{"data":[{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"So, like I said, this is a sideshow, but you're wrong, so let's do it anyway.\n\n>Soares et al excluded human population divergence dates that A) weren't archaeologically date-able and B) Where the mtDNA dating doesn't match the archaeoloigcal dates \n\nAll B means is that those alleles were not lost in that bottleneck. Which makes sense, since the survival of alleles through a bottleneck is random. So in some cases, specific alleles are lost, facilitating specific TMRCA calculations for specific haplotypes, and in others they aren't, which means no such calculations can be made. \n\nWhat this *doesn't* mean is that they excluded cases that contradicted their expectations. They just only used the instances that allowed for such calculations. \n\nAnother explanation [here](https://www.reddit.com/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duateyw/), only slightly longer. \n\n \n\n>But the rates are still nowhere near your 200ka.\n\nImmaterial. The point is that you can't use that region to calculate TMRCA. \n\n \n\nNow if you want to argue about Soares 2015 some more, make a new thread. It's off topic here. ","can_gild":true,"controversiality":0,"created_utc":1519075445,"distinguished":null,"edited":1519076096,"gilded":0,"id":"duid3g2","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duic12n","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duid3g2/","retrieved_on":1520023591,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duid3g2","ups":2},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":">The only remaining caveat to the present results is whether the mutation rate reported in Ding et al. (2015) represents a germline rate rather than a somatic mutation rate. \n\nThat's an admission that it's too unreliable to use. That sentence is the ballgame. You can make excuses for why we should still trust those data when they're used in this way, but the onus is on Jeanson to *demonstrate* that such calculations are appropriate, and he's clearly not interested in doing that. \n\n \n\nNone of the rest of what you wrote matters, because, again, this OP was about Jeanson and Jeanson only. So you are more than welcome to continue to try to poke holes in *other* mtDNA work, but it's completely irrelevant to the question of Jeanson's work.\n\nSo I'll address this last round of wrongness in a new subthread here, and then you need to make a new topic if you want to keep talking about it; it's just obfuscation in the context of this OP. ","can_gild":true,"controversiality":0,"created_utc":1519075313,"distinguished":null,"edited":false,"gilded":0,"id":"duicykl","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duic12n","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duicykl/","retrieved_on":1520023528,"score":3,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duicykl","ups":3},{"author":"JohnBerea","author_flair_css_class":null,"author_flair_text":null,"body":"I read that line about somatic vs germline mutations at the end of Jeanson's [2015 paper](https://answersingenesis.org/genetics/mitochondrial-genome-mutation-rate/) as admitting that multiple-generation data would simple be less error-prone.  Not that the Ding et al data was too unreliable to use.  I still don't think we have a reason to not think that Ding et al's homoplasmic mutations won't get us pretty close to the true mtDNA mutation rate.\n\nSoares et al excluded human population divergence dates that A) weren't archaeologically date-able and B) Where the mtDNA dating doesn't match the archaeoloigcal dates (they list H1 and H3 as example of this).  In another comment you hypothecized that they may also be C) excluding divergences where multiple mtDNA alleles went in both directions.  They probably are, even if they didn't mention that case.  But because they are excluding instances of B) that don't match, and there is a \"severe shortage\" that pass criteria A-C, you can't say that these divergences can be accurately used to create a clock.\n\n>  I've already answered your question here [about the percentage of mtDNA that must be subject to selection]\n\nLink me to it then, I must've missed it.\n\nYes, I now accept that the control region does indeed give a variety of rates.  It took me a while to find your source's source's source, but it was there after all.  But the rates are still nowhere near your 200ka.\n\n\n\n\n\n\n","can_gild":true,"controversiality":0,"created_utc":1519074400,"distinguished":null,"edited":false,"gilded":0,"id":"duic12n","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duiaguf","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duic12n/","retrieved_on":1520023019,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duic12n","ups":1},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"Regarding point 2, that's the point. You get a wide variety of rates. \n\nRegarding point 3, it's very much fair because *he's calculating a mutation rate*, not a substitution rate. He then portrays it as a substitution rate. (And anyone else confusing the terms needs to use them correctly as well, but let's keep this on topic. It's about Jeanson.)