular biology to go back in time, they simply back into these numbers.

    Ignorance cannot be replaced with exact equations—which is what you’re trying to do. Sorry.

    You don’t get it. The the coalescent method estimates Ne, the harmonic mean formula calculates Ne exactly under one variable (fluctuating population size). The FORMULA shows you Ne would be low in the scenario you dreamed up. If Ne was low the coalsencent estimator would recover that signal

    How does this respond to my statement

    You wanted to make something of the fact the coalescent is based on a neutral expectation. But, in fact, if selection was operating on these variants the coalsecnt approach would make Ne even smaller relative to the cenusus size. If this quiblle was meant to save the literal adam and eve (the poitn of this thread?) then if fails.

    I can find much joined-up-thinking in the rest of your comment, but in answer to your quesitons:

    I’m not a “Darwinist”, I”m an evolutionary biologist. Adatation is real, and there is abundant evidence for the the operation of natural selection in genomes and in teh wild. Darwin’s ideas are still important, but 21st century biology is much more than Darwinism.

    I presume you mean “caterpillar and butterfly” not moth. But I still don’t know why you’d think that was a problem for population genetics.

  43. 43
    bornagain77 says:

    Response to John Wise – October 2010
    Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called “saturation mutagenesis”1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans–because none of the observed developmental mutations benefit the organism.
    http://www.evolutionnews.org/2.....38811.html

  44. 44
    bornagain77 says:

    Hey wd400, You’re Going the Wrong Way – video
    https://www.youtube.com/watch?v=_akwHYMdbsM

  45. 45
    Eric Anderson says:

    For neutral evolution, population size doesn’t matter, correct? At least not in terms of having a particular change becoming fixed in the population.

  46. 46
    Eric Anderson says:

    Dumb question about neutral evolution:

    There are three basic types of changes: deleterious, beneficial, and neutral.

    1. Deleterious everyone knows what will happen.

    2. Beneficial can help the organism and be subject to selection.

    3. Neutral is just that — neutral to the organism and invisible to selection.

    It is argued by some that most changes/mutations are neutral. Let’s assume for a moment that is true.

    Why then are neutral changes sometimes held up as an example of evolution? By very definition, they are neutral — meaning they are, by very definition, not causing any evolution.

    Indeed, the existence of numerous neutral changes in an organism demonstrates that the organism robust against change. In other words, it is resistant to evolution.

    All of this follows rather naturally and, it seems, inexorably from the idea of pervasive neutral changes/mutations.

    Thus, at most, neutral changes are just that — neutral — and not relevant for evolution. On the other side, however, one could quite easily argue that neutral changes demonstrate that organisms can undergo significant perturbations in the genome and otherwise, while still not exhibiting any meaningful organismal change, and therefore neutral changes/mutations are actually evidence against the “plasticity” of organisms that is important to evolutionary theory.

    Thoughts?

  47. 47
    scordova says:

    The theory of neutral evolution came about based on the question: “is the diversity in a species due to natural selection or lack thereof”. Then they began to explore things like Haldane’s dilemma, the cost of natural selection (i.e. how many individuals do you kill off to maintain features).

    For example, with a genome of 4 giga base pairs, how many people do you have to kill off per generation to maintain conformity? If for example you have a mere 6 mutations per individual that deviate from a “good” configuration, every female human would have to give birth to 800 kids!

    Thus, it became obvious most evolution had to be free of selection, if design appears, natural selection had to be mostly absent as a cause.

    I provided sample calculations here at the bottom of the essay.

    http://www.uncommondescent.com.....e-fittest/

    Were my claims novel? Hardly, I got it from the evolutionists themselves, but it seems they prefer to let confusion reign lest IDists and creationists put two and two together and realize selection doesn’t much work as a theory of evolution.

  48. 48
    Eric Anderson says:

    Thus, it became obvious most evolution had to be free of selection, if design appears, natural selection had to be mostly absent as a cause.

    Right. But with respect to neutral changes, it is called “evolution” only in a loose (and, frankly, slightly deceptive) sense, because, by definition, neutral changes aren’t causing evolution. At least not in any meaningful sense. It is “evolution” only if every change is evolution, in which case we have robbed the term of any substance. Evolution now means essentially “everything that happens”, even if it doesn’t affect the organism in the least.

  49. 49
    scordova says:

    It is “evolution” only if every change is evolution,

    By golly, I think you’ve got it. 🙂

  50. 50
    Joe says:

    If evolution = a change in allele frequency AND neutral mutations do not affect allele frequency, then no evolution takes place with neutral mutations.

    However if you define evolution as descent with modification then neutral mutations are a modification and therefor evolution.

    That said not all deletrious mutations get eliminated and beneficial is relative.

    And with neutral mutations population size does matter wrt becoming fixed. The larger the population the less likely anything will become fixed. No one has ever confirmed Kimura’s equations- not in the wild.

  51. 51
    Querius says:

    Typically, evolution is loosely defined as “change over time.” Once you’re bullied into agreeing that you believe things change over time, you are “baptised” as an evolutionist. The next part is that you’re supposed to accept without criticism the entire corpus of just-so stories that range from plausible to hilarious.

    One factor often overlooked is that a single beneficial mutation must occur in multiple individuals, a certain percentage of the population, without which chance alone will result in the mutation disappearing from the genome.

    -Q

  52. 52
    wd400 says:

    There’s a lot of comments here, so here are some brief and general answers.

    1. Population size matters in neutral theory. Othersiwse neutral coalescent methods couldn’t establish historical population sizes. The special case in which population size vanishes in calculation is when we work out the rate at which new variants fix (or differences btweeen sister species accrue).

    2. I don’t know why you would think neutral change was not evolutionary change. And neutral variants are alleles

    3. PaV and others want to seem to want to pit neutral theory, and the fact most variants are not subject to selection against “Darwinism” as if onyl one can win. In fact, neutral nearly-neutral and selective models represent a contium. They simply explain the behaviour of genomes and genes and organism under different slection intensities. We can use what we know of biology to detect natural selection (indeed, neutral thoery provides teh null hypothesis for such tests) but we can also show that most genetic change is neutral. There is no conflict there.

    4. The fact that most of the genome evolves close the neutral rate is certainly evidence that organisms can withstain mutations without fitness. That’s one fo the good arguemtns for junk DNA, for instance. BUt again, that doesn’t meant tehre aren’t genetic variants that are subject to selection.

    5 One factor often overlooked is that a single beneficial mutation must occur in multiple individuals, a certain percentage of the population, without which chance alone will result in the mutation disappearing from the genom

    Nah. Such “soft sweeps” may in fact be common. But nothng requires the same mutation to arise in multiple individuals before it is swept to fixation. Indeed, neutral theory shows us that mutations with no selective advantage can eventually take over a population.

  53. 53
    PaV says:

    BA77:

    Sorry. I was in a terrible rush at the time. I don’t know how that error eluded me. I meant a worm and a butterfly, not a “moth and a butterfly.”

    Sorry again. Wish I could edit that one out since someone might not read this post.

  54. 54
    Joe says:

    wd400:

    Indeed, neutral theory shows us that mutations with no selective advantage can eventually take over a population.

    That’s the propaganda anyway. But no one has shown such a thing.

    But anyway, thanks for the correction as I wrongly thought that most neutral mutations, wrt Kimura, were in non-coding regions. That said we now know that so-called silent mutations aren’t silent at all. It all depends and that would affect the neutral theory.

  55. 55
    PaV says:

    wd400:

    Kind of… but it’s effective population size at the last coalescence that matters. And that size reflects the history of that population as well.

    Really. Let’s remember that all of this is sort of dreamed up. These equations are chosen for various reasons. That doesn’t make them TRUTH STATEMENTS.

    But, as usual, you’ve missed my point. I gave an example to two scenarios for a population having 10,000 generations. One starts out small and grows quickly. Almost 10,000 generations later, per the equation (not “truth statement”),under the scenario I depict, the “effective population size” would be the very same as for one that started out at 28,000 and remained the same for 9,990 generations, but then was decimated, and had a population size of only 100 for the last 10 generations. Isn’t it quite clear that this last scenario represents what is meant by a “bottleneck” while the other did not? Yet, basically the same numbers. Do you get it yet?

    You don’t get it. The the coalescent method estimates Ne, the harmonic mean formula calculates Ne exactly under one variable (fluctuating population size). The FORMULA shows you Ne would be low in the scenario you dreamed up. If Ne was low the coalsencent estimator would recover that signal.

    Look above at the formula for Probability of Coalescence. There are two variables: Ne and t=time. Now tell me, do they plug in a value of Ne and solve for time, or do they plug in a value for ‘t’ and then solve for Ne? Maybe this will help you see things more clearly.

    You wanted to make something of the fact the coalescent is based on a neutral expectation. But, in fact, if selection was operating on these variants the coalsecnt approach would make Ne even smaller relative to the cenusus size. If this quiblle was meant to save the literal adam and eve (the poitn of this thread?) then if fails.

    You missed my point completely. So what if the Ne is slightly lower. It’s almost meaningless since you can’t look beyond it, and you have no way of knowing what, and how anything, happened.

    My point was that Darwinists casually jettison the “theory of evolution”=Darwinism, when it suits their purposes. IOW, prove “evolution” happened no matter what means you employ, and no matter what contradictions it erects. And, of course, this “proof” is, like ‘beauty’ (and anything else that is SUBJECTIVE!) only in “the eye of the beholder.”

    I’m not a “Darwinist”, I”m an evolutionary biologist. Adatation is real, and there is abundant evidence for the the operation of natural selection in genomes and in teh wild. Darwin’s ideas are still important, but 21st century biology is much more than Darwinism.

    If you’re an “evolutionary biologist”, and want to move on from Darwin, that what, exactly, is the “theory” you employ? Can you explain this for all of us here at UD? Just exactly what is your theory. And, of course, since you’ve moved on from Darwin, don’t bother mentioning random variation and NS, because that’s Darwinism. So, give us your theory, please.

    And, I suspect it will take many years, probably decades, well after my death, before my notions will be prove correct; however, when you say “abundant evidence for the operation of natural selection in genomes,” this would be better stated: “there is abundant evidence for the apparent operation of natural selection in genomes.”

    I fully suspect that when the final chapter on all of this is written, we will discover that the genome ‘adapts’ itself to the environment, and the entire ‘adaptive’ process relies on information provided by the genome itself, and that NS—which is no more than lack of viability of an organism—is simply a by-product of the adaptive response.

    Nevertheless, that biochemical pathways can be turned ‘on’ and turned ‘off’ via the decimation of a population doesn’t mean that this process can be used in a directed way for the building up of, let’s say, ‘new’ biochemical pathways.

    As I’ve stated before, if a human being at age 5 can jump over a basketball, and at age 12 jump over a wheelbarrow, and at age 22 jump over an upright oil barrel, doesn’t mean that at age 75, he will be able to jump over roof-tops. Do you get my analogy?

    P.S. I’ve stated over and over again, that if Darwin had titled his book “Origins of Adaptations,” I would find very little fault with it. But ‘adaptations’ do not ‘evolution’ make!

    I presume you mean “caterpillar and butterfly” not moth. But I still don’t know why you’d think that was a problem for population genetics.

    I find it almost astonishing that you can’t think this problem through.

    The theory of evolution, =Darwinism in various forms, tells us that genetic change within the genome can build up over time and result in the kinds of changes in phenotype that we see in the fossil record over time.

    And, yet, the EXACT, SAME GENOTYPE—-NO GENETIC DIFFERENCES–is responsible for two, entirely different–hugely different–phenotypes, including different morphology, locomotion, feeding habits, and instincts. The unavoidable conclusion is that morphological changes CANNOT be simply equated to genomic changes. And, in the case of the caterpillar and the butterfly, this is so glaringly apparent as to make nonsense of the field of population genetics.

