A brief history of the lies of Ugo Perego: the author of the Church’s Book of Mormon and DNA Studies essay.

[I Have Questions]

Simon calls Perego’s statement “It is increasingly likely around 6+ generations back that you have no DNA in your genome at all from many of your ancestors in that generation.” false. It isn’t false. The complete loss of all DNA from some ancestors does increase the further you look back from 7th generation ancestors onwards. One might quibble that Perego should have used “some” instead of “many” but that quibble doesn’t make the statement “false”.

Perego's wording is misleading but calling his claim false is too strong a word. I have edited my post to reflect that. The wording "you have no DNA in your genome at all from many of your ancestors in that generation" seems to imply that you don't carry DNA from many in the 6th generation. Clearly, beyond the 6th generation you start to lose ancestors until the 10th generation when about 50% are lost.

Fair enough.

In his book "Who We Are and How We Got Here" David Reich has a Figure (4) that illustrates how many of our ancestors at earlier generations contributed to our DNA. When I asked David Reich in an email what the figure was based on he sent me a website link which I cited in my post. The figure below comes from that website. It shows how the percentage of ancestors who contributed DNA to you starts to drop off beyond 6 generations and by the 10th generation only about 50% contribute DNA.

I agree there’s a much more accurate and unambiguous way he could have phrased it. He was, in my opinion, just trying to create a Lamanite sized hole in the DNA record so that faith in the Book of Mormon wasn’t 100% ruled out by DNA science.

It’s worth noting that Perego was writing for a layman, Mormon audience, not presenting a paper to a geneticist convention. Of course he will dumb it down. His main point that Lamanite DNA might have disappeared from today’s population on the basis that 100% of some ancestors DNA drops out of today’s populations DNA is accurate. It is also accurate, within that context, to say that the number of ancestors whose DNA drops out of your own record increases the further back you look. 10 ancestors is, what, a 250 year timespan? Lamanite ancestors would be what 1,500 years ago. Looking over that timespan, many of your ancestors DNA traces would be completely missing. (I think this paragraph is arguably to strongest argument in defence of Perego’s statement).

Its not just Lamanite DNA that has miraculously vanished off the face of the Western Hemisphere. Jaredite DNA and Mulekite DNA has also vanished as well. All three Book of Mormon civilisations were very large. There must have been significant admixture from all three groups. Autosomal DNA would easily pick it up. Its harder to pick up admixture with mtDNA.

Yes but <dons apologist hat> they were many generations earlier and so have had longer to disappear. Especially if they didn’t interbreed with indigenous populations.

How did the Area leader know about the correspondence, and why did you share private correspondence without seeking Woodward’s approval to do?

The Area leaders put me in touch with Scott Woodward. That's how they knew I was corresponding with him.

Our correspondence wasn't private. My brother-in-law was copied on all of my emails so he had copies of all of Scott's emails. Scott was perfectly comfortable with that. So it seemed reasonable when my Area Leader requested a copy that I provide it. I had no reason to believe it would cause any problem for Scott. That assumption turned out to be incorrect because of the actions of Hinkley.

How do you feel about Ugo Perego's accusation that I lied to a general authority in order to harm Scott Woodward's career? Its been on the FAIR website for over a decade. Why would I want to hurt the career of a fellow scientist? Scott and I were on friendly terms and had been trying to identify an apostle we could talk to about the DNA science. My brother-in-law was fully aware of all our correspondence. Where is the motive?

I still think Woodward had an expectation of privacy between the three of you. A simple “Hi Scott, an Area Authority has asked to see copies of our correspondence. Are you okay with him seeing it?” would have been both polite, and an insurance against being accused of stitching him up. Personally I think sharing them with an Area Authority, outside of the 3 people in the email group, without asking him, was a breach of privacy.

I think in your position I’d have been asking him to support that accusation with evidence, or retract it. Had he refused to do so I’d have sent him a legal notice about an intention to sue him for deformation or slander or whatever was an actionable term.

I’d be taking the same position with FAIR.

Have they given any specific examples of you doctoring the emails?

