Carter, Lee, Sanford’s ICC 2018 Adam and Eve paper, Congratulations Bill Basener

Bill Basener (a participant here) co-authored a paper with John Sanford. He was given the honor of delivering a KEYNOTE ADDRESS at an international SECULAR biology conference. A video of his presentation is available in a link inside my write up of his presentation below. He alluded to some of the helpful input from his critics at TheSkepticalZone in his talk:

http://crev.info/2018/07/keynote-speech-falsifies-darwinism/

John Sanford is sort of the “Papa John” of creationist genetics. It is customary for the leader of a research group to be listed as the last author in a publication. That convention is seen in a variety of papers and books such as Rupe & Sanford; Basener & Sanford; Carter, Lee & Sanford; Montanyez, Fernandez, Marks & Sanford; and let’s not forget the Legendary High Velocity Team of Klein, Wolf, Wu & Sanford that permanently ensured the infusion of intelligently designed genes into a sizable fraction of Genetically Modified Organisms on planet Earth.

And perhaps one day in the distant future there will be a paper, “Cordova & Sanford”! 🙂

Below is a link of a paper from Papa John’s team about Adam and Eve which will be presented this week, July 29,2018 – August 1, 2018 at the 8th International Conference on Creationism

http://www.creationicc.org/2018_papers/15%20carter%20Y%20chromosome%20final.pdf

The existence of a literal Adam and Eve is hotly debated, even within the Christian body. Now that many full-length human Y (chrY) and mitochondrial (chrM) chromosome sequences have been sequenced and made publicly available, it may be possible to bring clarity to this question. We have used these data to comprehensively analyze the historical changes in these two chromosomes, starting with the sequences of people alive today, and working backwards to the ancestral sequence of the family groups to which they belong. The analyses of the chrY and chrM histories were done separately and in parallel. Remarkably, both analyses gave very similar results. First, the pattern displayed in both datasets supports a massive expansion of the human lineage, with multiple new branches forming from closely related individuals. Second, for both chromosomes, the mutation rate along each branch has not been the same through time. Third, both phylogenetic trees display a starburst pattern that centers around specific historical individuals, nearly all of whom lived in the Middle East. Fourth, we can know with a very high degree of confidence the actual sequences of the historical individuals that gave rise to each branch in both family trees. Fifth, within a reasonable margin of error we can approximate the sequence of Y chromosome Adam/Noah and Mitochondrial Eve. Sixth, given a few reasonable assumptions, we can estimate the time to Y Chromosome Adam/Noah and Mitochondrial Eve. Both individuals lived less than 10,000 years ago, which is most consistent with a biblical timeframe. Lastly, recurrent mutations are extremely common, and many of them are associated with epigenetic CpG sites, meaning mutation accumulation is not free of environmental influence and many mutations may have accumulated in different lineages in parallel. The genetic evidence strongly suggests that Y Chromosome Adam/Noah and Mitochondrial Eve were not just real people, they were the progenitors of us all. In this light, there is every reason to believe that they were the Adam/Noah and Eve of the Bible.

NOTE: Paul Nelson’s family was instrumental in the founding of the International Conference on Creationism which meets every 5 years. Paul is one of the few ID proponents openly associated with YEC. Nelson gave the 2013 ICC Keynote Address on Orphan Genes.

277 thoughts on “Carter, Lee, Sanford’s ICC 2018 Adam and Eve paper, Congratulations Bill Basener

  1. fifthmonarchyman: The paper is much more noncommittal about those groups

    I can’t imagine how you could have read that paper without understanding that, to the authors, denisovans and neandertals are descendants of Adam and Eve. Is it something analogous to beer goggles?

  2. John Harshman: do see a starburst pattern, though in fact I was unfamiliar with the term. Even had I known, I wouldn’t have known what you meant by it, and your answer suggests that you attributed some real significance to it rather than it being just a graphic style.

    Anyway, the center means nothing, as your source itself said. You apparently disagree, but on what basis?

    Well, I’m glad you actually learned something for a change. But unlike you, I don’t call people utterly ignorant like you’ve called me. But, that is beside the point.

    To your credit, as I reviewed your objections and the paper, I would prefer to form an alternate approach to the question of bottle neck. Ok, so you win this exchange as far as me saying, “I’d like to see more data and even stronger arguments than laid out in the paper.” However, I’m not ready to say it’s a bad paper, since, as you and others can see, Carter, Lee, and Sanford devoted a lot of effort combing through 1000 human genomes.

    That said, there are two starburst patterns of approximate shape. At least a few “soft polytomies” that were resolved into dichotomies, that sill nonetheless suggest the founders of the major branches were essentially a small population.

    Setting aside briefly the question of Adam and Eve, and a bottleneck for the entire human race, let me for the time being talk about the major macro haplogroups that can be seen in the starburst pattern.

