ICC 2018, mtDNA hetero and homoplasmy

In the link below are the abstracts with links to the papers presented at the International Conference on Creationism 2018 in Pittsburgh, PA July 29-August 1, 2018. Those presenting are professors at Christian colleges, professors already expelled from secular colleges, or professors at secular colleges who (by God’s grace) can’t be expelled. 🙂

http://www.creationicc.org/icc18_abstracts.php

A topic I will raise among the population geneticists there (John C. Sanford, Rob Carter, Nathaniel Jeanson, and others) is the issue of heteroplasmy in mtDNA as they are presenting on these topics.

Mature human cells have 100,000 to 600,000 mitochondrion. So how can a cell be mostly homoplasmic yet have mtDNA mutations that are reflected in lineages whereby an individual has a mostly homoplasmic mtDNA that enable us to identify the 7 daughters of Eve (to quote Oxford Geneticist Bryan Sykes).

I would think we would have not-so-discrete-one-or-the other situation but substantially more degrees of heteroplasmy given there are 100,000-600,000 mitochondrion in a cell.

One possible solution that was unwittingly suggested by an NIH grant is that some gametes have only 1-3 mitochonrion by extreme accident, hence we can have an mtDNA change in an lineage.

These issues must be considered when trying to calibrate mtDNA clocks by direct sampling of grandparents and grand children. Also, what is the effect of somatic mutations in the calibration of the clock since we usually sample somatic cells to calibrate the speed of germline mutations of mtDNA. I do not have answers to these questions, so this thread is a place marker for discussion for what I hope to glean at ICC 2018 regarding mtDNA.

40 Replies to “ICC 2018, mtDNA hetero and homoplasmy”

  1. Mung Mung
    Ignored
    says:

    Speaking of the Seven Eves:

    https://www.amazon.com/dp/0062190377

  2. J-Mac
    Ignored
    says:

    Welcome back Sal!
    I hope you are well…
    Have you expanded your knowledge of QM? 😉

  3. stcordova
    Ignored
    says:

    J-Mac:
    Welcome back Sal!
    I hope you are well…
    Have you expanded your knowledge of QM?

    Thanks J-mac. Nice to see you again.

    I actually need to re-learn QM before even expanding knowledge on that front. I’ve been having to focus, in connection with Dr. Sanford’s work, on other things in the meantime.

    My posts here at TSZ might now become insufferably boring because of the technical nature of some of the topics I bring up. I bring them up because they are of interest to the 3 people I named in the OP and maybe I could actually get an expert commentary on the issue I raised.

    So, apologies in advance for my new boring persona at TSZ.

  4. PeterP
    Ignored
    says:

    sal:

    Mature human cells have 100,000 to 600,000 mitochondrion.

    Not true at all.

    Want to try another number? (hint: you are about 2 orders of magnitude off)

  5. stcordova
    Ignored
    says:

    PeterP,

    Thank you for your response. I’ve seen numbers for gametes around 100, but for somatic cells 100,000-600,000.

    Did I mis-interpret this. Thanks in advance:

    https://www.researchgate.net/publication/16900133_Mitochondrial_DNA_copy_number_in_bovine_oocytes_and_somatic_cells_1

    In mammals, the number of mitochondria increases dramatically as the oocyte grows. In cattle, a 45-fold increase in mitochondria occurs from the primordial germ cell to the preovulatory follicular stage (Smith and Alcivar, 1993), with a mean 260,000 mitochondrial copies in mature oocytes ( Michaels et al., 1982). After fertilization and through the early stages of embryonic development, mitochondrial biogenesis ceases and their number remains constant until embryo implantation ( Dumollard et al., 2007). …

  6. PeterP
    Ignored
    says:

    stcordova: Did I mis-interpret this

    Yes.

    Why the switch from your claim of mature human cells to bovine oocytes?

  7. J-Mac
    Ignored
    says:

    stcordova: Thanks J-mac.Nice to see you again.

    I actually need to re-learn QM before even expanding knowledge on that front.I’ve been having to focus, in connection with Dr. Sanford’s work, on other things in the meantime.

    My posts here at TSZ might now become insufferably boring because of the technical nature of some of the topics I bring up.I bring them up because they are of interest to the 3 people I named in the OP and maybe I could actually get an expert commentary on the issue I raised.

    So, apologies in advance for my new boring persona at TSZ.