\n\n \n\n>But without pedigree or some other estimate of the divergence date, you can't calculate a rate.\n\nThat's where the archeology comes in. If we can date certain diverges to *specific* migration events for which we have *specific* dates, we can calculate a rate. Which is exactly what was done. \n\n \n\n>The data from Ding et al (cited by Jeanson)...put mtEve about 6000-6500 years ago.\n\nNo, they don't. Ding et al. don't actually generate data that allow you to do those calculations. Jeanson does so anyway because he either doesn't know better or doesn't care. \n\n \n\n>But I still don't see how you can get a rate of 200k without assuming that > 90% of nucleotides within mtDNA are subject to selection, which I don't think you will agree is the case. Thoughts?\n\nI think you need to take a class on phylogenetics rather than think you can read a few dozen papers and think you understand how this works. I've already answered your question here; if you don't realize that, well, that might be part of the problem.\n\n \n\nBut all of that isn't really material, for one very simple reason: Jeanson acknowledged he couldn't account for somatic vs. germline. And that invalidates everything else he did, even if all of it was perfectly kosher (which, it should be clear at this point, it was not). This is something I asked about earlier, and you ignored the question:\n\n>I highlighted a shortcoming in the data Jeanson used to arrive at a recent TMRCA. Jeanson also acknowledged this shortcoming, but disregarded it in his calculations.\n\n>Are you saying we're both wrong?\n\nSo...are we both wrong? *You* know better than *both of us*?","can_gild":true,"controversiality":0,"created_utc":1519072886,"distinguished":null,"edited":false,"gilded":0,"id":"duiaguf","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_dui504f","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duiaguf/","retrieved_on":1520022121,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duiaguf","ups":1},{"author":"JohnBerea","author_flair_css_class":null,"author_flair_text":null,"body":"1.  Can you think of a likely scenario in which Ding et al's subtraction of homoplastic mutations (as they use the term--across many cells) would not give a very close estimate of the germline mutation rate?  It's possible that hteroplasmy was inherited from the mother, but Ding et al accounted for that by comparing heteroplasmies shared by mother and offspring.\n\n2.  I've read your [link](http://www.evolutionpages.com/Mitochondrial%20Eve.htm) before.  His cited [Ingman et al](http://www.eva.mpg.de/documents/Nature/Ingman_Mitochondrial_Nature_2000_1556221.pdf) are just calculating the rate by comparing with chimps (page 709 bottom right).  The author also cites Gibbons 1998, which mentions a paper by \"Stoneking and Gyllensten\" which I'm guessing is [this one](https://www.nature.com/articles/ng0298-109).  They do indeed note big differences in d-loop mutation rates among pedigree studied, but all of them are still 5-10x faster than the rate calculated by comparing with chimps. \n\n3.  I fully agree that \"It's always the case that the substitution rate is slower than the mutation rate.\"  Some of the papers we're discussing also refer to the substitution rate as the \"mutation\" rate, so I don't think it's fair to fault Jeanson for doing the same.\n\n> If you survey two very distantly related individuals and count the differences, that's direct observation of the substitutions that have accumulated since they diverged.\n\nCertainly.  But without pedigree or some other estimate of the divergence date, you can't calculate a rate.  Thus why I said the observed rate and the observed date.\n\nThe data from Ding et al (cited by Jeanson) and Parsons et al put mtEve about 6000-6500 years ago.  The studies cited in the Ingman et al review give mutation rates 5-10 times slower, which would be 32k to 65k years ago.  But I still don't see how you can get a rate of 200k without assuming that > 90% of nucleotides within mtDNA are subject to selection, which I don't think you will agree is the case.  Thoughts?\n\nEdited to fix link.","can_gild":true,"controversiality":0,"created_utc":1519067523,"distinguished":null,"edited":1519073557,"gilded":0,"id":"dui504f","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_dufu3yg","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/dui504f/","retrieved_on":1520018954,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_dui504f","ups":2},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"I also want to point out that your objection here is nonsensical, and also misrepresents what I said:\n\n>Above you said that Jeanson's \"discounting heterplasmic variation doesn't solve the problem\" because a somatic mutation could become homoplasmic across an entire cell and thus \" Jeanson's number sweep up all instances like this.