    If the major macrohaplo groups of Y-chr and M-chr coincide, the fact that there were at least soft polytomies, that the branching was sudden, wouldn’t that suggest the founders of the major macrohaplo groups were small groups of individuals that spread out geographically? I mean, what WOULD rapid radiation from a small founding group look like in terms of parallel haploid lineages like Y-chr and M-chr.

  3. stcordova: Well, I’m glad you actually learned something for a change.But unlike you, I don’t call people utterly ignorant like you’ve called me.But, that is beside the point.

    Now I just wish you would learn something for a change. The difference between us is that you actually are utterly ignorant on the various subjects we discuss here.

    To your credit, as I reviewed your objections and the paper, I would prefer to form an alternate approach to the question of bottle neck.Ok, so you win this exchange as far as me saying, “I’d like to see more data and even stronger arguments than laid out in the paper.”However, I’m not ready to say it’s a bad paper, since, as you and others can see, Carter, Lee, and Sanford devoted a lot of effort combing through 1000 human genomes.

    Effort doesn’t make a paper good unless it’s the right sort of effort. Theirs is the wrong sort of effort. What alternate approach would you prefer, and why?

    That said, there are two starburst patterns of approximate shape.At least a few “soft polytomies” that were resolved into dichotomies, that sill nonetheless suggest the founders of the major branches were essentially a small population.

    Approximate shape is meaningless. Any tree can be arranged as a starburst. And this touchy-feely approach to population genetics is worthless. There are tests for bottlenecks, which do leave signatures in genomes. But the authors have attempted none of them.

  4. John Harshman: Approximate shape is meaningless. Any tree can be arranged as a starburst. And this touchy-feely approach to population genetics is worthless. There are tests for bottlenecks, which do leave signatures in genomes. But the authors have attempted none of them.

    I bet those tests are based on the “right” assumptions… as they should to make the tests outcomes “right”… to support preconceived ideas…

    What do you think, Sal?

  5. J-Mac: I bet those tests are based on the “right” assumptions… as they should to make the tests outcomes “right”… to support preconceived ideas…

    J-Mac demonstrates us how to avoid “optimism bias” and to follow the evidence wherever it leads.

    Thank you, J-Mac

  6. Corneel: J-Mac demonstrates us how to avoid “optimism bias” and to follow the evidence wherever it leads.

    Thank you, J-Mac

    Really?! In this case I’m pessimistically biased not only because of the great track record of unfounded assumptions by population genetics, but more so, by Harshman himself…
    He apparently has no problem with many “miraculous” insertion of whole genes into the tree of life, why would he have a problem with making the “right” assumptions, as he sees fit, to prove whatever he is trying to prove…
    What could be the consequences? Nobody is going to cut off his head… Some may even applaud it…

  7. J-Mac: Really?! In this case I’m pessimistically biased not only because of the great track record of unfounded assumptions by population genetics, but more so, by Harshman himself…
    He apparently has no problem with many “miraculous” insertion of whole genes into the tree of life, why would he have a problem with making the “right” assumptions, as he sees fit, to prove whatever he is trying to prove…
    What could be the consequences? Nobody is going to cut off his head… Some may even applaud it…

    Excuse me, can you tell me where to find the person who posted this

    From what I have been able to observe, and even test, to a degree, the great majority of commentators at TSZ, UD and many similar blogs, come here to support their preconceived beliefs… They don’t come here to learn something new, unless it is within their belief system…

    Anything that threatens their well-established beliefs is either rejected, mocked or ignored….

    [snip]

    Antony Flew, a professor of philosophy and a long promoter of atheism and evolution for over 50 years said the following after he has changed his mind and accepted the existence of a Creator:

    ” We must follow the argument wherever it leads us…”

    In other words, we MUST not use the Optimism Bias and “follow the evidence where we would like it to lead…

    The goal of scientific research, as well as religious, should be to find the truth, not to support preconceived ideas… Does it?

    To accept this, one has to be honest with himself/herself…

    …twice.

    Because I don’t believe you – who rejects a test before you even know what it is – are him

  8. J-Mac,

    And to top it off .. you asked Young Earth Creationist Salvador Cordova for confirmation. Let’s repeat that: confirmation, because of course DNA_Jock was right and confirmation bias is what you actually mean whenever you say “optimism bias”. But you told him off (quite rudely), because you perceive him as a threat to your preconceived beliefs. The irony is so thick, you could put a fork in it.

  9. J-Mac: He apparently has no problem with many “miraculous” insertion of whole genes into the tree of life, why would he have a problem with making the “right” assumptions

    That the emergence of a novel gene during the course of evolution is “miraculous” is a biased assumption. But to you, that is of course the “right” assumption to make.

    Corneel is right, you are no better than anyone else here at this and the irony of you constantly bringing up other people’s biases and assumptions comes in sliceable loaves.