    No worries Sal…It’s good to have you back… I mean it 😉 While we disagree on some issues, I really would like to attend the conference and meet you in person (provided you don’t post my picture here. It would ruin all the fun… 😉
    We have more than boring OPs here including some of mine but I found that the simpler the subject is presented (if possible) the more likely it is to be popular…
    Just look at the “Why does the soul need the brain? OP… it has almost become as popular as Daytona 500 also called Gruppcio 500 by Joe Felsaintstain…

  8. keiths keiths
    Ignored
    says:

    J-Mac, to Sal:

    I really would like to attend the conference and meet you in person…

    For once, I actually feel a little sorry for Sal.

  9. J-Mac
    Ignored
    says:

    keiths:
    J-Mac, to Sal:

    For once, I actually feel a little sorry for Sal.

    Do you really feel that anyone here cares what you have to say? We all know you can’t “feel’ anything…Why would we care? Don’t you get it?
    Your god evolution made you what it should have made you: crap

  10. OMagain
    Ignored
    says:

    J-Mac: Your god evolution made you what it should have made you: crap

    But, logically, given that’s not at all what you think happened you should in fact be questioning your foundation for saying the world that your presumed deity/Intelligent Designer made contains a crap thing.

    Keiths is exactly as your guiding intelligent wanted him to be. Agree or disagree?

  11. stcordova
    Ignored
    says:

    Why the switch from your claim of mature human cells to bovine oocytes?

    Cows are mammals, that was the one reference where I saw the large number. I thought I saw numbers for human oocytes 100,000-600,000 somewhere, but I don’t remember the reference.

    Anyway, this is not me promoting an idea, I’m soliciting information. So thanks for pointing out errors on my part.

  12. stcordova
    Ignored
    says:

    https://embryo.asu.edu/pages/mitochondrial-dna-mtdna

    Mitochondrial DNA (mtDNA) is a type of DNA located outside the nucleus in the liquid portion of the cell (cytoplasm) and inside cellular organelles called mitochondria. Mitochondria are found in all complex or eukaryotic cells, including plant, animal, fungi, and single celled protists, which contain their own mtDNA genome. In animals with a backbone, or vertebrates, mtDNA is a double stranded molecule that forms a circular genome, which ranges in size from sixteen to eighteen kilo-base pairs, depending on species. Each mitochondrion in a cell can have multiple copies of the mtDNA genome. In humans, the mature egg cell, or oocyte, contains the highest number of mitochondria among human cells, ranging from 100,000 to 600,000 mitochondria per cell, but each mitochondrion contains only one copy of mtDNA. In human embryonic development, the number of mitochondria, the content of mtDNA in each mitochondrion, and the subsequent mtDNA activity affects the production of the oocytes, fertilization of the oocytes, and early embryonic growth and development.

    So what does that figure mean? That’s obviously the same one I used in the OP. I’m not an embryologist or developmental biologist.

  13. stcordova
    Ignored
    says:

    Oocyte is not a somatic cell right, so somatic cells lose mitochondrion numbers???

  14. keiths keiths
    Ignored
    says:

    Sal,

    I suggest a disguise so that J-Mac won’t recognize you at the conference.

  15. stcordova
    Ignored
    says:

    keiths:
    Sal,

    I suggest a disguise so that J-Mac won’t recognize you at the conference.

    You mean like my casino pimp outfit? 🙂

  16. stcordova
    Ignored
    says:

    I thought more on the problem that inspired me to post. The problem is estimating mutation rates in the germ line in a way that we factor out the effect of somatic cell mutations since, as far as I know we test somatic cells like say between mother and daughter, not the actual germ line cells. So the germline might have gone 1 generation, but the somatic cells???? maybe 60-120 based on the Haflick limit? Is that right? Does that make sense?

  17. keiths keiths
    Ignored
    says:

    Sal,

    Your reasoning and reading comprehension skills are pitiful.

    Sal:

    Mature human cells have 100,000 to 600,000 mitochondrion [sic].

    PeterP:

    Not true at all.

    Want to try another number? (hint: you are about 2 orders of magnitude off)

    Sal:

    Thank you for your response. I’ve seen numbers for gametes around 100, but for somatic cells 100,000-600,000.

    Did I mis-interpret this.

    <quotes passage on bovine oocytes>

    PeterP:

    Yes.

    Why the switch from your claim of mature human cells to bovine oocytes?

    Sal:

    Cows are mammals, that was the one reference where I saw the large number.

    So your reasoning is “cows are mammals, therefore bovine oocytes are human somatic cells”? You make the baby Jesus cry when you reason like that, Sal.

    Then Sal finds a quote that applies to humans:

    In humans, the mature egg cell, or oocyte, contains the highest number of mitochondria among human cells, ranging from 100,000 to 600,000 mitochondria per cell,

    So your reasoning is “human oocytes contain 100,000 to 600,000 mitochondria; therefore human somatic cells contain 100,000 to 600,000 mitochondria”?