\" However, Ding et al measured homoplasmy across multiple cells so you made an incorrect claim about the methodology of Jenason's source (Ding et al).\n\nFirst, why not quote my *entire* statement, instead of chopping it up like that? I was very clearly providing a hypothetical example. \n\nSecond, homoplasmy literally means \"same within a cell\". [That's the definition.](https://en.wikipedia.org/wiki/Homoplasmy) So I don't know what you're trying to say here. But whatever it is, it doesn't make sense. Stay on topic, though. Somatic vs. germline. Jeanson can't tell. Ding et al. couldn't tell. Therefore no valid mutation rate from those data, therefore no valid mtTMRCA. ","can_gild":true,"controversiality":0,"created_utc":1519008198,"distinguished":null,"edited":false,"gilded":0,"id":"duh0s16","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duf9op5","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duh0s16/","retrieved_on":1519996398,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duh0s16","ups":2},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"1) Wrong question. The right question is \"do we have strong evidence that only using homoplasmic mutations eliminates somatic mutations?\" The answer is no. Jeanson could, like, *do science* if he wanted to show it's the case, but we can't just assume that we're controlling for a variable without direct evidence to that effect. \n\n2) Again, the problem with the D-loop isn't the high rate per se. It's the variation across multiple studies. There is a fairly detailed discussion of that [here](http://www.evolutionpages.com/Mitochondrial%20Eve.htm) with plenty of references. \n\n3) I see the problem. It's the question of mutations vs. substitutions. Go back to that simple figure I posted. You don't need selection to have only a sub rate much lower than the mutation rate. It's *always* the case that the substitution rate is slower than the mutation rate. This gets at Jeanson maybe not knowing the difference?\n\nRelated point, you keep saying *observed* as though substitution rates that disagree with a young earth aren't, and while a neat rhetorical trick, this is wrong. If you survey two very distantly related individuals and count the differences, that's direct observation of the substitutions that have accumulated since they diverged. Pedigree studies don't own the \"observed\" label. \n\n \n\nBig picture: Points 2 and 3 are not relevant to the question. It's all about demonstrating that we're only counting germ-line mutations, which we cannot do based on the Ding data, and Jeanson acknowledges (and disregards) this shortcoming. ","can_gild":true,"controversiality":0,"created_utc":1518962991,"distinguished":null,"edited":false,"gilded":0,"id":"dufu3yg","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duf9op5","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/dufu3yg/","retrieved_on":1519869933,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_dufu3yg","ups":1},{"author":"JohnBerea","author_flair_css_class":null,"author_flair_text":null,"body":"Above you said that Jeanson's \"discounting heterplasmic variation doesn't solve the problem\" because a somatic mutation could become homoplasmic across an entire cell and thus \" Jeanson's number sweep up all instances like this.\"  However, Ding et al measured homoplasmy across multiple cells so you made an incorrect claim about the methodology of Jenason's source (Ding et al).\n\nThis is what I think are our remaining key points:\n\n1.  Is there still any reason to think that taking the hompolasmic mutations from Ding et al is not a reasonably good way to estimate the rate of germline mutations?  The part where you, me, and Jeanson seem to agree that a multi-generational study would still be superior.\n\n1.  Jeaonson claims the published control region (d-loop) mutation rates agree with his own calculated whole mtDNA genome rates, thus confirming it.  Do you know of any observed (i.e. pedigree) control region dates that disagree?\n\n2.  Unless you can provide an observed mutation rate that is much slower than Jeanson's, that means you need strong selection to filter out most mutations over deep time, and thus almost all of the mtDNA is subject to selection.  Do you agree or disagree?","can_gild":true,"controversiality":0,"created_utc":1518932075,"distinguished":null,"edited":false,"gilded":0,"id":"duf9op5","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duf8y54","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duf9op5/","retrieved_on":1519856600,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duf9op5","ups":1},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":">You incorrectly claimed Ding et al had only done this across a single cell (a forgivable offense) but instead of admitting this you're now accusing me of possible dishonesty.