Valerie: Questions about TMR4A

When I was a child, I spoke as a child, I understood as a child, I thought as a child; but when I became a man, I put away childish things.

No, you like to pick out little bits that fit your preconceptions, while ignoring everything that doesn’t. That’s not research.

The way of a fool is right in his own eyes,
But he who heeds counsel is wise.

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Weird… I’ve not had problems reported with e-format from publisher or Mr Amazon. Did you download from some other source?

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Nope, direct through the Logos software. I will flag it to them later, I just found your extended copy of Job to be amusing enough to share :smiley:

@thoughtful you are showing a child like faith in creationism, which is different than a child like faith in Jesus…

Don’t you agree Jesus is greater than creationism?

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Probably written by the same guy who did the Sumerian king lists…

The following is from Human Y Chromosome Mutation Rate: Problems and Perspectives
Note that Jeanson does reference some of these papers, but diverges wildly from the accepted range of mutation rate.

Table 1. Methodology used, number of Mb analysed, mutation rate in bp-1y-1 and TMRCA in thousand years of age, in some relevant studies on human Y chromosome.

Reference Methodology n° of Mb Mutation Rate TMRCA

Thomson et al. 2000 [37] chimp/human 0.064 1.24×10-9 bp-1y-1, 50 ky

Kuroki et al. 2006 [62] chimp/human 13 1.50×10-9 bp-1y-1, n.a

Xue et al. 2009 pedigree 10.15 1.00×10-9 bp-1y-1, n.a

Mendez et al. 2013 pedigree 0.24 0.62×10-9 bp-1y-1, 338 ky

Francalacci et al. 2013 archaeology 8.97 0.53×10-9 bp-1y-1, 180-200 ky

Poznik et al. 2013 archaeology 10 0.82×10-9 bp-1y-1, 120-156 ky

Helgason et al. 2015 pedigree 23.1 0.87×10-9 bp-1y-1, n.a

Karmin et al. 2015 aDNA 10.8 0.74×10-9 bp-1y-1, 150 ky

Trombetta et al. 2015 aDNA 1.5 0.72×10-9 bp-1y-1, 291 ky

What I note in above table is that the estimates for TMRCA run from 50 to 291 thousand years, as opposed to ~4,500 years per Jeanson.

More recent relevant papers include The Divergence of Neandertal and Modern Human Y Chromosomes where Mendez reports the time to the most recent common ancestor of modern humans and Neandertals as ~588 thousand years ago, two orders of magnitude greater than Jeanson’s result. A preprint from this spring, The evolutionary history of Neandertal and Denisovan Y chromosomes may be of interest.

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I clicked on some of these, but again, like @swamidass you’re missing the point as well.

For instance, the first link references y-chromosome and then goes to this:

Genomic mutation rates can be estimated either by direct observation of mutations in present-day families (de novo mutation rate), by calibrating genetic variation against archaeological/historical records (evolutionary rate), or by using a sequence extracted from ancient human remains of known chronology.

But YEC believes many nuclear DNA differences are a result of created differences, not mutations only. So the only direct measurement YEC can use to argue an approximately 6000 year timeline is Y-chromosome de novo mutation rate, and mtDNA de novo mutation rate. Mainstream genomic rates are a strawman against a YEC position.

Jeanson is saying that there are only 4 studies that captured the y-chromosome rate. It’s not as if it an evolutionary conspiracy - mainstream scientists just don’t care about proving wrong some creationist scientists they’ve never heard of, and they’re all relying on the same set of assumptions using an evolutionary time scale most of the time. And it appears to me, there’s not really a big motivation for them to capture this y-chromosome data.

But all creationists (it was in the Dismantled firm) point to this below. Mainstream science agrees that the de novo mtDNA mutation rate is young (and this was 23 years ago!). And you guys think I don’t accept your theory because I’m ignorant? It’s because I realized creation scientists have already been proven right, and evolutionary origins theory makes less sense to me the more I study it. I’m copying the quote from an article where Jeanson quoted it because I don’t feel like buying the article.

“Thus, our observation of the substitution rate, 2.5/site/Myr [i.e., 2.5 mutations per mitochondrial DNA position per million years], is roughly 20-fold higher than would be predicted from phylogenetic analyses. Using our empirical rate to calibrate the mtDNA molecular clock would result in an age of the mtDNA MRCA [i.e., the mitochondrial DNA Most Recent Common Ancestor—the time at which modern *Homo sapiens* began] of only ~6,500 y.a. [i.e., years ago].”

https://www.nature.com/articles/ng0497-363

I read it, and I’m not sure if it’s the translation I’m reading, but there’s nothing of “where these things already exist.” And if you posit that thorns and thistles are not the result of sin, then the crown Jesus wore on the cross has significance for him as King, but it doesn’t complete the metaphor that Jesus is King of creation as well and mediates its restoration through the cross.