  56. 56
    Eric Anderson says:

    Thanks, wd400:

    Population size matters in neutral theory. Othersiwse neutral coalescent methods couldn’t establish historical population sizes. The special case in which population size vanishes in calculation is when we work out the rate at which new variants fix (or differences btweeen sister species accrue).

    Yes, I was referring to the fixation of new variants in the population. So, given a starting population, in order fix a number of new changes occurring in, say, a genome over time, the size of the population would presumably be irrelevant? I’m not arguing over coalescent methods, just trying to make sure I’m clear on the fixation of new variants.

    I don’t know why you would think neutral change was not evolutionary change. And neutral variants are alleles.

    Oh, sure. It is all “evolution.” As long as we are so loose with our definitions as to lump virtually everything that happens under the heading of “evolution.” And then we engage in the deceptive (whether purposeful or negligent) rhetoric of implying that these evidences of “evolution” demonstrate the truth of “evolution” broadly speaking. Things like new body plans, new functional systems, new information-rich sequences. All of which are the real fundamental requirements of producing new life forms on Earth, and none of which — by definition — come about through neutral changes.

    This is the kind of muddled approach that leads many supporters to pound the table and proclaim the “fact of evolution!”, even though none of the real fundamental questions has ever been observed or demonstrated.

    So, yes, we can call neutral changes “evolution.” As long as we are willing to acknowledge that evolution in that sense really means nothing of consequence and is just a surrogate for some change, any change, an observation that something happened.

    We can use words like “neutral evolution” to try and bring the observation of neutral changes under the umbrella of evolution. But an objective review might suggest that, if anything, the existence of many neutral changes in an organism means that the organism is robust against substantive change — a real life example of not evolving in any meaningful sense.

  57. 57
    PaV says:

    Joe:

    That said we now know that so-called silent mutations aren’t silent at all. It all depends and that would affect the neutral theory.

    That’s right, Joe. It’s good that you’re pointing this out. Now, the Darwinists—oops, the “evolutionary biologists”—have another conundrum they must face. It’s never ending. As I say: “Another day, another bad day for Darwinism.”

  58. 58
    wd400 says:

    PaV,

    I really see no point in carrying this on. You said in your first post that you weren’t an expert in this field, and so it has proved.

    I understand that in the scnarios you dreamed up the Ne (and so genetic diversity) would be approximately the same at the end. I don’t know why I shuold care. Again, if there had been a time in which the human population was 2 people in last million years these methods would detect it.

    The rest is wild and whirling words. The idea that gene expression is important (polyphenism) is hardly new to evolutionary biology (Wilson and King famously suggested gene expression differences would be the principal differnces between humans and chimps in the 1970s). But gene expression differences are tehmselves driven by genes (regulatory sequences and tanscription factors and even fashionable but probably less important things like miRNA and DNA methyl-transferases).

  59. 59
    bornagain77 says:

    “You said in your first post that you weren’t an expert in this field, and so it has proved.”

    aka “You just don’t understand evolution’. 🙂

  60. 60
    bornagain77 says:

    The Mismeasure of Man: Why Popular Ideas about Human-Chimp Comparisons Are Misleading or Wrong – Ann Gauger March 10, 2014
    http://www.evolutionnews.org/2.....83011.html

  61. 61
    Joe says:

    wd400:

    Again, if there had been a time in which the human population was 2 people in last million years these methods would detect it.

    If those methods apply. That is the question and we say they do not.

  62. 62
    PaV says:

    wd400,

    I watched the video of Dr. Robert Carter’s presentation, and he obviously takes these calculations seriously. So, I think I should afford them more propriety than I have so far.

    Yes, they tell us something. And, yes, prima facie they point to a “population” and not “two people.” But Dr. Carter makes clear that, from a biblical point of view, at least two factors must be considered when interpreting the data. The first is the Biblical Flood, which, in all likelihood (I’m not a YEC) occurred after the last Ice Age around 12,000 years ago, and also the Tower of Babel phenomenon, which, in secular terms would simply mean that primitive populations broke off from one another and became geographically, and reproductively, isolated. This alone could account for a large portion of the diversity and require us to view these numbers differently.

    I still stand by this statement wd400: “These equations are not ‘truth statements.'” Even if a Christian like Francis Collins accept these data as determining for certain that “man” arose from a population of at least 2,250, he could EASILY be wrong, as others could. This is NOT EXACT science. Just because numbers are being dealt with here does not mean that they constitute some kind of ‘mathematical proof.’ They do not. They have to be understood properly. Their limits in scope have to be taken into account. Dr. Carter makes clear that under certain, perhaps reasonable, assumptions, these conclusions can be interpreted “oppositely” to how they have been interpreted. So, to say the least, leeway in interpretation certainly exists.

    Let me point this out. I ran some numbers for a population that 790 of the 800 generations, had a population size of 10,000. The first seven generations were less, and the final three were less. What was the effective population size? 793. Does this make sense?

    Not really. Why? Because since we’re dealing with a sum, we can shift the last three generations to the front—the order of the sum (per the equations used) does not make a difference. This would mean that for 10 generations the population size was, on average (not harmonic mean!), 1,000, and then it was 10,000 for 790 generations! Think about this, wd400.

    Do you really want to tell me that random genetic drift didn’t take place within a Ne of 10,000? Do you really want to stick to this claim? Think it through. Think about the size of the population, the mutation rate, the number of mutations entering the genomes of that population. Are you telling me that the amount of heterozygosity does NOT reflect a population size of 10,000, but, rather, a population size of 793? Is that what you want to tell me?

    IOW, everything in this discussion hinges on using the harmonic mean to establish an effective population size. And, so, the question then arises: how accurate is this assumption? And, a related question arises? Why is this formula used? And, then, one more question: What are the limitations of using this formula?

    And, now, let’s remember a little bit of history: in the 90’s, they went looking for “mitochondrial Eve”, and were certain that they would find more than ONE such “Eve.” But that’s not what happened. Why did they believe this. Was it population genetics, or simply that they wanted to prove the Bible wrong? I think I know the answer.

    Then they went looking for “Y-Adam,” again convinced that they would find more than ONE such “Adam.” And they thought for sure they would find more than one because they were sure that the Bible was wrong. And what happened? Yes, indeed, only ONE “Y-Adam.”

    Now it’s “there couldn’t have been just one Adam and one Eve because the ‘bottleneck’ shows the Ne as being 2,250.” Darwinists have been wrong twice already. I fully suspect that when the final chapter is written, they will turn out to be wrong again—not wrong in the sense of coming up with wrong numbers, but in having interpreted those numbers wrongly.

    If Francis Collins wants to say, with Jerry Coyne, that we have “proof,” that’s his business. But I say, let’s wait until more data are available, and more analyses done: then we can see where the science is pointing.

  63. 63
    PaV says:

    wd400:

    Here’s something to think about.

    Ne of 2,250. We assume neutral drift and not NS at play. How much time will it take for ONE!!!! mutation to become “fixed” in the population? Answer: 2Ne.

    So, 2 x 2,250 x 25yrs/gen = 112,500 yrs!!!

    So, just think what the brilliant population geneticists are telling us. That from the time than humans lived in Africa, only ONE!!! allele has become fixed, and only ONE!!!mutation within that allele!!!!

    What a great story of macro-evolution this is!!!!

    Would you care to respond?

  64. 64
    wd400 says:

    The derrivation of the forumlae for Ne are not straightforward, but are covered in many textbooks. It’s not true, or even possible so far as I can tell, that Wilson and Cann though there would be more that one MRCA mitochondrial DNA (or Y-chom). How would that even work?

  65. 65
    wd400 says:

    PaV,

    Ne of 2,250. We assume neutral drift and not NS at play. How much time will it take for ONE!!!! mutation to become “fixed” in the population? Answer: 2Ne.

    So, 2 x 2,250 x 25yrs/gen = 112,500 yrs!

    This is a common error. It would take ~112,500 years for any given mutation to fix. But there many mutations in each generation. In fact, the fixation rate is equal to the per-individual mutation rate. The brilliant population geneticists are telling us ~100 mutations fix in each generation.

  66. 66
    PaV says:

    wd400:

    Jerry Coyne tells us that 2,250 is bigger than 2.

    So, let’s look at an effective population of 2.

    Here’s what it looks like: 2/2/2/2/2/2/2/2/2/2/2/2/2/ …….ad infinitum.

    Is this what Jerry Coyne is looking for?
    Isn’t it obvious that an effective population size of 2 is invisible?
    Isn’t it clear the ‘population’ would have died off at some point?

    Do you think about these things? Or, are formulas sufficient?

  67. 67
    PaV says:

    wd400:

    The brilliant population geneticists are telling us ~100 mutations fix in each generation.

    But, remember, NS isn’t working. These are “neutral mutations”. What does 100 neutral mutations buy you?

    If you respond that the mutations are there at the ready, then you are effectively saying that NS is there at the ready. But you can’t invoke NS. So now what?

  68. 68
    PaV says:

    wd400:

    The derrivation of the forumlae for Ne are not straightforward, but are covered in many textbooks.

    I’m not asking you to tell me how the formula is derived. It appears to simply be the reciprocal of the reciprocal of the arithmetic mean. So, kind of N=N/N(1/N).

    Why is it used here? Can you answer that question. I think I know, so I will be interested in your answer.

    It’s not true, or even possible so far as I can tell, that Wilson and Cann though there would be more that one MRCA mitochondrial DNA (or Y-chom). How would that even work?

    It’s not clear to me what you’re getting at here. What are you saying exactly?

  69. 69
    wd400 says:

    I mean the derrivation of the forumula for this effective population size. As I say, it’s not straightforward but you can look it up in most popgen texts.

    It’s not clear to me what you’re getting at here. What are you saying exactly?

    it’s (a) not true that ‘in the 90?s, they went looking for “mitochondrial Eve”, and were certain that they would find more than ONE such “Eve.”’
    (b) not even possible that there could be more than one “eve”

  70. 70
    Joe says:

    wd400:

    The brilliant population geneticists are telling us ~100 mutations fix in each generation.

    Except that “brilliant” shpuld never be used to describe population geneticists as they are far from it.

    And their methods do not apply to a Special Creation.

  71. 71
    PaV says:

    wd400:

    This is a common error. It would take ~112,500 years for any given mutation to fix. But there many mutations in each generation. In fact, the fixation rate is equal to the per-individual mutation rate. The brilliant population geneticists are telling us ~100 mutations fix in each generation.

    This is NOT an error. It is the time required for a neutral mutation to be fixed at a particular location along the length of the genome.

    4,500 generations x 100 mutations per generation = Total Mutations over 112,500 years = 4.5 x 10^5.

    These are “randomly” distributed along the length of the genome (if we assume NS is turned off, it can even happen in the just 5% of the genome that codes for protein). So, to change a protein, you would need a nucleotide change at a particular location = .05 X 3.0 x 10^9 nucleotides within protein coding regions=1.5 x 10^8 nucleotides.

    The probability of such a genome occuring during 112,500 years of “neutral evolution” is …….drum rolls please:

    4.5 x 10^5/1.5 x 10^8 = 0.003.

    Now the Ne is 2,250. So the odds of such a mutation actually occurring in the population is 2,250/3,000. So there is less than ONE chance of ONE needed mutation to occur in this population over 112,500 years. But, wait a second. It’s supposed to be “neutral”, so it’s likely not a single amino acid will be changed by this mutation—should it even occur.