  10. John Harshman:

    there are tests for bottlenecks, which do leave signatures in genomes. But the authors have attempted none of them.

    If L0 and A0 are concentrated the same population today to the exclusion of other populations, let us designate such population as L0A0, would that suggest L0A0 passed through a bottleneck?

  11. stcordova: If L0 and A0 are concentrated the same population today to the exclusion of other populations, let us designate such population asL0A0, would that suggest L0A0passed through a bottleneck?

    No, it would not.

  12. John Harshman: No, it would not.

    Why not? Is that because this could be a sampling error, or confirmation bias to see A0L0 in the same sample? Ok, but what if they are in the same geographical region?

  13. Rumraket: That the emergence of a novel gene during the course of evolution is “miraculous” is a biased assumption.

    It’s not an assumption, it’s an inference.

  14. Rumraket: How is that inferred?

    Probably something like this. Dead people do not usually come back to life. This dead person was raised from the dead, back to life. That must have been a miracle, and it must have been God doing it.

    Do you not see the inferences?

    Now see if you can turn them into assumptions and show me how that works.

  15. stcordova: Why not?Is that because this could be a sampling error, or confirmation bias to see A0L0 in the same sample?Ok, but what if they are in the same geographical region?

    I don’t understand your reasoning, perhaps because you haven’t explained it. Why would two widely divergent haplotypes in one population imply a bottleneck?

  16. Mung: Probably something like this. Dead people do not usually come back to life. This dead person was raised from the dead, back to life. That must have been a miracle, and it must have been God doing it.

    Do you not see the inferences?

    You can certainly make inferences based on a lot of assumptions, sure. But I’m waiting for you to tell me how this applies to the origin of genes during the course of evolution.

    Also, though it is irrelevant to the origin of genes it seems to me your statement contains multiple assumptions, among them:
    1. This dead person was raised from the dead, back to life.
    2. That must have been a miracle.
    3. It must have been God doing it.

    There’s even more. That there even was a person. That the person died. That the person returned to life later.

    Possibly even the first statement is an assumption, but I could give it some leeway due to the use of the word “usually”, since at least some times people who have died have come back to life provided they weren’t dead for too long, or too damaged in whatever killed them.

  17. John Harshman: I don’t understand your reasoning, perhaps because you haven’t explained it. Why would two widely divergent haplotypes in one population imply a bottleneck?

    Can we or can’t estimate the age of a macrohaplotype?

  18. Hey stcordova

    I was completely unaware of Joshua Swamidass’s existence a few months ago and now his name is coming up everywhere in these discussions

    Here is a paper from him that articulates the position on Adam and Eve that I have been exploring for few years now most recently in this very thread

    https://www.asa3.org/ASA/PSCF/2018/PSCF3-18Swamidass.pdf

    I am very interested in any Biblical objections you may have as a YEC to the genealogical Adam approach he is detailing. Keep in mind that he does not rule out special creation of the first couple.

    thanks in advance.

    peace

  19. stcordova: Can we or can’t estimate the age of a macrohaplotype?

    What is a macrohaplotype?

    No, we can’t estimate the age of a haplotype, though we can estimate the age of divergence of two haplotypes. What does that have to do with your previous claim about a bottleneck, the one I asked you about?

  20. John Harshman: What is a macrohaplotype?

    No, we can’t estimate the age of a haplotype, though we can estimate the age of divergence of two haplotypes. What does that have to do with your previous claim about a bottleneck, the one I asked you about?

    The Macro Haplotype is the major haplotype carried by several branches. Carter explains it in his paper, which, as all papers at ICC 2018 are now behind a paywall. Bummer.

    You bring up good objections. One testable prediction however, if the root of the tree is indeed toward the center of the starburst is that the African populations must have a higher mutation rate.

    I found this paper:
    https://www.ncbi.nlm.nih.gov/pubmed/9353974

    Global studies of within-group genetic variation have revealed a tendency for some traits, but not all, to show higher heterozygosity in sub-Saharan African populations. Although excess African diversity has been interpreted as reflecting a greater “age” of sub-Saharan African populations, more recent research has shown that this excess is more likely a consequence of a larger African long-term effective population size. The observation that certain traits, particularly classic genetic markers and RFLPs, do not show this pattern has been interpreted as ascertainment bias. Here, I examine another possible factor: that excess African heterozygosity is in part a function of mutation rate. Simple equilibrium and nonequilibrium models of absolute excess heterozygosity are examined. The results indicate that there is little excess African heterozygosity for traits with low mutation rates and greater excess heterozygosity for traits with moderate to high aggregate mutation rates. Observed data are consistent with these models. Also, depending on population size and time depth, traits with high levels of mutation might show less excess heterozygosity than those with moderate to high mutation rates. Another measure of diversity, mean sequence divergence, shows an increase in excess diversity for traits with high mutation rates.

    PMID: 9353974

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