[simon southerton]

Its not just Lamanite DNA that has miraculously vanished off the face of the Western Hemisphere. Jaredite DNA and Mulekite DNA has also vanished as well. All three Book of Mormon civilisations were very large. There must have been significant admixture from all three groups. Autosomal DNA would easily pick it up. Its harder to pick up admixture with mtDNA.

Yes but <dons apologist hat> they were many generations earlier and so have had longer to disappear. Especially if they didn’t interbreed with indigenous populations.

The Americas were widely populated at least 10,000 years ago. The apologetic claim that the Lehites MUST have encountered others and mixed with them must surely apply to the Jaredites and Mulekites, as they were much larger populations.

Time does not necessarily cause DNA to disappear. Humans admixed with Neanderthals and Denisovans tens of thousands of years ago and their DNA can easily be detected today using autosomal DNA. If Middle Easterners contributed DNA to Native American populations, it would be easy to detect it today using autosomal DNA. Low levels of Middle Eastern DNA have been found in indigenous populations all over South and Central America. But it arrived on Spanish galleons.

I still think Woodward had an expectation of privacy between the three of you. A simple “Hi Scott, an Area Authority has asked to see copies of our correspondence. Are you okay with him seeing it?” would have been both polite, and an insurance against being accused of stitching him up. Personally I think sharing them with an Area Authority, outside of the 3 people in the email group, without asking him, was a breach of privacy.

All very easy to say with the benefit of hindsight hey? I repeat. I was on good terms with Scott. Our exchange was polite. He had said nothing that could possibly reflect poorly on him. How could I possibly have anticipated that the prophet of the church would sack Scott to hide the DNA evidence from the members of the church.

Can you not see that President Hinckley is the cause of Scott's pain?

Do you believe that I edited Scott's emails to harm his career?

I think in your position I’d have been asking him to support that accusation with evidence, or retract it. Had he refused to do so I’d have sent him a legal notice about an intention to sue him for deformation or slander or whatever was an actionable term.

I’d be taking the same position with FAIR.

Have they given any specific examples of you doctoring the emails?

I wrote to Perego and he blocked me. Perego wouldn't have copies of my email correspondence with Scott. I wrote to FAIR and they ignored me. I'm not interested in what you would have done in my position with the benefit of hindsight.

[I Have Questions]

I still think Woodward had an expectation of privacy between the three of you. A simple “Hi Scott, an Area Authority has asked to see copies of our correspondence. Are you okay with him seeing it?” would have been both polite, and an insurance against being accused of stitching him up. Personally I think sharing them with an Area Authority, outside of the 3 people in the email group, without asking him, was a breach of privacy.

All very easy to say with the benefit of hindsight hey?

Absolutely. I realise I’m being smart after the event with the benefit of hindsight.

I repeat. I was on good terms with Scott. Our exchange was polite. He had said nothing that could possibly reflect poorly on him. How could I possibly have anticipated that the prophet of the church would sack Scott to hide the DNA evidence from the members of the church.

You couldn’t.

Can you not see that President Hinckley is the cause of Scott's pain?

I think Woodward himself shares some responsibility for that. By not covering his own ass by checking with a grown up that what he was sharing was okay in the eyes of the institution that he was employed by, he’s gone out on a limb. Again, I note that this is all with hindsight. His sacking seems to be less about him and more about reducing the credibility of the DNA evidence. Woodward should have known the Church will always throw individuals under the bus when it suits.

Do you believe that I edited Scott's emails to harm his career?

I don’t think it’s about belief. Either you did or you didn’t. I can definitely see a floundering Woodward on the verge of being dismissed trying to save himself by saying you altered the e mails. I will say that I cannot see how you could alter them in such a material way that it resulted in his sacking and which he couldn’t demonstrate by simply showing the original sent email to Hinckley. If Woodward was unable to show Hinckley an unaltered original sent email that was materially less dangerous to the Church, which obviously he wasn’t, then I’d say the suggestion that you had altered the emails to make the content look bad is likely untrue.