    Again, you’re making the baby Jesus cry.

  18. stcordova
    Ignored
    says:

    Your reasoning and reading comprehension skills are pitiful.

    That may be true, and that’s why I came here for brilliant guys like you to set me straight.

    So your reasoning is “human oocytes contain 100,000 to 600,000 mitochondria; therefore human somatic cells contain 100,000 to 600,000 mitochondria”?

    That’s what I thought, but so a variety of somatic cells are generated with on the order of 100 less mitochondrion than oocytes???

    Unlike you I’m willing to re-orient my understanding and say I’m wrong, but it would be nice if a biologist chimed in offered some references. I mean that’s an enormous variation.

    Here is the mechanistic issue. As I read it, at some stage maybe as little as 1-3 mitochondria exist in a reproductive cell, though typically it’s 100, then when it becomes an oocyte it goes to 600,000 and then a somatic cell it goes to 4000????? Is that right. If no more than “I tell you different” would be helpful.

  19. stcordova
    Ignored
    says:

    From an NIH grant:

    https://grants.nih.gov/grants/guide/pa-files/PA-16-087.html

    Oocytes develop from primordial germ cells in the embryo. Primordial germ cells possess approximately 100-200 mitochondria per cell, and each cell will have only one or two copies of mitochondrial DNA (mtDNA). During oogenesis, there is increase in both the number of mitochondria and the mtDNA copy number. A mature, fertilizable metaphase II oocyte will have approximately 100,000 mitochondria, and correspondingly will have >200,000 copies of mtDNA. Mitochondrial DNA (mtDNA), unlike the nuclear genome, is transmitted to the offspring from the population of mitochondria present in the oocytes at the time of fertilization.

    Ok so, thanks to Keiths I see where I’ve confused my terms. Unlike Keiths, however I will say I was confused, I mis-interpreted, I was wrong. In contrast Keiths will go for thousands of posts defending his mistake. He’s so much fun to debate because he must save face at all costs and try to give the appearance he’s infallible.

    A professor evolutionary biology over a Reddit disputed the meaning of this:

    Primordial germ cells possess approximately 100-200 mitochondria per cell, and each cell will have only one or two copies of mitochondrial DNA (mtDNA).

    Mitochodria without mtDNA??????

  20. keiths keiths
    Ignored
    says:

    Sal,

    That’s what I thought, but so a variety of somatic cells are generated with on the order of 100 less mitochondrion than oocytes???

    Assuming you meant to say “100 times fewer mitochondria than oocytes”, then yes. Why do you find that so astonishing?

  21. keiths keiths
    Ignored
    says:

    Sal,

    Ok so, thanks to Keiths I see where I’ve confused my terms. Unlike Keiths, however I will say I was confused, I mis-interpreted, I was wrong.

    You acknowledged a mistake. That’s good. Why spoil it by immediately following it with a lie?

  22. keiths keiths
    Ignored
    says:

    Sal,

    A professor evolutionary biology over a Reddit disputed the meaning of this:

    Primordial germ cells possess approximately 100-200 mitochondria per cell, and each cell will have only one or two copies of mitochondrial DNA (mtDNA).

    Mitochodria without mtDNA??????

    No, all mitochondria have mtDNA. I think the author meant to write this:

    Primordial germ cells possess approximately 100-200 mitochondria per cell, and each cell mitochondrion will have only one or two copies of mitochondrial DNA (mtDNA).

    [correction in bold]

  23. OMagain
    Ignored
    says:

    Sal,

    or professors at secular colleges who (by God’s grace) can’t be expelled.

    Presumably those that were expelled were also expelled because that’s what your god wanted to happen? So on the one hand you praise god for stopping their expulsions but on the other hand you seem to have forgotten to blame it for the explosions that did happen.

    I guess it’s a bit like those people who praise de lard for saving them for a tornado, but never seem to question why de lard sent it in the first place.

  24. stcordova
    Ignored
    says:

    Ok, let me state some my errors so far in this discussion and thus set a good example to Keiths how to behave rather than constantly try to save face:

    Error 1:

    Mature human cells have 100,000 to 600,000 mitochondrion.

    The proper term is Ooocyte, it probably would not be considered a representative cell. According to wiki, the number is 4,000 for other cells, but to my credit, from a university website:

    in humans, the mature egg cell, or oocyte, contains the highest number of mitochondria among human cells, ranging from 100,000 to 600,000 mitochondria per cell,

    PeterP said I misinterpreted. Ok, so I misinterpreted. I was wrong wrong wrong.

    There, see Keiths, it’s not so hard to say, “I’m wrong.” or “I mis-interpreted.” or “I was uninformed” or “I made a terrible mistake.” or “I certainly need to learn more.”