Both you and others should consider this piece in addition, which I thought is a pretty thorough refutation. I came across it today when searching for Irenaeus. I didn’t realize Jon had already given me his reference.

http://theoutlet.us/The’FallofNature’inScriptureandEarlyTradition.pdf

You ask good questions. I was thankful God brought a passage to mind earlier this morning in a few minutes. The answer is that the “restoration of Eden” and the “restoration of Israel to its promised blessings” is perhaps a distinction without a difference:

The restoration includes both the New Jerusalem and the tree of life. Eden and Israel are restored. Notice the echo of Acts 3:21 in Revelation 21:5 and Revelation 22:2

Revelation 21

Then I saw a new heaven and a new earth, for the first heaven and the first earth had passed away, and the sea was no more. 2 And I saw the holy city, new Jerusalem, coming down out of heaven from God, prepared as a bride adorned for her husband. 3 And I heard a loud voice from the throne saying, “Behold, the dwelling place[a] of God is with man. He will dwell with them, and they will be his people,[b] and God himself will be with them as their God.[c] 4 He will wipe away every tear from their eyes, and death shall be no more, neither shall there be mourning, nor crying, nor pain anymore, for the former things have passed away.”

5 And he who was seated on the throne said, “Behold, I am making all things new.” Also he said, “Write this down, for these words are trustworthy and true.”

Revelation 22

Then the angel[a] showed me the river of the water of life, bright as crystal, flowing from the throne of God and of the Lamb 2 through the middle of the street of the city; also, on either side of the river, the tree of life[b] with its twelve kinds of fruit, yielding its fruit each month. The leaves of the tree were for the healing of the nations. 3 No longer will there be anything accursed, but the throne of God and of the Lamb will be in it, and his servants will worship him. 4 They will see his face, and his name will be on their foreheads. 5 And night will be no more. They will need no light of lamp or sun, for the Lord God will be their light, and they will reign forever and ever. 6 And he said to me, “These words are trustworthy and true.

So you’re requiring several migrations, the first of which is under a layer of glaciation, Neanderthal remains later, etc. I think this only takes centuries not millennia. Think how much has happened in the last 500 years of modern history.

Watch 11:30 to 22 minutes and see if you think it is plausible.

Who says that? It’s not, as I understand it, Jeanson’s favored model. You’re presumably talking about the idea that Adam had all sorts of prefabricated genomes in his gametes, enough to simulate a whole population. By its nature, there can be no evidence for or against this notion in the Y chromosome data.

In a word, yes. Willfully so, and the reason behind that is that you don’t want to know because it contradicts your ingrained notions.

If I recall, Jeanson takes the rate of the D-loop hypervariable region and extrapolates that to the entire mitochondrial genome. That’s not a reasonable thing to do. It’s like estimating the evaporation rate of a pond by checking a pot of boiling water on a stove.

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It’s Ken Ham. You can’t expect anyone to take what he says seriously. You certainly can’t expect anyone to watch any of it.

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As I have answered the other 2-3 times you asked me this: Yes, Jesus is greater than any of man’s ideas of science. Do you agree?

I’d be careful when you see a non-believer using scripture or biblical language to criticize a fellow Christian. Let’s assume he does not wield it correctly, and if he does, it can be used falsely as when Satan tried to tempt Jesus. I saw the compliment in the criticism - that he resented that I used my faith to filter how to use evidence. I thought God was gracious in that, as I think John uses sophisticated spiritual attacks sometimes.

The use of faith to filter evidence is specifically why I wrote this in my review of your book:

@John_Harshman I think quickly realized his mistake, and tried a new type of criticism. But again John, your problem is with how I think, right? He focused on that and not what my faith was in - to him it makes no difference whether it is in God or creationism but only what I think about science. Do you care what my faith is in - or just how it makes me think about scientific evidence?

No. The quote was not from Jeanson. It’s from this.

https://www.nature.com/articles/ng0497-363

Well that is obviously not quite the case.

Several papers have multiple authors, the Karmin Paper lists a hundred author attributions. For many reasons, there is a great deal of motivation around the Y chromosome mutation profile.

Then find me another one that captures it separately besides those 4, if it’s not “quite true.”