    So, how, exactly, is “evolution” supposed to happen?

    That’s starting at 112,500 years ago. So, starting 112,500 years ago, if you push back another 112,500 years, again, less than one chance of a needed mutation occurring.

    How do you propose overcoming these dismal statistics?

    Michael Behe and Snoke rans some of these kinds of numbers, looking just for a two amino acid substitution, assuming immediate fixation, but also elimination of deleterious mutations, and they came up with staggeringly huge amounts of time required for simple a.a. substitutions to occur; and this only occurs if your population size is enormous.

    That study led to “The Edge of Evolution.” Have you read that book?

    I’ll have more to say about harmonic means and effective population sizes tomorrow.

  72. 72
    jerry says:

    I am on a tour in Africa. Our tour guide is from South Africa and like all good tour guides provides interesting tidbits about the local culture etc. He said there is a theory proposed by some South Africans researchers that there was a mass killing off of the human species several thousand years ago and the species was reduced to a small group along the eastern coast of South Africa.

    My comment was that he was saying South Africa was/is paradise. I have no ideas if this is bunkum or not but will ask him if he knows of the source of the data. The tour guide is well educated and was a computer programmer before heading off to the bush to live with the animals.

    My reaction to this is that science is a Whack a Mole process. Just when one thinks they have killed off one theory another comes out of nowhere that may be the answer.

  73. 73
    wd400 says:

    You said this
    So, just think what the brilliant population geneticists are telling us. That from the time than humans lived in Africa, only ONE!!! allele has become fixed,

    Which is clearly not the same as “the time required for a neutral mutation to be fixed at a particular location along the length of the genome”.

    You now seem to be mistaken in a new way. though it’s hard to follow precisely what youa are trying to calculate. What exactly are you trying to calculate, and who is specifying these “needed” changes?

  74. 74
    PaV says:

    wd400:

    Which is clearly not the same as “the time required for a neutral mutation to be fixed at a particular location along the length of the genome”.

    That’s right. It isn’t. But the “time required for a neutral mutation to be fixed at a particular location along the length of the genome” is the only way you can BEGIN to have “evolutionary change.” So what if one million “neutral” mutations are fixed all over the length of the genome. As I’ve already asked you—and you have yet to respond—what, exactly, does this buy you? What value is there?

    You now seem to be mistaken in a new way. though it’s hard to follow precisely what youa are trying to calculate. What exactly are you trying to calculate, and who is specifying these “needed” changes?

    You admit that you don’t know what I’m trying to calculate, and you admit you don’t know why the changes are “needed”, yet you’re convince, it would appear, that “I’m mistaken in a new way.”

    Why am I mistaken? Because what I point to is something that Darwinists/evolutionary biologists refuse to look at?

    Here’s an example. I have a genetic defect within my hemoglobin protein coding area that results in defective hemoglobin molecules, which makes me chronically anemic.

    Now, let’s say you’re a geneticist, and it’s your goal in life to ‘cure’ this disease. So you look along the length of the HG coding area and see the actual loci (there are two bad a.a.s involved) where these wrongly-coded nucleotides are found. You then devise an entirely new technique which allows you to replace these two or three (possibly four) “bad” nucleotides with the “correct” ones. The person is cured.

    Now, using random processes to ‘cure’ the same person requires that, at a minimum, two EXACT locations along the genome must be replace with the “CORRECT” nucleotide.

    The probability of replacing the nucleotide with the “correct” nucleotide via random genetic drift is 1/3 x 2,250/3,000 as calculated above. But this is ONLY HALF the problem.

    You need TWO mutations. So, for the probability of ONE of getting the “correct” replacement at the first location along the length of the genome, 3,000/2,250 x 3 x 112,500 years will be needed = 450,000 years. Now the FIRST mutation is in place. If you’re lucky, and the FIRST mutation doesn’t change itself again in the intervening 450,000 years (although it is likely that this will happen based on neutral drift —REMEMBER: 100 mutations are fixed EACH generation, and all over the genome), it will take an additional 450,000 years to get the SECOND mutation. And, of course, much more than that if, which is likely, the FIRST mutation disappears.

    So,almost ONE MILLION YEARS to change TWO mutations. And, in my case, these two mutations are NEEDED. You don’t mind if I do the specifying, do you?

    So, tell me, the time it took to go from a ‘chimp’ to a ‘human’, what is it? 6 million years? Per my calculation, via random genetic drift, this “buys” you 13 a.a.s in places where the ‘chimp’ to ‘human’ transition happens.

    Just out of curiosity: are there more than 13 a.a. differences between chimps and humans?

    The answer is: Of course! Don’t you think, then, that there’s something wrong in presenting this supposed method as a way of bringing about “macro-evolution”?

  75. 75
    wd400 says:

    That’s right. It isn’t

    Progress, you’ve admited to getting something wrong 🙂

    Why am I mistaken? Why am I mistaken? Because what I point to is something that Darwinists/evolutionary biologists refuse to look at?

    Because the equations following your sentences don’t appear to be related in any obvious way. You get yourself in another mess in this post which I don’t have time to umtangle.

    If you wan to know what’s the proability that pre-sepcified mutation will fix in a population by dirft in less that a million years then the answer is close enough to zero to make no difference. After all, chimps and humans have been evolving apart for 6 million years (=12 million years of evolution) and we have very few fixed differences.

    But why is that important? No one things drift is responisble for adaptation. Using neutral models to explain demography of genomic patterns doens’t preclude us from using selective models to explain other parts of biology. As I’ve said from the start, there is a lot of evidence for the fact natural selection has been at work in our genome.

    So, tell me, the time it took to go from a ‘chimp’ to a ‘human’, what is it? 6 million years? Per my calculation, via random genetic drift, this “buys” you 13 a.a.s in places where the ‘chimp’ to ‘human’ transition happens.

    Just out of curiosity: are there more than 13 a.a. differences between chimps and humans?

    Well, your calculations are wrong.

    Let’s look at it per gene, as the numbers are easier to follow, and you have the exonic portion of DNA wrong in your ealier comments. The average polypeptide is 400 amino acids long = 1200 nt.

    Using back-of-an-envelope numbers, the per nucleotide mutation rate is ~2.2e-8 and ~25% of mutations are synonymous. Over 6 million years, each lineage would have 240 000 25yr generations so we’d expect

    1200 nt * mu = 2.2e-8 * 240000 gen * 2 lineages ~ 13 substitutions per protein.

    13 per protein rather than 13 per genome.

    In fact, the observed number is smaller that the one we just calculated, due to the effect of purifying selection. The rate at which non-sysnomous mutation fix is ~1/5 the rate at which synomous ones fix (and 13/5 is 2.6 which is about the average number of amino acid differnce between human and chimp proteins). So the neutral rate would generate more differences than we observe, the fact we don’t see so many is evidence for the operation of selction.

    he answer is: Of course! Don’t you think, then, that there’s something wrong in presenting this supposed method as a way of bringing about “macro-evolution”?

    When did I do that? I said we can use a neutral methods to infer demographic histories. That doesn’t mean neutral theory explains all of “macro-evolution”, what ever that term means to you.

  76. 76
    PaV says:

    wd400:

    I’ve asked you why the ‘harmonic mean’ was used in calculating Ne. You told me that I should look at how it is derived.

    I’ve done that. Now I’m reporting back.

    First of all, we’re dealing with the theory of random genetic drift that is attributed to Sewall Wright and R.A. Fisher. It’s been around since the 30’s and 40’s.

    It is based on the “infinite allele” model. This model assumes an infinite population that produces an infinite number of alleles, that is then subdivided into N sub-populations, each of which itself produces an ‘infinite’ number of alleles. So this is quite an ‘idealized’ model.

    Therefore, when implementing it, one has to move from the ‘ideal’ population model and actual populations. Corrections, therefore, must be made in applying the model; one of these has to do with population size, and Ne, effective population arises within the context of making this correction.

    Any quotes I include in the following come from a Nature’s Review article by Armando Caballero, published in Heredity in 1994.

    “Under the simple conditions of the idealized population, sampling of gametes is binomial and the variance of the change in gene frequency is:

    ?²(&#916 q) =q(1-q)/2N,

    where q is the allele frequency of a gene in the infinite base population. The coefficient of inbreeding at generation t, the probability that two gametes which unite to produce a zygote in generation t carry identical by descent copies of a gene (Wright, 1922; Malecot, 1948), is:

    F_t = 1/2N + (1-1/2N)F_t-1,

    where the first term denotes identity by descent from copies of a gene of an individual in generation t-1 and the second, that from copies of a gene of an individual in previous genrations. The rateof incresae in inbreeding per generation is thus:

    &#916 F = 1/2N

    where &#916 F =F_t-F_t-1/1-F_t-1.

    The observable consequence of this increase in inbreeding is a reduction in the expected heterozygosity (H) each generation,

    &#955=H_t/H_t-1 = 1-&#916F ……… (3),

    or, relativ to that in the base population,

    H_t/H_t-1 = 1 – F_t = (1-&#916F)^t. …………..(4)

    [(N.B. the 1-F_t is from a straight substitution of the equation above (3) directly into (3). And, since, this equality is true for EACH generation, gen 0 to gen t, then the power of “t” is arrived at) PaV]

    . . .”

    Caballero gives a few more equations that won’t be interesting us, and then says:

    “It is obvious that real populations are very unlikely to meet the conditions of the idealized population defined above and, therefore, the number of breeding individuals does not describe appropriately the effects of inbreeding and gene frequency drift in most practical situations. The concept of effective population size (Ne) was introduced by Sewall Wright (1931, 1938, 1939) to overcome this problem and has been developed subsequently by others, mainly James F. Crow and coworkers (Crow & Kimura, 1970, pp. 345-364; Crow & Denniston, 1988).”

    How do we get effective population size, Ne?

    “If the variance of change in gene frequency or the rate of increase in inbreeding are known, because the genotypes can be distinguished and hence the genotypic fequencies estimated or because pedigrees are available, the effective population size can be estimate or computed directly from the expressions above. For example, if we can trace an observable quantity such as the heterozygosity so that we know its rate of decay (H_t/H_t-1), we can use eqns (2) and (3) to estimate the asymptotic N_e. . . .

    When information on genotypic frequencies or pedigrees is not available, effective size can still be predicted under certain circumstances (in which one or more assumptions of the idealized population are removed) when demographic data such as census numbers and variances and covariances of the number of progeny per parent are available. Effective size can be derived following a sampling drift approach or an inbreeding approach when the matter of interest is in the gene frequency drift or the increase in homozygosity, respectively (Crow 1954).”

    So, just as I suspected, and as I stated above, one either had the numbers and information, or one “backs into” N_e. When you have to estimate it without available information, then you have to remove “one of more assumptions of the idealized population). This is exactly where the HARMONIC MEAN comes in.

    We move down in the paper:

    “4. Variable population size over generations

    In the idealized population the number of breeding individuals (N) is constant over generations. Let us consider a situation where the population size varies over generations, with size N_i in generation i. From eqns (3) and (4), the expected heterozygosity in generations t relative to that in the base population is H_t/H_t-1=&#928i=1-t (1-1/2N_i). This can be equated to the relative heterozygosity in the idealized population (eqns (2) and (4), replacing N by N_e, i.e., (1-1/2N_e)^t. When population sizes are large and t much smaller than any of these, this latter equality can be approximated by

    1-&#931_i (1/2N_i)&#8776 1-t/2N_e, from where:

    1/N_e&#8776 1/t &#931_i [1/N_i]

    (PaV: summations are from i=1 to i= t)

    (Wright, 1938; Crow & Kimura, 1970pp. 109-110),
    i.e., using the harmonic rather than the geometric mean.