\n\nYeah, see, I actually didn't claim that, if you go back and read what I wrote. \n\nI'm going ignore all the other fluff in the interest of keeping this on topic. \n\nI highlighted a shortcoming in the data Jeanson used to arrive at a recent TMRCA. *Jeanson* also acknowledged this shortcoming, but disregarded it in his calculations. \n\nAre you saying we're *both* wrong? Because saying the Ding data don't allow for us to distinguish between somatic and germline mutations is probably the only thing Jeanson and I agree on. ","can_gild":true,"controversiality":0,"created_utc":1518930994,"distinguished":null,"edited":false,"gilded":0,"id":"duf8y54","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duf8orr","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duf8y54/","retrieved_on":1519856241,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duf8y54","ups":1},{"author":"JohnBerea","author_flair_css_class":null,"author_flair_text":null,"body":"My point is that homoplastic mutations (as measured across multiple cells) is a good proxy for measuring the germline mutation rate.  You have not provided a reason to think otherwise.  You incorrectly claimed Ding et al had only done this across a single cell (a forgivable offense) but instead of admitting this you're now accusing me of possible dishonesty.\n\nI was rather unclear in the paragraph you took offense at, so let me state it in clearer terms:  \"On the D-loop, I've seen 3 or 4 studies that produce mtDNA divergence estimates, but never one that is based on observed mutation rates (not deep-time evolutionary assumptions) that differed very far from ~~them~~ **YEC estimated mtEve dates**. Do you know of any?\"\n\n> \"Deep evolutionary time\" (i.e. the timeframe supported by all the data) is not an assumption. Radiometric dating is real. Paleontology is real.\n\nGenerally about every other line of evidence I take a look at ends up being wildly discordant.  Soft tissue and carbon-14 in dinosaur bones so far.  Yet many alleged lines of evidence I haven't yet explored.  Because of this discordance, my position is that these past timelines cannot be known with any confidence.  Not that anything is a specific age.\n\nOn mtDNA and most mutations being selected away:  It matters very very much for this discussion, because the only way you can get the 200k age of mtEve is if almost all mutations are selected away over time.  How else can you account for the pedigree and the deep time mutation rate estimates of the control region to differ by 20-50x?\n\n\n\n","can_gild":true,"controversiality":0,"created_utc":1518930625,"distinguished":null,"edited":false,"gilded":0,"id":"duf8orr","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duf7hwi","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duf8orr/","retrieved_on":1519353742,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duf8orr","ups":2},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":">You're incorrect about Ding et al--in each person they're sampling mtDNA from many different cells. In thatt paper, \"heteroplasmy\" means differences in the mtDNA across all those samples, not just within a single cell. So your \"example of why this matters\" doesn't apply.\n\nI don't know how to say this a different way, so I guess I'll say it the same way? Homoplasmic vs. heteroplasmic and somatic vs. germline are two different things. Ding et al. made the former distinction, but not the latter. Jeanson acknowledges this, but disregards it in his calculations, in effect assuming all observed mutations were germline. \n\n \n\n>but never one that is based on observed mutation rates (not deep-time evolutionary assumptions)\n\n\"Deep evolutionary time\" (i.e. the timeframe supported by all the data) is not an assumption. Radiometric dating is real. Paleontology is real. \n\nI mean...are you saying \"assumption\" because you really don't know about the data that support that position, or because you want to undermine that position with rhetorical tricks? Because option 3, that it is actually an assumption with no empirical foundation, isn't a real thing. This is why I find you so frustrating, and such a paradox. You're clearly well informed in some ways, but it often seems exceptionally narrow. So I can't make up on mind on \"uninformed\" vs. \"dishonest\" in cases like this. I genuinely can't tell if you think these are actual assumptions, or if it's for show. \n\n \n\n>You've argued that most mutations in mtDNA are selected away\n\nI would like for you to quote where I have made this argument. In other words, I don't believe I have done so. But for what it's worth, I also don't think it matters for this discussion. ","can_gild":true,"controversiality":0,"created_utc":1518928953,"distinguished":null,"edited":false,"gilded":0,"id":"duf7hwi","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duf6j69","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duf7hwi/","retrieved_on":1519353169,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duf7hwi","ups":2},{"author":"JohnBerea","author_flair_css_class":null,"author_flair_text":null,"body":"You're incorrect about [Ding et al](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005306)--in each person they're sampling mtDNA from many different cells.  