OK. I see all your attributions above, but they use evolutionary arguments as far as I could tell when I clicked on a few. Accepting their POV is self-defeating.

Agrees?

The Parsons paper that you quoted also states…

This disparity cannot be accounted for simply by substitutions at mutational hot spots, suggesting additional factors that produce the discrepancy between very near-term and long-term apparent rates of sequence divergence.

And sure enough, further study elucidates the long term rates [bold is mine]…

From Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times

Using Bayesian analysis with a relaxed-clock model, we estimated rates for three groups of mitochondrial data: avian protein-coding genes, primate protein-coding genes, and primate d-loop sequences. In all three cases, we found a measurable transition between the high, short-term (<1–2 Myr) mutation rate and the low, long-term substitution rate. The relationship between the age of the calibration and the rate of change can be described by a vertically translated exponential decay curve, which may be used for correcting molecular date estimates. The phylogenetic substitution rates in mitochondria are approximately 0.5% per million years for avian protein-coding sequences and 1.5% per million years for primate protein-coding and d-loop sequences. Further analyses showed that purifying selection offers the most convincing explanation for the observed relationship between the estimated rate and the depth of the calibration. We rule out the possibility that it is a spurious result arising from sequence errors, and find it unlikely that the apparent decline in rates over time is caused by mutational saturation. Using a rate curve estimated from the d-loop data, several dates for last common ancestors were calculated: modern humans and Neandertals (354 ka; 222–705 ka), Neandertals (108 ka; 70–156 ka), and modern humans (76 ka; 47–110 ka).

Mainstream science does not agree with Jeanson on either Y chromosome or mtDNA clocks. At all.
You seem to think that there is evidence against evolution and the age of the earth right there in front of scientists, but they are somehow blind to the big picture truth that the evidence supports the earth and all life therein being young. The consilience of science massive supports the great antiquity of the planet, and the researchers uncovering the actual data are best positioned to contextually interpret the findings.

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Thanks Valerie, I will check that out
Will you be reading the book as well as those articles?

Who am I, a tool of Satan? This is a paranoid fantasy, and one fears for your mental health. There was of course no compliment. What you apparently consider a virtue, I consider a vice.

Sorry, what mistake?

You will note that it’s talking about the D-loop. Unfortunately, the article is paywalled, so I can only see the abstract. They do suggest explanations, apparently, that don’t involve the world being 6000 years old. Do you disagree with their explanations? Have you read the paper?

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Possibly. I have a lot to read on my list currently. :neutral_face: But I definitely always think it’s good to be aware of ideas I don’t agree with. Just need the capacity to engage with them - I’d rather spend all my time thinking about ideas rather than doing laundry, but my kids need clothes to wear. :sweat_smile: I need to invest in audiobooks I think…

I definitely feel your pain on the too many books on the reading list side of life. A benefit of being single is the ability to spend more time reading, but even then there just isn’t enough time. Just figured that it would be good to not just rely on a rebuttal paper without reading the book itself to see if the criticisms are fair.
Not always doable with limited time, though

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No, it still doesn’t. You’ve had this explained to you multiple times. You can’t generalize one part of the mitochondrial genome to the entire mitochondrial genome, just like you can’t generalize the y-chromosome to all other chromosomes.

And then you have to factor-in the long-term effects of natural selection. Deleterious mutations will be weeded out by natural selection. Hence the long-term mutation rate must be lower. This result is so basic and unassailable only an insane person would seek to oppose it.
If a mutation lowers your reproductive rate compared to others(and some mutations do), then that mutation will eventually be outcompeted and go extinct.

There are no ifs or buts here. If you deny it, you have left the arena of rational discourse.

I don’t know which or to what extend ignorance or something else explains your apparent inability to put two and two together here, I’ll leave that to your own devices to figure out. Suffice it to say you’re not impressing anyone by making the same easily debunked, vacuous assertions every time.

No, still no. You can’t generalize the D-loop of the mitochondrial genome to the rest of the mitochondrial genome. No, you can’t just ignore the effects of natural selection. No, natural selection isn’t an assumption, it’s a demonstrable reality. It is so basic one can know it from reason alone.

The attributes of organisms are encoded in their DNA.
Changing that DNA changes their attributes(such as survival and reproductive success).
Those attributes can get worse.
Hence some mutations unavoidably, logically necessarily must have deleterious fitness effects. You can’t get around it. It won’t go away just because you don’t want to think about it.

You can ignore it, which you seem to be doing. But that only reflects badly on you.

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