I think in your position I’d have been asking him to support that accusation with evidence, or retract it. Had he refused to do so I’d have sent him a legal notice about an intention to sue him for deformation or slander or whatever was an actionable term.

I’d be taking the same position with FAIR.

Have they given any specific examples of you doctoring the emails?

I wrote to Perego and he blocked me. Perego wouldn't have copies of my email correspondence with Scott. I wrote to FAIR and they ignored me. I'm not interested in what you would have done in my position with the benefit of hindsight.

That’s fair enough. I do realise I’m being smart after the event. But that is where we are at. We do have the benefit of hindsight at this point in time.

That said, I’d still go after FAIR right now to either put up the evidence that you tampered with the emails, or take the statement down with a noted retraction.

Yes but <dons apologist hat> they were many generations earlier and so have had longer to disappear. Especially if they didn’t interbreed with indigenous populations.

The Americas were widely populated at least 10,000 years ago. The apologetic claim that the Lehites MUST have encountered others and mixed with them must surely apply to the Jaredites and Mulekites, as they were much larger populations.

Time does not necessarily cause DNA to disappear. Humans admixed with Neanderthals and Denisovans tens of thousands of years ago and their DNA can easily be detected today using autosomal DNA. If Middle Easterners contributed DNA to Native American populations, it would be easy to detect it today using autosomal DNA. Low levels of Middle Eastern DNA have been found in indigenous populations all over South and Central America. But it arrived on Spanish galleons.

Let me be clear, I think there’s more chance of discovering that the moon really IS made of cheese than there is of finding any genetic, archeological, biological, historical…and so on traces of Book of Mormon peoples. There is sufficient evidence within The Book of Mormon itself to show that it isn’t what it claims to be. I think the burden of proof lies with Perego to find Lamanite, etc. DNA rather than hot airing about why it might not have been found. I’m surprised he’s not a laughing stock in geneticist circles.

[simon southerton]

RE: Perego and Hinckley's sacking of Woodward

There are additional factors that probably impacted Woodward's situation at BYU. Woodward was made a professor at BYU in 1989, only a few years after getting his PhD. In 1994 Woodward announced that he had extracted and typed DNA (mitochondrial) from an 80-million-year-old Cretaceous dinosaur bone. This discovery was published in Science and attracted a huge amount of publicity. Woodward was a rock star.
https://www.science.org/doi/10.1126/science.7973705

However, within a month of publication, several leading research groups wrote to the journal and clearly showed that Woodward had really sequenced human DNA. Woodward wasn't aware that parts of the human mitochondrial genome have been incorporated into the rest of the genome where they are picking up lots of new mutations because they are essentially non-functioning. At the time Woodward tried to defend his paper but it was absolutely clear he had not discovered Dinosaur DNA. This would have been a huge embarrassment for Scott.

I have only briefly mentioned this whole sad episode a couple of times (including now), many years after I left the church. If I had wanted to hurt Scott's career, I could have widely publicised his discredited dinosaur paper. I can absolutely guarantee you that if I had a DNA skeleton like that in my career, you would know about it. Apologists would be publicising it at every possible opportunity. In my 25 years of experience with apologists, I have observed that many of them have almost zero integrity.

By perpetuating the claim that I lied to a general authority (altered his emails) to hurt Scott's career, Perego may have incorrectly linked Gordon B. Hinckley to the Native American DNA problem. There were other problems with Scott's DNA research that had embarrassed the church. In 2001 Scott's group was collecting thousands of DNA samples from people all over the world. They did a bunch of collections in New Zealand without bothering to get approval from the appropriate ethics board. Its quite possible that this was what motivated Hinckley to move Scott out of BYU. But Perego's lie quite clearly implicates Hinckley to the Native American DNA problem. And I can live with that.

[drumdude]

Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for sequencing technologies. The oldest DNA sequenced from physical specimens are from mammoth molars in Siberia over 1 million years old. In 2022, two-million-year-old genetic material was recovered from sediments in Greenland, and is currently considered the oldest DNA discovered so far.