    So, there you have it: the derivation and the reason for using the harmonic mean.

    But, we’re not through yet.

    I’ve argued here, over and over again, that it is plain silly to say that a growing population represents a “bottleneck.”

    Well, here’s what Caballero has to say to us:

    Because N_e is a harmonic mean, two important points similar to those explained for eqn (7) appear. [N.B., eqn (7) deals with a different assumption of the idealized population, and its only relevance here is that as in the case of using the harmonic mean, caution must be exercised when applying this deviation from the idealized model] Firstly, the maximal N_e, given a total &#931_i N_i, is achieved with constant population size over generations. Secondly, N_e is most strongly affected by periods of reduced population size. In other words, if a bottleneck occurs, causing an increase in inbreeding, this is not restored by a later expansion of the population size. . . .

    As was mentioned before, genetic drift begins one generation (if selfing is allowed) or two (if not) earlier than inbreeding. If population size varies over time, for a given generation, genetic drift depends on the number of individuals in that generation whereas inbreeding depends on the number of their parents (if selfing is allowed) or their grandparents (if not).”

    So, when I describe a population that grows from 2 individuals to 28,000 individuals over a 7 or 8 generation time frame, this means that only (depending on the mutation rate) 1,400 to 1,600 mutations will have been fixed. Then after that, it’s “harmonic mean” will be that of its maximum value since it will have a “constant population size” for the next 9,900 generations.

    To summarize:

    (1) I was right about scientists having to “back into” the N_e when actual information is lacking.

    (2) I was right about a ‘constant’ population size over many generations.

    (3) This means I was also correct in saying that an “effective population size” of 2,250, or even, 28,000 can be reached in a very few number of generations, and is, therefore, blind to the method being employed.

    (4) Just to underline all of this, from an earlier post, an “effective population size” of 2 looks like this (generation numbers as well as generations, separated by slash marks:

    2/2/2/2/2/2/2/2/2/2/ …………………2/2/2/2/2/2/2/ …………………..2/2/2/2/2/2/ …………..

  77. 77
    wd400 says:

    (2) Nope. Your own source, which you pasted here, says “Secondly, N_e is most strongly affected by periods of reduced population size. In other words, if a bottleneck occurs, causing an increase in inbreeding, this is not restored by a later expansion of the population size.”

    (3) Nope. See above.

    (4) Sure. Why is this important?

    Actually, can you succinty point out what you are trying to do with any of this? I’ll remind you that orignal paper finds now evidence of a severly small population in more than a millon years, the newer one extend back less far but still no sign of a severely small population. We know that Ne is “strongly affected by periods of reduced population size”, so if there was a bottle beck prior to these evens it would still show up these studies. It hasn’t.

    You might be able to create some post hoc reason that saves a literal Adam and Eve, just like it’s possible to say the world was invented yesterday complete with memories, but it’s clear genetic evidence doesn’t support such a couple.

  78. 78
    PaV says:

    wd400:

    Progress, you’ve admited to getting something wrong 🙂

    The ONLY mistake I made was in saying “a particular place along the genome” instead of “a specified place along the genome.” For some reason you EBs like “pre-specified.” I think it only confuses things. Why not just use “specified”?

    Let’s look at it per gene, as the numbers are easier to follow, and you have the exonic portion of DNA wrong in your ealier comments. The average polypeptide is 400 amino acids long = 1200 nt.

    Yes, the “exonic portion” is probably about 3%; but, as usual, I give the EBs a break and used a higher percentage. And for this, you tell me I got it wrong.

    Using back-of-an-envelope numbers, the per nucleotide mutation rate is ~2.2e-8 and ~25% of mutations are synonymous. Over 6 million years, each lineage would have 240 000 25yr generations so we’d expect

    1200 nt * mu = 2.2e-8 * 240000 gen * 2 lineages ~ 13 substitutions per protein.

    13 per protein rather than 13 per genome.

    My calculations used 4,500 generations. Sticking with only one lineage, since the only reason to include 2 lineages is if, as you stay further on, if you want to study when they separated, then we get:

    1200 nt * 2.2 * 10^-8 *4,500 = .122 which, though different, means that during those 4,500 generations it is likely that no mutation occurred in any of the protein coding area.

    Using your same numbers, but looking at just ONE lineage, there are about 6 mutations per exon.

    That’s 6 nucleotides within an exon of 1200 exons. Now what percentage of the average exon is conserved? We’re talking here about NGD, so are we not talking about “neutral” substitutions?

    But you go on to note that non-synonymous mutations “fix” at 1/5 the rate of synonymous mutations. So that means, on average, 6/5, or, ONE nucleotide per exon; or, at most, ONE a.a. difference per exon.

    Now this is with purifying selection turned on.

    I guess this means that if you compare two exons, one from a chimp and a corresponding one from a human, out of the 1400 nucleotides only ONE nucleotide is different. And this is what converts a chimp into a human. Is this what you want me to believe?

    and 13/5 is 2.6 which is about the average number of amino acid differnce between human and chimp proteins)

    But, just a little bit more. You’ve made your calculation using 2 lineages. The reason for that, I presume, is that you’re considering the NGD that takes place within the chimp population. So this means that the chimp lineage changed from what it was like 6 million years prior by about ONE a.a., while the human lineage changed from what the chimp lineage was like 6 million years prior.

    So if you want to say that NGD is responsible for changing chimps into humans, then, in the same amount of time (you’ve assumed this) the chimps, having undergone an equal amount of change, nevertheless, still remain chimps! Why haven’t they changed into something different?

    If the numbers impress Darwinists/EBs to have confidence in macro-evolution, wherein a chimp, little bit by little bit, changes into a human, then why didn’t chimps change, little bit by little bit, into something else more similar to themselves, not as profoundly different as mankind? IOW, is there a chimp species that shows itself diverging from another chimp species less than 6 million years ago?

    I don’t know. I’m asking the question. But if there isn’t, then this absence appears to be rather peculiar.

    Another curiousity. Is the effect of purifying selection that of reducing the mutation rate of non-synonomous mutations to one-fifth that of synonomous mutations determined mathematically, stemming from some kind of first principles; or do you just simply back yourself into it by noticing the a.a. differences between humans and chimps and then calculating the numbers?

    Again, what mechanism, exactly, are you proposing for macro-evolution to take place. And, again, if you leave Darwin behind, saying that the EBs have moved on from his original theory, then surely science requires you to propose some new mechanism. And, of course, science would further require you to propose a sensible, logical mechanism.

    Is there one you would now propose?

  79. 79
    PaV says:

    wd400:

    (2) Nope. Your own source, which you pasted here, says “Secondly, N_e is most strongly affected by periods of reduced population size. In other words, if a bottleneck occurs, causing an increase in inbreeding, this is not restored by a later expansion of the population size.”

    (3) Nope. See above.

    Believe it or not, I can actually read. You’ll notice I included the quote you’ve posted. But I didn’t underline it. There are two caveats: one about ‘bottlenecks’ and one about ‘constant population size.’ You choose to focus on the ‘bottleneck’ and I choose to focus on the “constant population size.’

    Please explain to me how going from 2 to 50 to 500 to 2,000 census population, and then remaining at N = 2,250 for the next hundred generations, represents a ‘bottleneck’. In what way?

    (4) Sure. Why is this important?

    One reason is that Jerry Coyne said that 2,250 is greater than 2. Does this mean he thinks that effective population sizes of 2 can actually exist?

    Second reason: it is silly to think that one can look at what came before a “bottleneck”. I’ve already shown this a number of times. You seem not to want to accept this reality.

    You might be able to create some post hoc reason that saves a literal Adam and Eve, just like it’s possible to say the world was invented yesterday complete with memories, but it’s clear genetic evidence doesn’t support such a couple.

    Clear genetic evidence? Really? What’s so ‘clear’ about it? As I’ve stated over, and over, and over again, you can’t see what’s ‘in front’ of a “bottleneck”. The only reason that they talk about a population size of 10,000 going back in time, is because of the Out of Africa theory. So, you use one population, the African one, as the ancestral population, and then you compare the European populations with that of the African one. When you compare Europeans, you go back, what, was it 67,000 years. That’s where the “bottleneck” supposedly occurred, based on heterozygosity and assuming NGD; and, meantime you’ve backed into a N_e. Isn’t that how the computer simulation is done?

    But the point is is that this doesn’t allow you to look back past the 67,000 year mark using the European population data alone.

    If, in the original paper, they said something like the effective population of the African population is 10,000 going all the way back in time, why, then wasn’t it 9,350?

    Probably because that is their best guess for N_e. Then you use that to figure out some time to a “bottleneck” based on the heterozygosity of the African populations. And what comes before the 10,000 at it’s earliest? I’m sure they have no idea. It’s guesswork. And, so, the same is true of the European data set.

    Bottlenecks end in blindspots, not actual population sizes. Unless, of course, you’ve actually done some kind of field study. Using an infinite allele model–as does NGD—I don’t see any other alternative understanding.

  80. 80
    wd400 says:

    Believe it or not, I can actually read. You’ll notice I included the quote you’ve posted. But I didn’t underline it. There are two caveats: one about ‘bottlenecks’ and one about ‘constant population size.’ You choose to focus on the ‘bottleneck’ and I choose to focus on the “constant population size.’

    They aren’t caveats, they are consequences of the fact the harmonic mean gives us the value of Ne under these circumstances. Ad you can’t ‘choose to focus’ or one thing or the other, they’re both true. With the harmonic mean long-term stable populations have higher Ne, and populations recovering from a period of very low populatin retain low Ne for a long time.

    Please explain to me how going from 2 to 50 to 500 to 2,000 census population, and then remaining at N = 2,250 for the next hundred generations, represents a ‘bottleneck’. In what way?

    Because there is much less diversity in such a population than one that has been at 2,250 for ever. As the text you quoted says, it takes a long time for the population to get back towards the equilibrium

    So, you use one population, the African one, as the ancestral population, and then you compare the European populations with that of the African one. When you compare Europeans, you go back, what, was it 67,000 years. That’s where the “bottleneck” supposedly occurred, based on heterozygosity and assuming NGD; and, meantime you’ve backed into a N_e. Isn’t that how the computer simulation is done?

    This is extradondairy. No, this is not how the study was done. Inf fact, the Li and Durban paper uses a single genome to infer past population sizes. These methods use the distrbutions of times-to-coalescnce of blocks of chromosomes to to inder past populatin sizes. When effective population size is small you get many such coalesences quickyl, when it’s large that are more spaced out.

    It should be obvious from this that bottlenecks are not ‘blindspots’ or barriers through which such methods can’t see. For wthat it’s worth an Ne of 10,000 is most commonly used for humanity as it is calculated from observed genetic diversity in modern populations.

    I don’t see any other alternative understanding.

    And that, ultimately, is the problem. You’ve laboured in this entire thread, attacking your own misunderstanding of how these method work,without, it seems, considering the idea that specialists in population genetics know what they are talking about and don’t extend their estimates back beyond ‘blindspots’.

  81. 81
    PaV says:

    wd400:

    They aren’t caveats, they are consequences of the fact the harmonic mean gives us the value of Ne under these circumstances. Ad you can’t ‘choose to focus’ or one thing or the other, they’re both true. With the harmonic mean long-term stable populations have higher Ne, and populations recovering from a period of very low populatin retain low Ne for a long time.

    This is just “preachy”. It’s like you’re in a classroom teaching some young 19-year old. I’m sure they’ll accept your answers. I don’t. You’ll have to do better than you’ve done so far.