In thatt paper, \"heteroplasmy\" means differences in the mtDNA across all those samples, not just within a single cell.  So your \"example of why this matters\" doesn't apply.  So I expect that their methodology gets us pretty close to the actual per-generation germline mtDNA mutation rate, although a multi-generation pedigree would still be an improvement.  It also seems unlikely the somatic mutation rate would be much higher than the germline rate.\n\nOn the D-loop, I've seen 3 or 4 studies that produce mtDNA divergence estimates, but never one that is based on observed mutation rates (not deep-time evolutionary assumptions) that differed very far from them.  Do you know of any?\n\n> nobody's assuming that all mtDNA is functional\n\nYou've argued that most mutations in mtDNA are selected away, and therefore most mtDNA must functional.  If you can tell me what rates you are supposing for the per-generation and deep time substitution rates, we can calculate how much mtDNA must be subject to selection in your view.","can_gild":true,"controversiality":0,"created_utc":1518927686,"distinguished":null,"edited":false,"gilded":0,"id":"duf6j69","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duai6ik","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duf6j69/","retrieved_on":1519352682,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duf6j69","ups":2},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"So what do we think? Will we get a \"huh, I guess you're right\" or nothing until the next time this comes up and John uses the same old talking points?","can_gild":true,"controversiality":0,"created_utc":1518914817,"distinguished":null,"edited":false,"gilded":0,"id":"duew1z3","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duai6ik","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duew1z3/","retrieved_on":1519347662,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duew1z3","ups":2},{"author":"QuestioningDarwin","author_flair_css_class":null,"author_flair_text":null,"body":"Yes, that's what I thought, thanks for the clarification.","can_gild":true,"controversiality":0,"created_utc":1518722564,"distinguished":null,"edited":false,"gilded":0,"id":"duatoqv","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duateyw","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duatoqv/","retrieved_on":1519277199,"score":3,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duatoqv","ups":3},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"It means we can't use those events to inform the dates.\n\nHere's what going on:\n\nWe have archeological events that are crystal clear bottleneck events due to migration. For example, the settlement of specific islands, the crossing into North American from Siberia, etc.\n\nIf we have specific mtDNA alleles, or combinations of alleles, that are present only in the group that did a specific migration, we can then use the date of the migration to calibrate the mtDNA sub rate. But if an allele is on both sides of a bottleneck, like say it's present in Native American populations, but also Siberian populations, then we can't use the date of that migration to calibrate the rate, since the MRCA of that allele doesn't correspond to the known date of the bottleneck.\n\nWhen that's the case, that isn't evidence against any specific rate. It just means the specific alleles and migrations in question can't be used to calculate the sub rate.\n\nOn the other hand, if we have an allele that is only on an island, and it's spread through everyone on that island, and we know the date of the settlement of that island, that establishes an upper bound for the TMRCA for that allele, and we can therefore use it to calibrate our sub rate.","can_gild":true,"controversiality":0,"created_utc":1518722314,"distinguished":null,"edited":1518722840,"gilded":0,"id":"duateyw","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duamioz","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duateyw/","retrieved_on":1519277071,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duateyw","ups":2},{"author":"QuestioningDarwin","author_flair_css_class":null,"author_flair_text":null,"body":"So u/JohnBerea was wrong to imply that it had anything to do with dating? Am I correct in deducing that undermines his whole argument?