    Hopefully in the process of me highlighting my errors you learned something from my shining example of humility. 🙂

  25. stcordova
    Ignored
    says:

    So what’s the ulterior motive behind this seemingly innocuous discussion. Well it relates to this dispute posted by a professor of evolutionary biology:

    https://www.reddit.com/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/

  26. colewd
    Ignored
    says:

    stcordova,

    Hopefully you learned something from my shining example of humility.

    There is always hope and I remain optimistic 🙂

    Good to see you post here Sal. Have you read Ewert’s paper?

  27. stcordova
    Ignored
    says:

    colewd,

    I’ve read parts of it, I actually have a more far reaching hypothesis which extends Ewert’s ideas. I sketched it out in the link below. I call it the “Hackability Hypothesis.”

    https://www.reddit.com/r/Creation/comments/92kjcy/common_descent_vs_the_hackability_hypothesis/

    Nice to see you too! Nice to be back. I hope you are well.

  28. keiths keiths
    Ignored
    says:

    Sal,

    There, see Keiths, it’s not so hard to say, “I’m wrong.” or “I mis-interpreted.” or “I was uninformed” or “I made a terrible mistake.” or “I certainly need to learn more.”

    I know. I’ve been trying to get you to follow my lead for years.

    I’m happy to see you doing so, and at the same time disappointed (but not at all surprised) that you immediately resort to lying in order to make the bitter pill of correction easier to swallow.

    It’s a typically Cordova-ish move. Such behavior is among the many reasons you are so widely disrespected.

  29. John Harshman John Harshman
    Ignored
    says:

    Start with this:

    Birky C.W., Jr. Evolution and population genetics of organelle genes: Mechanisms and models. In: Selander R.K., Clark A.G., Whittam T.S. editors. Evolution at the Molecular Level. Sunderland, MA, Sinauer Assoc., 1991. p. 112-134.

  30. stcordova
    Ignored
    says:

    Thanks John, much appreciated.

  31. Mung Mung
    Ignored
    says:

    keiths: I’ve been trying to get you to follow my lead for years.

    What are you talking about. You don’t admit when you are wrong or when you’ve misinterpreted something.

    ETA:

    keiths: Why spoil it by immediately following it with a lie?

    Ah. I get it now.

  32. keiths keiths
    Ignored
    says:

    Mung,

    What are you talking about. You don’t admit when you are wrong or when you’ve misinterpreted something.

    Sure I do. What is it with doofuses like you and Sal? Do you think you can alter the past simply by wishing for it to change?

  33. Mung Mung
    Ignored
    says:

    keiths: Do you think you can alter the past simply by wishing for it to change?

    I’m more interested in how you will act in the future. Whether you will ever admit your mistakes and learn from them. Your track record in that regard leaves something to be desired. The idea that someone can learn from you how to admit mistakes is hilarious.

  34. keiths keiths
    Ignored
    says:

    Mung:

    You never admit mistakes.

    keiths:

    Sure I do.

    Mung:

    But I don’t want that. I don’t want that! I need you to stop, so I can criticize you.

    keiths:

    (Rolls eyes)

  35. Mung Mung
    Ignored
    says:

    Mung: The idea that someone can learn from you how to admit mistakes is hilarious.

    For sure someone can mimic your words about how you admit your mistakes. I’m talking about actions. Where you actually do admit to making a mistake.

  36. keiths keiths
    Ignored
    says:

    I’m talking about actions. Where you actually do admit to making a mistake.

    Christ, Mung. It happened just a few minutes ago:

    Oops — that should be “Thou canst not teach a dumb rock new tricks.”

    Predicted Mung response, as indicated above:

    But I don’t want that. I don’t want that! I need you to stop [acknowledging your mistakes], so I can criticize you.

  37. Mung Mung
    Ignored
    says:

    keiths: Christ, Mung. It happened just a few minutes ago:

    LoL. You made a typing mistake. So you can admit when you make a typing mistake.

    My bad.

  38. keiths keiths
    Ignored
    says:

    Not just typos, of course.

    But you’ve got to admit that it’s funny. You make a claim, not realizing that there’s a counterexample from just a few minutes earlier. Typical Mung fail.

  39. stcordova
    Ignored
    says:

    I had a conversation with Nathaniel Jeanson over mtDNA.

    First, there is a developmental bottlneck where cells have only 9 mitochondrion. It was one of the papers cited in Jeanson’s work. I don’t have it handy. THAT’S one piece of the puzzle I was trying to solve!!!! Whoohoo!

  40. Mung Mung
    Ignored
    says:

    This is good news. We need more reasons to believe in a young earth.

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