    Because there is much less diversity in such a population than one that has been at 2,250 for ever. As the text you quoted says, it takes a long time for the population to get back towards the equilibrium

    I’m sure you really think this. And I’m sure you think this because it’s the prevailing dogma. But I’m looking for answers, not just dogma.

    Let me illustrate what I mean.

    You have made no attempt whatsoever to try and understand the objections I have made in terms of the model being used. You’re content to give me bromides.

    The model that is in play is the “infinite allele” model, is it not? This model says that you begin with an “infinite population” with EACH generation itself producing an INFINITE number of “alleles.” The next generation is randomly selected from this host of “infinite alleles.”

    Now, where on earth will you find an “infinite sized population” that each generation produces an “infinite” number of alleles? Nowhere. (And, yes, I know about permutations of a genome that is billions of nucleotides long is quasi “infinite”, etc. I understand all that. So no lectures, please) So, when dealing with actual populations, but, in particular, populations that fluctuate over time, an “effective population” calculation is used to correct for the idealized assumptions.

    However, as far as I can see, you fail to engage the implications of the model. That is, the ENTIRE CONCERN is that when the population size is reduced, the notion of an infinite number of individuals producing an infinite number of alleles is thrown way off. Another way of looking at it is to simply say that when there is a “bottleneck”, a lot of diversity is lost because the diversity ‘exists’ over the entire population. Once it is lost, it will take a long time to recover it. In fact, depending on the lineage, and how far back in time it goes, you may never fully recover it.

    Now that is all you’ve been saying. But, that’s not the end of the story. For you, however, that is the end of the story. And when I get you to think it through more carefully, I get one lecture after another. Yes, indeed, the Ivory Tower is quite high.

    I will now point out how you are completely unresponsive to what I’m trying to point out.

    Answer this simple question: which of the two populations below has suffered from a “bottleneck”?

    (1) Population A: here is part of its history (population sizes of each generation separated by slashes):

    100/200/600/2,000/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250 and so on for another 5,000 generations.

    (2) Population B: here is part of its history (slashes again separate generation size):

    9,450/9,200/9,760/8,760/3,700/2,700/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250/2,250 and so on for 5,000 generations.

    I won’t wait for your answer, because I don’t think you’ll want to answer. So I’ll just avoid all the gamesmanship.

    According to you, both of these should be considered “bottlenecks.” Right?

    And what does this mean? It means what I’ve been saying now for over a week. It’s saying that if there is a “bottleneck” then you have no idea whether the population size of the population before the “bottleneck” was ten times greater or ten times smaller than the calculated N_e. If you a before and after picture, and you can’t tell whether something gets ten times bigger or ten times smaller, then I suggest you must be ‘blind’.

    Are you willing to admit that my interpretation is the correct one?

    PaV:

    So, you use one population, the African one, as the ancestral population, and then you compare the European populations with that of the African one. When you compare Europeans, you go back, what, was it 67,000 years. That’s where the “bottleneck” supposedly occurred, based on heterozygosity and assuming NGD; and, meantime you’ve backed into a N_e. Isn’t that how the computer simulation is done?

    This is extradondairy. No, this is not how the study was done. Inf fact, the Li and Durban paper uses a single genome to infer past population sizes. These methods use the distrbutions of times-to-coalescnce of blocks of chromosomes to to inder past populatin sizes. When effective population size is small you get many such coalesences quickyl, when it’s large that are more spaced out.

    I don’t see what you think is so extraordinary.

    Let me tell you what I see that is extraordinary:

    I am not talking about Li and Durban. I’m talking about Sheehan’s paper and they use more than one genome. But this is not big thing, since both are basically using a newest variation of the “coalescent” method.

    And what are they doing with the method? They’re going back in time using some rule for RGD, instead of going forward in time. And what is it they’re looking at which is going to “coalesce”? They’re simply taking some consensus genome for the European population and another consensus one from the African and using some form of simulated Markov method until the present day chromosome length “coalesces” to the “original” allele.

    Here’s what they say in their Discussion section:

    Applying our method to a 2 Mb intergenic region of chromosome 1 from ?ve Europeans and ?ve Africans, sequenced as part of the 1000 Genomes Project, and using a per-generation mutation rate of µ = 1.25×10?8 per site, we have inferred a severe (out-of-Africa) bottleneck in Europeans that began around 117 kya, with a drop in the e?ective population size by a factor of 12. In contrast, we have observed a much more mild population size decrease in the African population. We remark that our estimate of the timing of the bottleneck may not be very accurate, since we used only 16 discretization intervals and 7 free population size parameters. Furthermore, all of our inferred times and population sizes would be smaller by a factor of two if we had used µ = 2.5 × 10?8.

    What is the difference between “inferring” these numbers and “backing into them”?

    So, it’s a bit extraordinary that you get so worked up by what I stated.

    Did you notice it wasn’t “one” genome, but five; and it wasn’t just one population, but both African and Central European. And the factor of 12 they’re talking about is a drop from their calculated N_e for Africans at the time of split of 28,000, and the 2,250 they calculated as the N_e for the Europeans.

    Isn’t it quite obvious that based on Sheehan’s paper, from which Coyne (remember him? That’s how this all got started) then said that 2,250 is greater than 2, implying that Europeans are directly descended from Adam and Eve, rather than what is quite obvious from Sheehan’s paper, that the Europeans are descended from the African lineage.

    So, we go back to Africa, and then we go back in time, and then we estimate an effective population size of 10,000, and then we say, “Obviously we’re not descended from Adam and Eve, but some chimp lineage that numbered around 10,000.”

    This isn’t science. This is assuming evolutionary theory to be true, and then interpreting everything accordingly, and then saying that this is all demonstrable.

    The fact of the matter is we don’t know enough, and probably will never know enough. But when scientists want to trumpet “effective population sizes” as evidence that there was never an Adam and Eve, well, this sounds to me much like what it must sound like to you when a true Creationist says that the world was created in six days.

    It has been against this improper extension of science that I’ve been railing against.

  82. 82
    wd400 says:

    The infinite allele model does not include an infiniate population size. In fact, the most famout eqn in the paper is

    F = 1 /[ 4Ne.u + 1]

    I think(?) you are talking about the idealised Wright-Fisher model. The infinite thing in an infinite sites model is the number of possible alleles (i.e. each mutation is making a new allele).

    You yourself described the derrivation of why both populatins have genetic reduced diversity, so I don’t why you keep on going on about the semantics of ‘bottle necks’. The thing I think you haven’t quite grasped is the difference between an instantaneous value for Ne (which could be arrived at from many histories) and the histroical reconstruction of Ne over many time periods that these coalescent methods produce. That’s why these graphs extend out past the OOA bottlenecks in non-African populations.

    Anyway. It’s become increasingly clear you are so wedded to your ideas that you want give them up (do you at least admit no one though there would be multiple mtEves?). So I think I’m going to find something better to do than this.

  83. 83
    PaV says:

    wd400:

    This is from Caballero’s 1994 article:

    The simplest possible conditions under which the
    dispersive process can be studied are met in the
    Wright—Fisher idealized population (Fisher, 1930; Wright, 1931). This consists of an infinite, randomly mated base population subdivided into infinitely many subpopulations, each with a constant number, N, of breeding individuals per generation

    Yes, the “subpopulation” is not infinite (I’m sure the infinite population is being used to justify some kind of mathematical trick). And, yes, it is the Wright-Fisher model. I stated that somewhere along the line. And, yes, that’s not the coalescent theory, but coalescent theory is built upon the foundation of the neutral theory. And, yes, as I stated twice already, each generation produces an infinite number of alleles.

    The thing I think you haven’t quite grasped is the difference between an instantaneous value for Ne (which could be arrived at from many histories) and the histroical reconstruction of Ne over many time periods that these coalescent methods produce. That’s why these graphs extend out past the OOA bottlenecks in non-African populations.

    It seems to me that “coalescence” takes place when you run out of ‘heterozyogisity.’ You end up with one allele, or one form, etc. That’s where you’re going to determine where the MRCA is. This number obviously depends on the methodology employed, and it is not always going to be the same estimated time. And, of course, these methods suffer— as all methods involving molecular biology do, like molecular clocks and phylogenies—with inconsistencies. Nevertheless, some helpful information is gained, and it is certainly gained in as scientific a manner as is available.
    Again, I just notice the limitations of such methods, and we’re wrong to not notice them.

    (do you at least admit no one though there would be multiple mtEves?)

    Can you rephrase this? There may be a word missing.

    As to the discussion, I would agree that it has been more than thoroughly hashed out.

  84. 84
    wd400 says:

    You said this.

    And, now, let’s remember a little bit of history: in the 90?s, they went looking for “mitochondrial Eve”, and were certain that they would find more than ONE such “Eve.”

    Can you admit you got this wrong?

  85. 85
    Querius says:

    PaV might not be wrong at all—but you might be, wd400.

    From what I’ve read, there seems to have been a reaction by paleoanthropologists in the 1990s against the 1987 Mitochondrial Eve theory.

    While Darwinists claimed that ME was represented by many women, Paleoanthropologists observed genetic traits in Homo erectus fossils simultaneously in various parts of the world—arguably MEs in Asia, Africa, and Europe (Neanderthals).

    Interestingly, there actually *three* primary mitochondrial lineages that are observed in the world today (M, N, R) that could nicely correspond with the three fertile mothers on Noah’s arc, and also explain the genetic bottleneck as due to a global flood.

    For anyone’s interest, Dr. Robert Carter speaks on mitochondrial DNA and other genetic topics starting at 30:30) at http://www.youtube.com/watch?v.....38;t=9m40s.

    -Q

  86. 86
    PaV says:

    wd400:

    From what I know, aren’t you about 30? That means you were what, ten years old when all this was going on, while I was in my forties. Do you want me to deny reality? Is that what you’re asking me?

    It was in the papers. It was a topic of discussion. I remember it vividly. I waited expectantly for their results exactly because if there were multiple origins of “Eve” this would prove troubling. And then they were surprised when it turned out that there was only ‘one’ Eve. I remember all of this very well. We’re not in a communist state, yet; so I’m in no way going to deny reality.

    Unless you’re older than forty, I’m not going to accept a word you say. Darwinists, like Communists, rewrite history to please themselves. Don’t drink the Kool-Aid, wd400.

    Now, shifting back to our discussion: I hammered away at making the point that science cannot see clearly enough beyond these “bottlenecks.” However, there’s another way of looking at all of this.

    When we look at Genesis, Cain, after killing Abel, is sent off. He’s afraid that he will be killed; so he is given a special ‘mark.’ It sure sounds like we’re dealing here with other human-like primates.

    Let’s remember that what gives us freedom, and the use of reason, is our consciousness. Without this, we are mere animals. Think of someone who sleepwalks: they move around, talk with people, and do other things; but they’re not at all self-aware of what they are doing. It is consciousness that elevates us above all the other animals.

    It is entirely possible that the account of man’s creation in the second chapter of Genesis has to do with God infusing consciousness into human-like primates.

    If this is true, then genetically, these “persons”—human-like primates now having “consciousness” (likely changed in some ways)—would be linked to the genetic history of the group from which they were formed.

    The Bible, in my estimation as a Catholic, is not a history book at all times (it is quite a good history book at other times), and this applies to the Genesis accounts of Creation. It says there that God formed man out of the clay. But, of course, in Chapter 1 it just finished saying that God made men and women and told them to fruitful and multiply. So there is really no clear and unequivocal understanding here, and so caution as to how we understand all of this is in order.

    But, I invite your comments about the genetic history perspective I’ve presented.