\n\nIf the chronologies are sound *and* align the substitution rate must be sound, right?","can_gild":true,"controversiality":0,"created_utc":1518715877,"distinguished":null,"edited":false,"gilded":0,"id":"duamioz","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duakzxd","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duamioz/","retrieved_on":1519273778,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duamioz","ups":1},{"author":"Denisova","author_flair_css_class":null,"author_flair_text":null,"body":"Gee, even at this instance where the man has overtly and unambiguously shown to be flawed and even, when confronted with this mistake, manages to just continue his course, despite being an educated Ph.D. in Cell biology, no-one here has the simple courage to admit. It reminds me of the sister and uncle of North Korean Kim Jong-un attending the Olympics who, when they will be back home, after experienced the wealth of South Korea, when home, still will tell their people that they live in the Worker's Paradise and everything is bad outside.","can_gild":true,"controversiality":0,"created_utc":1518714450,"distinguished":null,"edited":false,"gilded":0,"id":"dual0ga","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duai6ik","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/dual0ga/","retrieved_on":1519273058,"score":3,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_dual0ga","ups":3},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"It means that no mtDNA alleles were lost in the bottleneck in question, so you can't correlate the MRCA of any lineage specific alleles to a specific migration event. ","can_gild":true,"controversiality":0,"created_utc":1518714436,"distinguished":null,"edited":1518722298,"gilded":0,"id":"duakzxd","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duajyqp","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duakzxd/","retrieved_on":1519273051,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duakzxd","ups":2},{"author":"QuestioningDarwin","author_flair_css_class":null,"author_flair_text":null,"body":"I'm by no means an expert, so pardon me if I'm misreading something, but I don't immediately see how \"not sufficiently well linked to mtDNA lineages\" means the same as \"not matching the expected date\"? Or am I missing something here?\n\n>The episodes that they propose are either archaeologically controversial (as in the case of the first settlement of Australasia, or Sahul, which they tie to haplogroup P), or **not sufficiently well linked to mtDNA lineages**—an example being H1 and H3, already alluded to above, which they surprisingly date to the Last Glacial Maximum (rather than the Late Glacial) without any clear justification.\n","can_gild":true,"controversiality":0,"created_utc":1518713457,"distinguished":null,"edited":false,"gilded":0,"id":"duajyqp","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_du9wi8n","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duajyqp/","retrieved_on":1519272557,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duajyqp","ups":1},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"First, on the D-loop, I mean inconsistent in the absolute sense. Different studies, different populations, different rates. So it isn't usable as a molecular clock. \n\n \n\nSecond, you can count or discount homo- or hetero-plasmic mutations however you want. That's a different distinction from somatic or germline. The line I quoted, the *only* line in which Jeanson even touched on this issue, indicates that *he* knows the difference. Which means he's doing some handwaving with homo- vs. heteroplasmic to make it seem like a non-issue, when it still very much is.\n\nIn other words, homo- vs. heteroplasmic is not directly relevant to the question of somatic vs. germline, so discounting heterplasmic variation doesn't solve the problem. \n\nTo give you a specific example of why this matters, say you have a mutation during development in a single mitochondrion. The cell in which this occurs is now heteroplasmic. But if that mitochondrion or its descendants end up *on their own* inside a descendent cell, that cell will be homoplasmic, even though that variant was due to a *somatic* mutation. Jeanson's number sweep up all instances like this, artificially elevating the substitution rate. In other words, he's simply calculating a mutation rate and *calling it* a substitution rate. \n\n\n \n\nLastly, nobody's assuming that all mtDNA is functional. What Soarse et al. show is that there are hallmarks of selection in *parts* of the mt genome, and you have to take that into consideration when using mtDNA for coalescence analysis. Please stop overstating results like that. ","can_gild":true,"controversiality":0,"created_utc":1518711746,"distinguished":null,"edited":false,"gilded":0,"id":"duai6ik","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duah6y0","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duai6ik/","retrieved_on":1519271706,"score":3,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duai6ik","ups":3},{"author":"JohnBerea","author_flair_css_class":null,"author_flair_text":null,"body":"Ok I had skimmed [Jeanson's paper](https://answersingenesis.org/genetics/mitochondrial-genome-mutation-rate/) once before but now I've given it a read all the way through.  