    BTW, this is why I said earlier that I don’t see linkages of humankind (as we now know it) to chimps and such as a problem. Now, do I consider this to be “common descent”? I don’t think so. I think it is very likely that God intervened in some manner. For example, in order to accomodate “consciousness” was a larger cerebral cortex needed? Etc.

    I don’t know that we will ever have a full story of this. As I see it, neither religion nor science, neither Darwinism nor Intelligent Design, will ever know enough as to make a definitive conclusion about all of this. We’re all called to understand this as best we can, and in the best way possible.

    Anyway, your comments.

  87. 87
    PaV says:

    Thanks, Querius, for your comments.

    I remember all of this happening in the early 90’s, but it could have easily been the late 80’s too.

    Of course, then it was off to “Y-Adam.” And another surprise.

  88. 88
    PaV says:

    wd400:

    We’ve lived through Darwinists pounding away at IDists, night and day, for years and years, that the presence of so much “junk-DNA” is proof that Darwinism, and not ID, was correct. Then, when they could do this no longer in the face of so much conflicting evidence, they now, quite conveniently, just say: “Oh, when did we ever say that?”

    This sounds very much like your: “Oh, they never expected there to be just ONE “mitochondrial Eve.”

    When they asked Nixon how history would view him, he replied: “It depends on who the historians are.”

  89. 89
    wd400 says:

    It’s not possible for their to be more than one mitochondrial eve. How could that possibly work? Since Cann and Wilson and other geneticists in the 1980s were not idiots I think we can safely rule out the claim that they were expected to find multiple eves, and put all this “Darwinists are like communists,re-writing history” stuff aside.

    I guess you are confused by the difference btween multi-regionalism and Out of Africa. But neither of those schools thought there would be mulitple eves (and indeed, even in out of africa there are regionally unique mitochondrial lineages)

    So, you were wrong again. I won’t hold my breath waiting for an apology about all this childishness comparing evolutionary biology to communnism and Nixon…

    (Oh, and it hardly matters, but the best evidence still points to most of the genome being junk, and this is indeed evidence for that fact out genomeis the product of evolution.)

  90. 90
    goodusername says:

    PaV:

    A woman alive today will be a future mitochondrial eve. Every woman alive today is a mitochondrial lineage. Each generation from now, there will be women who either don’t have children, or have sons but no daughters. Thus, each generation from now, there will be fewer and fewer women of today that can claim any mtdna descendants. Eventually it will be just one woman.

    So the question simply was, how far back do we have to go before there is a single woman who is the mdna ancestor of all women today? (Note that the answer to who’s Mito Eve is irrelevant to the question of human origins. It’s also not a fixed individual. The mito eve of humans a hundred years from now might be someone different.)

    If you go back to a point where there are still several mito lineages from which mdna today originates, than, by definition, you haven’t gone back far enough. So not only is it not true that several mito eves were expected, it doesn’t even make any sense. It’s nonsensical. What would it even mean?

    Here’s an article from Science mag 1987:
    “The Unmasking of Mitochondrial Eve”:
    “Because mitochondria pass from generation to generation only through the female line… the phylogenies inferred from mtDNA data essentially trace maternal inheritance: ultimately, a single female is reached at the root of the tree, hence the reference to Eve.”
    http://www.sciencemag.org/cont.....24.extract

    It’s the same for Y-Adam. At some point in the past there is a man who’s the Y-chromosome ancestor of all men today. It’s not much of a prediction that such a man exists, it’s what HAS to happen, for the same reason a mito Eve must exist.

    In Dawkins’ “River Out of Even” (1995) he predicts that the Y-Adam will be a man who probably lived long after mito Eve. This was (IIRC) about 5 years before the results of the first Y-Adam study were announced.
    http://news.sciencemag.org/200.....osome-adam

    If you can find any articles that predicted otherwise, I’d really love to see them – it would be fascinating to see what on earth they were talking about.

  91. 91
    PaV says:

    wd400:

    You still have not answered how old you are.

  92. 92
    wd400 says:

    And I’m not going to. My own experience is irrelevant to the fact that speaking of mulitiple mitchondrial eves makes not sense. To suggest (without evidence, I might add) that genetcists expected to find multiple eves is very strange indeed.

  93. 93
    PaV says:

    goodusername:

    Thanks for the link. Here is what is in the third column of the 1987 Science paper:

    Because the origins of modern humans was thought to have occurred at some time in the past half million years, mtDNA seemed to offer a genetic route to answering a question that had eluded anthropologists for decades.

    The question was not just when the first modern humans evolved, but also how. Did they evolve simutaneously throughout the Old World, deriving from populations of archaic sapiens already established there from Homo erectus forerunners? Or did they arise in one location and then migrate throughout the rest of the world, replacing poulations of archaic sapens as they went? ……….. One this was clear,” says Brown (a student of Wilson, who led the investigation–pav), “the degree of variation between individuals was much less than might have been expected, given the variation known fro the great apes for instance.”

    This low level of mtDNA variation was a surprise, not least because it appeared to preclude deep genetic roots for Homo sapiens.

    Would you like to rephrase your remarks concerning this, wd400? You see, Communism prevails.

    And goodusername, what I was stating was right there in the article. So I won’t have to point anything out to you.

    (Note that the answer to who’s Mito Eve is irrelevant to the question of human origins. It’s also not a fixed individual. The mito eve of humans a hundred years from now might be someone different.)

    Expecting a war are we, goodusername? Does this mean you believe in the flood? Same phenomena, isn’t it?

    So, you were wrong again.

    No, you were wrong again. Wilson had his own ideas, as the article points out; but there was plenty of uncertainty in the methods and other competing points of view at the time. And those views were being bandied around in the media all the time. So, start listening to your elders, please.

    (Oh, and it hardly matters, but the best evidence still points to most of the genome being junk, and this is indeed evidence for that fact out genomeis the product of evolution.)

    You will one day have to ‘eat’ those words, I’m afraid.

    A woman alive today will be a future mitochondrial eve. Every woman alive today is a mitochondrial lineage. Each generation from now, there will be women who either don’t have children, or have sons but no daughters. Thus, each generation from now, there will be fewer and fewer women of today that can claim any mtdna descendants. Eventually it will be just one woman.

    Sorry to ‘rain on your parade,’ but will it turn out that this eventual “one woman” came out of Africa? You know what I mean.

  94. 94
    goodusername says:

    PaV,

    Would you like to rephrase your remarks concerning this, wd400? You see, Communism prevails.
    And goodusername, what I was stating was right there in the article. So I won’t have to point anything out to you.

    It appears that WD400 was right in #89, this is confusion regarding the multi regional theory vs the out-of-africa theory.

    No one – including the proponents of the multiregional theory – were saying that there wouldn’t be a single mito Eve at some point going back. As explained, there HAS to be one due to the facts of how mtdna is passed on and that we’re a sexually reproducing species!

    Many of the proponents of the out-of-Africa theory did make much of the results of the study. Not because there IS a mito Eve (everyone knew that there would be one), it’s that she lived perhaps more recently than some predicted, and came from the very region where the out-of-Africa proponents were suggesting that modern humans originated from. It’s perhaps a point in favor of the out-of-Africa theory, but I’d say a small one, at best.

    Had the study said that mito Eve from from eastern Asia 400k years ago, it would perhaps be a point in favor of the multiregional theory, but again, a small one. It’s pretty random who mito Eve is going to be, and as explained, it’s a moving target. A thousand years from now, mito Eve may indeed be someone from Asia. Even as a proponent of the out-of-africa theory myself, I think much too much was made of this study. This is why I said it’s irrelevant to the question of human origins. As explained, someone today will someday be a “mito eve”, but it doesn’t mean that this is the start of a new species or anything.

    Sorry to ‘rain on your parade,’ but will it turn out that this eventual “one woman” came out of Africa? You know what I mean.

    It can be any woman today that has, or will have, daughters. (If you meant something else by the question I’m afraid I missed it.)

  95. 95
    vjtorley says:

    Hi PaV and wd400,

    Professor Felsenstein was kind enough to respond to a query of mine regarding Adam and Eve, over at http://theskepticalzone.com/wp/?p=4200 . See especially
    http://theskepticalzone.com/wp.....ment-43066 ,
    http://theskepticalzone.com/wp.....ment-43193 and
    http://theskepticalzone.com/wp.....ment-43375 . You might find his remarks helpful. Cheers.

  96. 96
    wd400 says:

    Would you like to rephrase your remarks concerning this, wd400?

    No. It’s not possible for there to be more than one mtEve and multi-regionalists did not expect there to be more than one (rather, they thought mtEve would be much older than the OOA school did)

    You comments to goodusername suggest a lack of understanding about who mtEve is. The title can obviously change hands, and you don’t wars or famine or floods for other lineages to die out. In fact, there must have been an molder tEve for the population in which “our” mtEve lived!

  97. 97
    wd400 says:

    I wouldn’t listen to Joe – he’s an evolutionary biologist and and the son of communists! You know who those people re-write history 🙂

  98. 98
    Querius says:

    LOL PaV,

    Don’t embarrass wd400 regarding his age.

    Speaking of communists, many people can’t recognize their indoctrination. History is a great place to start. For example, according to a friend of mine who emigrated from the Soviet Union, Russia did not sell Alaska but leased it to the U.S.for 99 years, for which they were never paid. Also, that Abraham Lincoln imported large numbers of Irish to help him win the Civil War. Choose your historian . . .

    When wd400 claims

    It’s not possible for their [sic] to be more than one mitochondrial eve. How could that possibly work?

    This is because his imagination is limited to what he reads in his text books.

    From Homo erectus in each region, Africa, Asia, and Europe, emerged a female most recent common ancestor (MRCA) to Homo sapiens, each with unique mtDNA. The emergence was independent and at a similar, though not identical point in time. These three independent Eves were genetically similar, although the European and Asian Eves suffered a recent genetic bottle neck while the African Eve did not.

    It’s easy if you try.

    -Q

  99. 99
    wd400 says:


    From Homo erectus in each region, Africa, Asia, and Europe, emerged a female most recent common ancestor (MRCA) to Homo sapiens, each with unique mtDNA. The emergence was independent and at a similar, though not identical point in time. These three independent Eves were genetically similar, although the European and Asian Eves suffered a recent genetic bottle neck while the African Eve did not.

    Where did African, Asian and European Eve’s get their mtDNA from?

  100. 100
    Querius says:

    Where did African, Asian and European Eve’s get their mtDNA from?

    Their respective mothers.

    And where did Pan troglodytes mtDNA come from? 😉

    -Q

  101. 101
    wd400 says:

    whoe in turn inherited their DNA from their mothers, and back to…. the inevetiable single common ancestor of mtDNA: the one and only mitochondrial eve.

    Chimps have their own mtEve, as does every species with strict matrilineal inheitence of mtDNA.

  102. 102
    PaV says:

    goodusername:

    No one – including the proponents of the multiregional theory – were saying that there wouldn’t be a single mito Eve at some point going back. As explained, there HAS to be one due to the facts of how mtdna is passed on and that we’re a sexually reproducing species!

    wd400:

    Querious: From Homo erectus in each region, Africa, Asia, and Europe, emerged a female most recent common ancestor (MRCA) to Homo sapiens, each with unique mtDNA. The emergence was independent and at a similar, though not identical point in time. These three independent Eves were genetically similar, although the European and Asian Eves suffered a recent genetic bottle neck while the African Eve did not.

    wd400:Where did African, Asian and European Eve’s get their mtDNA from?

    So, wd400, you’re suggesting that the “African, Asian and European Eves all received their mtDNA from ONE ancestral “Eve”.

    goodusername, you say I’m wrong. wd400 says I’m wrong. Both of you tell me that what I read and heard in the early 90’s, when all of this was hitting the popular press, is just my imagination. (I suspect that in the back of your mind, wd400, you’re thinking that I’m just not smart enough to follow this sort of stuff. This thought gives you comfort, I suppose)

    So, now, wd400, let me point out where you seem to be going wrong when denying my thesis. If, indeed, as you are implying, the African Homo erectus, and the Asian Homo erectus and the European Homo erectus all received their mtDNA from some ancestral Homo erectus, then the transition from Homo erectus to Homo sapiens had to have taken place—or, at the very least, could have taken place [after all, we wouldn’t know for sure until the DNA evidence was in]—in THREE different locations, meaning that “man” (human beings–intelligent, free, human beings) arose in three different locations: the VERY thesis I said was “in the air” at the time.

    [Let me just point out that in the early 90’s I hadn’t read a single population genetics book. Didn’t know the field existed. Wouldn’t have known the’Hardy-Weinberg Equation’ if I saw it in glowing letters.

    So, I’m simply telling you what was being reported in the press. Everyone was just waiting for ‘humanity’ to have arisen in more than one spot. You know, they wanted the notion of the “Garden of Eden” to be smashed.

    Now, most reporters have very little understanding of the subjects they’re writing about, and make mistakes in reporting all the time. So it is entirely possible that they were simply confused about what the experts were telling them. But that is how it was reported. And it sure sounded like there were a lot of different scientific views of all this.]

    I take it that you’re not going to aver that “Adam and Eve” were Homo erecti.

    Would you now like to backtrack a little?

    This is all for right now.

    P.S. vjtorley: did see your post, and did look at Felsenstein’s response. I guess there is no “scientific theory” of the soul. Can’t argue that one. Or can we? Hmmmm.

  103. 103
    wd400 says:

    Would you now like to backtrack a little?

    no, it remains true that it is not possible for there to be more than one mtEve.

    So, now, wd400, let me point out where you seem to be going wrong when denying my thesis. If, indeed, as you are implying, the African Homo erectus, and the Asian Homo erectus and the European Homo erectus all received their mtDNA from some ancestral Homo erectus, then the transition from Homo erectus to Homo sapiens had to have taken place—or, at the very least, could have taken place [after all, we wouldn’t know for sure until the DNA evidence was in]—in THREE different locations, meaning that “man” (human beings–intelligent, free, human beings) arose in three different locations: the VERY thesis I said was “in the air” at the time.

    I don’t what the press was reporting, or what you were reading. But the multiregional position did not suggest multiple origins for modern humans. Rather, they thought gene-flow among the different continents (the ‘lattice model’) pulled the whole species along from H. erectus to H. sapiens whle retaining some regional variants.

  104. 104
    wd400 says:

    Here’s Wolpoff himself making this point <a href="dx.doi.org/10.1002/(SICI)1096-8644(200005)112:13.0.CO;2-K”>Multiregional, not multiple origins.

    I don’t know if the press got it wrong, but it’s not true that when ‘they’ went looking for “mitochondrial Eve”, ‘they’ “were certain that they would find more than ONE such ‘Eve’.”

  105. 105
  106. 106
    Querius says:

    wd400,

    Chimps have their own mtEve, as does every species with strict matrilineal inheitence of mtDNA.

    Bingo!

    So as we move from Homo erectus to Homo sapiens, I’m suggesting the possibility that this step happened independently in three geographic regions, hence you now have a scenario for three different mtDNA sources with different mutation histories for Homo sapiens. If you imagine a micro version of parallel evolution, you’ve got the concept.

    -Q

  107. 107
    wd400 says:

    So as we move from Homo erectus to Homo sapiens, I’m suggesting the possibility that this step happened independently in three geographic regions, hence you now have a scenario for three different mtDNA sources with different mutation histories for Homo sapiens

    But all three regions had to inherit their own mtDNA from somwhere. Trace the lineages of the three “eves” back and they have to join up in the common ancestor to all human mtDNA…. the one the only mitochondrial eve.

  108. 108
    Querius says:

    wd400,

    I don’t what the press was reporting, or what you were reading. But the multiregional position did not suggest multiple origins for modern humans. Rather, they thought gene-flow among the different continents (the ‘lattice model’) pulled the whole species along from H. erectus to H. sapiens whle retaining some regional variants.

    That’s the heart of the issue. I’m suggesting that under similar environmental pressures and presumed mutation opportunities, it’s not impossible for more than one H. Sapiens mitochondrial Eve to emerge from H. erectus. In fact, it’s likely that there were many other “candidates” that didn’t survive due to pathogens, predation, infant mortality, etc. and not just one, unless you’re proposing divine intervention for a single, very lucky female. 😉

    The apparent lack of other mt Eves is also supportive of a severe genetic bottleneck from a catastrophic event or perhaps a disease that wiped out all but a few individuals.

    -Q

  109. 109
    wd400 says:

    That’s the heart of the issue. I’m suggesting that under similar environmental pressures and presumed mutation opportunities, it’s not impossible for more than one H. Sapiens mitochondrial Eve to emerge from H. erectus

    And you are wrong. The different ‘eves’ you imagine had the themselves inherit mtDNA. Trace thier histories back and you woul arrive at the shared common ancestor all modern human mtDNA – mitochondrial eve.

    In fact, it’s likely that there were many other “candidates” that didn’t survive due to pathogens, predation, infant mortality, etc. and not just one, unless you’re proposing divine intervention for a single, very lucky female.

    Ever single women that has every lived, including those alive today, is a candidate to be a future mtEve.

    The apparent lack of other mt Eves is also supportive of a severe genetic bottleneck from a catastrophic event or perhaps a disease that wiped out all but a few individuals.

    No,it’s not. It’s evidence that populations are infinitely large, and so lineages coalesce eventually.

  110. 110
    Querius says:

    wd400,

    The different ‘eves’ you imagine had the themselves inherit mtDNA. Trace thier histories back and you woul arrive at the shared common ancestor all modern human mtDNA – mitochondrial eve.

    The Eves that I imagine are H. sapiens. The common ancestor that you’re imagining is H. erectus . . . or earlier. That’s why I originally brought up chimpanzee mtDNA, which according to your conceptions are passed along through a common ancestor to humans.

    The math simply demonstrates that a small sample size compared to a total population that’s large in comparison yields probability results that are asymptotic to an infinite population. Also, the math assumes perfect mixing without any isolated communities or density variations. Since you believe in Darwinism, I don’t need to remind you that isolation is a major factor in speciation. So, to discount a genetic bottleneck using this method robs you of speciation: you can either have an “infinite” population or you can have speciation, but not both.

    But I’m willing to be convinced otherwise. Try the population experiment yourself using, let’s say 100 marbles of several colors. I’d be interested in your results.

    -Q

  111. 111
    wd400 says:

    The Eves that I imagine are H. sapiens. The common ancestor that you’re imagining is H. erectus . . . or earlier

    Yes. So?

    I really have no idea what you are talking about in the rest of this comment. I am not denying the existance of bottlnecks or genetic isolation. All I’m trying to say, and I don’t think it’s a hard point to grasp, is that your ‘eves’ themselves share a common ancestor from whom they must have inherited their mtDNA. Since ‘eve’ is the most recent common ancestor of human mtDNA that person would be today’s eve (even though she wasn’t eve at the time, and won’t be eve at some time in the future).

    This would be true even if African European and Asian humans were different species or arose independantly.The onyl way around the inevitability of this would be multiple special creations.

  112. 112
    Querius says:

    wd400,

    Me: The Eves that I imagine are H. sapiens. The common ancestor that you’re imagining is H. erectus . . . or earlier

    You: Yes. So?

    Me: Then, she wouldn’t be called a mitochondrial Eve, would she. Otherwise you could have a mitochondrial “Eve” for a planaria and a pussycat, which would be nothing more than the most recent common female ancestor.

    Regarding the math, it’s really not that hard. Google it. Here’s a sample link:

    http://emp.byui.edu/BrownD/Sta.....e_pops.htm

    You might want to start with Part 2 of David Brown’s paper.

    -Q

  113. 113
    wd400 says:

    Mitochondrial eve is the most recent common ancestor of all humanity. There is no requirement she be the same (chrono-)species as modern human. Indeed, there are several genes seggregating in human populations that coalesce at a time prior to the human-chimp split.

    If we want to recap this. The multiregionalists did not expect there to be multiple origins of humanity, even if they did such a scenario would not give rise to multiple eves, as, indeed mitochondrial lineages in any population will always be able to be traced back to a shared common ancestor. I don’t know why you are so invested in denieing these faces.

    I know well enough about populations and samples. I don’t know why you think it is relevant. To use your hundred marble example: Start with a population of 100 labled individuals. Now, sample that population with replacement to simulate a new generation. Of course, some indiviuals will have more than one offspring and some will have none (their lineages die). Repeat this again and again and you’ll keep losing lineages until only one ‘ancestor’ is represnted in the population. That’s ‘eve’, and she emerged from a population that didn’t shrink at all.

    It will take much longer for this process to happen in a lrage population (the expected time = 2N), but it can’t be avoided.

  114. 114
    PaV says:

    wd400:

    Here are three separate comments made in three separate posts. I want to try and understand the implications of these comments below:

    First:

    And you are wrong. The different ‘eves’ you imagine had the themselves inherit mtDNA. Trace thier histories back and you woul arrive at the shared common ancestor all modern human mtDNA – mitochondrial eve.

    Second:

    But the multiregional position did not suggest multiple origins for modern humans. Rather, they thought gene-flow among the different continents (the ‘lattice model’) pulled the whole species along from H. erectus to H. sapiens whle retaining some regional variants.

    Third:

    Since ‘eve’ is the most recent common ancestor of human mtDNA that person would be today’s eve (even though she wasn’t eve at the time, and won’t be eve at some time in the future).

    It seems that population geneticists firmly believe that as time marches on, tests run to determine mt-Eve will uncover a different Eve.

    Now, this must rest on the hypothesis that with time lineages simply ‘die out.’ I would think that the ‘idealized’ conditions of the model that is employed for RGD—viz, an ‘infinite number of alleles’ produced by each generation, out of which each ‘allele’ of the present generation is formed—adds to this likelihood.

    But I see the net effect of this as rendering the entire project bankrupt of meaning. It’s as if you’re saying (actually you are saying this, though I scratch my head as to why—in the sense of it being a bankrupt notion) 100,000 years ago, if we could have done this test, we would have found a DIFFERENT mt-EVE; and, if we run this test 100,000 years from now, we’ll turn up another mt-EVE.

    If you’re firmly convinced of that, then, as I say, this makes the whole technique devoid of content.

    But it also makes things worse IMO. For example: what if a 100,000 years from now they determine that mt-EVE came out of Asia. Then what ever happened to the Out-of-Africa theory? Is it now untrue? This completely trivializes this theory.

    And, as I try to remember back some 25 years or so, they were attempting to find out the various ‘sources’ of the human population; not necessarily ‘mt-EVE.’ IOW, they were testing individuals from various parts of the world knowing that the mitochondria are inherited along the maternal germ line, AND, if there had been multiple ‘origins’ of H.erectus, then this would mean they might find three completely different kinds of mt-DNA. When it turned out that all of the mt-DNA came from one single origin, Africa, they then began to speak of a mt-EVE. I don’t think the scientists were completely sure what they would find when they began the testing.

    You mention that chimps have their own mt-DNA. Couldn’t there have been three different mt-EVEs for H. erectus (before they started testing; not afterwards)?

    You said earlier that the RGD is used to determine ‘divergence times.’ Well, I guess it can do that. But, and this is you saying this, these ‘divergence’ times might almost be a constant over time—-which ends up telling us very little that we can put under the heading ‘certain.’