I'm skeptical of his citations of Guo and Rebolledo-Jaramillo because it sounds like they're not doing enough to distinguish between hetero- and homoplasmic mutations.  But Jeanson assumes there were zero which shifts his mutation rate estimate in favor of the evolutionary timeline, so he's being generous here.\n\nHowever, Ding et al **did** distinguish between hetero- and homoplasmic mutations!  They took multiple mtDNA samples to determine which were heteroplasmic.  Why did you say above that \"Jeanson counted all of the differences found between parents and offspring in this study\"?  Until now I had taken your word on this.  Jeanson wrote:\n\n1.  \"In the Ding et al. (2015) study, the authors... scored both heteroplasmic and homoplasmic mutations. Again, I ignored all mutations reported as heteroplasmic.\"\n\nJeanson also says:  \"Interestingly, the resultant rate was virtually identical to the calculated mutation rate for the D-loop based on pooled and statistically weighted data.\"  I have several papers saved that I plan to read on mtDNA d-loop mutation estimates, but why do you say that D-loop estimates should be disregarded for being inconsistent?  Inconsistent with the evolutionary model?  Jeanson says they are consistent with his YEC model.\n\nHowever, I still agree that:\n\n1.  Multi-generation pedigree studies would be superior to the method in Ding et al.\n2.  You can make the divergence dates be whatever you want depending on how much selection there is, if you first assume that almost all nucleotides in mtDNA genes are functional.\n\n**Edit:** I'll be away from my computer all day today, so it might be this evening or tomorrow before I can return to this.","can_gild":true,"controversiality":0,"created_utc":1518710783,"distinguished":null,"edited":false,"gilded":0,"id":"duah6y0","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duaeoea","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duah6y0/","retrieved_on":1519271234,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duah6y0","ups":1},{"author":"[deleted]","author_flair_css_class":null,"author_flair_text":null,"body":"[deleted]","can_gild":true,"controversiality":0,"created_utc":1518710544,"distinguished":null,"edited":false,"gilded":0,"id":"duagyh5","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duaeoea","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duagyh5/","retrieved_on":1519271123,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duagyh5","ups":1},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"Answer my questions rather than deflecting, please. Cite a study if you have one. ","can_gild":true,"controversiality":0,"created_utc":1518708334,"distinguished":null,"edited":false,"gilded":0,"id":"duaesjp","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duaemf4","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duaesjp/","retrieved_on":1519270088,"score":2,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duaesjp","ups":2},{"author":"DarwinZDF42","author_flair_css_class":null,"author_flair_text":null,"body":"[Here's the original piece.](https://answersingenesis.org/genetics/mitochondrial-genome-mutation-rate/) No, he does not address this. This is the last line of the discussion:\n\n>The only remaining caveat to the present results is whether the mutation rate reported in Ding et al. (2015) represents a germline rate rather than a somatic mutation rate. To confirm germline transmission in the future, the DNA sequences from at least three successive generations must be sequenced to demonstrate that variants were not artifacts of mutation accumulation in non-gonadal cells.\n\nSo clearly knows that what he's doing isn't appropriate. But he goes ahead and does it anyway. ","can_gild":true,"controversiality":0,"created_utc":1518708213,"distinguished":null,"edited":false,"gilded":0,"id":"duaeoea","is_submitter":true,"link_id":"t3_7xnjdv","parent_id":"t1_duadi25","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duaeoea/","retrieved_on":1519270033,"score":3,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duaeoea","ups":3},{"author":"JohnBerea","author_flair_css_class":null,"author_flair_text":null,"body":"So what percent of mtDNA nucleotides do you think are subject to selection?","can_gild":true,"controversiality":0,"created_utc":1518708158,"distinguished":null,"edited":false,"gilded":0,"id":"duaemf4","is_submitter":false,"link_id":"t3_7xnjdv","parent_id":"t1_duae8l7","permalink":"/r/debatecreation/comments/7xnjdv/mteve_was_not_6000_years_ago/duaemf4/","retrieved_on":1519270006,"score":1,"stickied":false,"subreddit":"debatecreation","subreddit_id":"t5_30pmo","subreddit_type":"public","name":"t1_duaemf4","ups":1}]}