  115. 115
    PaV says:

    Apparently others agree with my assessment of mt-EVE.

    Here’s this from Rick Groleau of PBS’s NOVAonline.

    Not surprisingly, there is currently a heated debate over the value of “mitochondrial Eve”—especially between history-hunting geneticists and some fossil-finding paleoanthropologists. According to these anthropologists, even if we could accurately gauge the age of the ancestor, that knowledge is meaningless because all she really is is the woman whose mtDNA did not die out due to random lineage extinctions. Furthermore, her status as the most recent common ancestor doesn’t mean that she and her contemporaries were any different from their ancestors. (Remember, she and all of her contemporaries had their own mitochondrial Eve.)

    Perhaps the most valuable finding regarding the “most recent common ancestor” is that she probably lived in Africa—a finding that supports the most popular theories about the worldwide spread of hominids.

  116. 116
    Querius says:

    wd400,

    Your first two sentences are self-contradictory. I don’t know how you would reconcile them. Also, I’m proposing that it makes sense in a Darwinist ideology for multiple emergences of H. Sapiens as well as aspects of multiregionalism.

    I’m not invested in any of this—none of these speculations are facts (I assume you meant facts, not faces).

    Take your 100 marbles and put them in an egg carton, dividing them into groups of zero to ten (or whatever fills a pocket in the tray). Now put the egg carton in your Prius, and drive over a bumpy road. The empty pockets are unfilled regions. Now do your sampling and replacement but do this pocket by pocket (along with adding some novelties without which Darwinism won’t work). You’ll find that the pockets protect genetic diversity.

    -Q

  117. 117
    wd400 says:

    PaV,

    Right – so the fact mtEve lived in Africa is not a great big deal. The findings that multiregeionalism can’t really account for are (a) she lived very recently and (b) almost all the basal mitochondrial lineages are found in Africa. That’s exactly the patter OOA predicts (with non African populations mainly being a sub-sample of African genetic diversity + whatever mutations they added along the way). The population was very highly structured then the time to coalescence would be much greater, and there is no real way to explain the much greater diversity in Africa.

    You mention that chimps have their own mt-DNA. Couldn’t there have been three different mt-EVEs for H. erectus (before they started testing; not afterwards)?

    No. Or, there are distinct mitochondrial lineages in restricted to geographical regions (7 duaghters of eve and all that), they just aren’t Eves.

    You said earlier that the RGD is used to determine ‘divergence times.’ Well, I guess it can do that. But, and this is you saying this, these ‘divergence’ times might almost be a constant over time—

    Nope. Times to coalescence within one population would be constant abesent selection, fulcuting population size etc (that’s, after all, how we know there was no sever bottleneck…). But times to divergence are different because gene flow ceases and the lineages can no longer coalsece. If you use a single gene the estimaes of divergence times will be slighltly biased upwards since they will coalesce on some ‘eve-like’ individual who lived prior to the ceasatoin of geneflow, but modern methods account for this.

  118. 118
    wd400 says:

    Querius,

    Your first two sentences are self-contradictory. I don’t know how you would reconcile them

    At this point I’m happy to mark that up as your failure rather mine. I don’t know why these facts are hard for you to reconcile.


    Take your 100 marbles and put them in an egg carton, dividing them into groups of zero to ten (or whatever fills a pocket in the tray). Now put the egg carton in your Prius, and drive over a bumpy road. The empty pockets are unfilled regions. Now do your sampling and replacement but do this pocket by pocket (along with adding some novelties without which Darwinism won’t work). You’ll find that the pockets protect genetic diversity..

    Structured populations lose genetic diversity, though they do make the time to coalescence in the ‘metapopulation’ longer, they don’t eliminate the absolutely inevetibaly phenomenom.

  119. 119
    Querius says:

    wd400,

    Your statement number 1:

    Mitochondrial eve is the most recent common ancestor of all humanity.

    This statement seems to indicate that mitochondrial Eve is human, in other words H. sapiens.

    Your statement number 2:

    There is no requirement she be the same (chrono-)species as modern human.

    This statement indicates that mitochondrial “Eve” could be a different species (or chronopecies) entirely, which is NOT H. sapiens. But if the MCRA of ALL humans is a chimpanzee-like animal, you would be claiming that there is no common H. sapiens ancestor to all humans, which contradicts your first statement. The only way to make your second statement true is by parallel and convergent evolution—otherwise there WOULD be a human mitochondrial Eve.

    You seem to be confusing the concepts of MCRA with mtDNA. They’re not the same thing.

    Structured populations lose genetic diversity, though they do make the time to coalescence in the ‘metapopulation’ longer, they don’t eliminate the absolutely inevetibaly phenomenom.

    Humbug. Especially for “infinite” populations. Go get 100 marbles of 3-4 different colors, an egg carton, and a Prius, and try it yourself!

    Segregate the marbles according to color in the egg carton to represent isolated populations with a mutational difference as Darwinists claim happened for evolution to have occurred. Allow some scattering. Introduce a new colored marble occasionally but rarely to represent mutational novelties as is supposed to have happened according to Darwinists.

    If you’re ambitious, write a simple app and show us. Have it count the number of generations. I think you’re in for a surprise. Remember, the more filled a pocket in the egg carton becomes, the more likely a marble will spill over into a neighboring pocket.

    -Q

  120. 120
    wd400 says:

    In youour statement number 1:

    Mitochondrial eve is the most recent common ancestor of all humanity.

    This statement seems to indicate that mitochondrial Eve is human, in other words H. sapiens.

    That you think this suggests you have a confused idea of either mitochondrial eve and population genetics or what a species is. I can’t tell which. (By the way, I should have said the most recent matrilineal common ancestor – the most recent common ancestor of humanity almost certinaly lived more recently than ‘eve’.)

    Here’s Joe Pickrell making the same point about Y-chr adam (although, note, it seems even some population geneticists have made this mistake)

    Humbug. Especially for “infinite” populations

    Which populations do know that are infinite?

    Segregate the marbles according to color in the egg carton to represent isolated populations with a mutational difference as Darwinists claim happened for evolution to have occurred. Allow some scattering. Introduce a new colored marble occasionally but rarely to represent mutational novelties as is supposed to have happened according to Darwinists.

    I really have no desire to prove entry level pop gen.Population structure extends the time to coalescence, in the extreme case with no gene flow (i.e. speciation) the lineages will coalesce just prior to the cessation of gene flow, otherwise at some more recent time. Expanding populations are known to hold on to more diversity, and mutations allow us to relate lineages to each other,neither of these processes remove the inevetiability of the fact lineages coalesce eventually.

  121. 121
    PaV says:

    wd400:

    I really have no desire to prove entry level pop gen.Population structure extends the time to coalescence,

    But how, exactly, do you ‘prove’ “entry level population genetics”?

    It’s all axiomatic. We’re using models, with idealized assumptions being made, and then refinements made to the idealized assumptions. You either have “confidence” in the models and their results, or you don’t.

    As I pointed out earlier, the value of all of this becomes questionable. That you have to make a distinction between the “most recent matrilineal common ancestor” and the “most recent common ancestor of humanity” is an indication of the theory’s limited value.

    See you tomorrow.

  122. 122
    Querius says:

    wd400,

    Yes, matrilineal. And you haven’t answered my challenge of how our MRMCA could possibly not be Homo sapiens.

    Statistically infinite populations were explained in the link that I provided:

    http://emp.byui.edu/BrownD/Sta.....e_pops.htm

    You should really try playing with the marbles. It will get you a feel for the dynamics. Besides direct observation should always trump theory. Right?

    PaV,

    Exactly!

    -Q

  123. 123
    wd400 says:

    And you haven’t answered my challenge of how our MRMCA could possibly not be Homo sapiens.

    That’s because you simpyl assert that being the MRMCA of humanity means Eve is necesarily a modern human. There is absolutely no reason for that to be the case. Without seeing why you think this is the case it’s very hard to guess where your confusion arises from.

    The statistical behaviour of samples from their large populations has almost nothing to do wit this question – as long as populations are actually finite then coalesnce will happen.

    I have done the equivalent of your marble simulation many many times, as have thousands fo population geneticists. If you want to deny the findings of this field you will need to do better than though experiments about egg cartons and marbles.

  124. 124
    Querius says:

    Nice try, wd400, but I didn’t say modern human. I said Homo sapiens. There is an important difference!

    The link that I provided indicated statistically infinite populations, and explained why. This is not my idea, and I object to the lack of factoring in genetically isolated groups, which I think is critically important.

    And the “equivalent of your marble simulations” as you put it are not the same as Actually Performing One with actual marbles in an egg carton in your Prius! You seem to be reluctant to even try it. Don’t be a grouch, it will be fun! 😉

    -Q

  125. 125
    wd400 says:

    This is a waste of time.

    Nice try, wd400, but I didn’t say modern human. I said Homo sapiens. There is an important difference!

    What’s the imprtant difference? Why do yout thinkthe MRMCA of humans today had to H. sapiens?

    The link that I provided indicated statistically infinite populations, and explained why. This is not my idea, and I object to the lack of factoring in genetically isolated groups, which I think is critically important.

    The link doesn’t “indicate” “statistically infinite populations” in any relevant way – it’s about sample statistics and the fact you can sometimes safely assume the population from which a sample was drawn was is infinite when you do statistical tests. It doesn’t apply to this question at all, so far as I can tell.

    I don’t ignore population strucutre, nothing about reduced gene flow prevents lineages form coalescening (thoug it slows that process). If populations are completely isolated then lineages will still coalesce at some time prior to the cessation of geneflow. Indeed if you treated humans and chimps as a single very structured population there would still be one “eve” for that combined population.

  126. 126
    Querius says:

    wd400 shot back:

    This is a waste of time.

    Don’t worry, I read your post regardless. 😉

    What’s the imprtant difference? Why do yout thinkthe MRMCA of humans today had to H. sapiens?

    I’m astonished that you don’t know the difference between what we still recognize as Homo sapiens (in context, early modern humans) versus contemporary humans. Sorry, but you left out a word or two in your second sentence, so I don’t know what you’re trying to say.

    The expressions that David Brown provided for a statistically infinite population does not recognize the effect of isolated populations—if you disagree, please point out the terms that do address them.

    Indeed if you treated humans and chimps as a single very structured population there would still be one “eve” for that combined population.

    Nonsense. We don’t treat humans and chimps as a single structured population! Humans and chimps don’t and never have bred together. You should know this, so I can only conclude that you’ve decided to become disingenuous.

    The marble experiment is a good place to help you understand the dynamics involved.

    Goodbye.

  127. 127
    wd400 says:

    I’m astonished that you don’t know the difference between what we still recognize as Homo sapiens (in context, early modern humans) versus contemporary humans. Sorry, but you left out a word or two in your second sentence, so I don’t know what you’re trying to say.

    I know the difference, I even know the difference between modern humans and contempory humans if you want to play silly games. What I don’t know if why you claim the MRMCA of contempory humans has to be H. sapiens. Please explain that.

    The expressions that David Brown provided for a statistically infinite population does not recognize the effect of isolated populations—if you disagree, please point out the terms that do address them.

    The expressions aren’t about biological populations, so they have nothing to do with genetic isolation. What are you talking about?

    Nonsense. We don’t treat humans and chimps as a single structured population! Humans and chimps don’t and never have bred together. You should know this, so I can only conclude that you’ve decided to become disingenuous.

    I’m taking an extreme versoin of your position (that population structure can create multiple eves) and showing even then you claim doesn’t hold.

    Now, please, in a simple sentence: why must the MRMCA of contempory humans be H. sapiens?

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