Wow. That's quite the mistake. If I believed I had found DNA that is almost 2 orders of magnitude older than the oldest known surviving DNA, I would double and triple check that before publishing.

But knowing Mormons and BYU, I'm not surprised that checking their fantastic claims wasn't a priority...

[I Have Questions]

RE: Perego and Hinckley's sacking of Woodward

There are additional factors that probably impacted Woodward's situation at BYU. Woodward was made a professor at BYU in 1989, only a few years after getting his PhD. In 1994 Woodward announced that he had extracted and typed DNA (mitochondrial) from an 80-million-year-old Cretaceous dinosaur bone. This discovery was published in Science and attracted a huge amount of publicity. Woodward was a rock star.
https://www.science.org/doi/10.1126/science.7973705

However, within a month of publication, several leading research groups wrote to the journal and clearly showed that Woodward had really sequenced human DNA. Woodward wasn't aware that parts of the human mitochondrial genome have been incorporated into the rest of the genome where they are picking up lots of new mutations because they are essentially non-functioning. At the time Woodward tried to defend his paper but it was absolutely clear he had not discovered Dinosaur DNA. This would have been a huge embarrassment for Scott.

I have only briefly mentioned this whole sad episode a couple of times (including now), many years after I left the church. If I had wanted to hurt Scott's career, I could have widely publicised his discredited dinosaur paper. I can absolutely guarantee you that if I had a DNA skeleton like that in my career, you would know about it. Apologists would be publicising it at every possible opportunity. In my 25 years of experience with apologists, I have observed that many of them have almost zero integrity.

That’s quite the howler! Presumably the peer review committee were equally embarrassed. Has Woodward ever admitted the mistake?

By perpetuating the claim that I lied to a general authority (altered his emails) to hurt Scott's career, Perego may have incorrectly linked Gordon B. Hinckley to the Native American DNA problem. There were other problems with Scott's DNA research that had embarrassed the church. In 2001 Scott's group was collecting thousands of DNA samples from people all over the world. They did a bunch of collections in New Zealand without bothering to get approval from the appropriate ethics board. It’s quite possible that this was what motivated Hinckley to move Scott out of BYU. But Perego's lie quite clearly implicates Hinckley to the Native American DNA problem. And I can live with that.

I’m wondering why Perego got involved in something that really wasn’t any of his business, did he have an axe to grind with you?

[simon southerton]

Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for sequencing technologies. The oldest DNA sequenced from physical specimens are from mammoth molars in Siberia over 1 million years old. In 2022, two-million-year-old genetic material was recovered from sediments in Greenland, and is currently considered the oldest DNA discovered so far.

Wow. That's quite the mistake. If I believed I had found DNA that is almost 2 orders of magnitude older than the oldest known surviving DNA, I would double and triple check that before publishing.

But knowing Mormons and BYU, I'm not surprised that checking their fantastic claims wasn't a priority...

In Woodward's defence, the development of methods for isolating DNA from ancient remains was in its infancy. It was very difficult to avoid contamination from people handling the ancient remains. But it doesn't reflect well on the review process at Science. His paper must have got past several leaders in the field. Science published about 4 rebuttals a few months later, (https://www.science.org/doi/epdf/10.112 ... ce.7605504) so everyone knew he'd published human DNA sequences. Woodward rejected the criticism and defended his work in response to the rebuttals. But the writing was on the wall.

The field of paleogenomics was just kicking off. Svante Pääbo was a pioneer in this field and published the Neanderthal mtDNA sequence in 1997. It was also several years before the human genome was published, so he may not have had human sequences to compare his sequences with. The paper had a significant impact on the field. People became obsessed with avoiding contamination.

Has Woodward ever admitted the mistake?

Not that I'm aware of.

I’m wondering why Perego got involved in something that really wasn’t any of his business, did he have an axe to grind with you?

I visited Scott Woodward's lab back in about 2004 and he took me on a tour of the Sorenson Molecular Genealogy facility in Salt Lake. Perego was a PhD student in his lab at the time and he sat in on a chat we had afterwards. Scott was very defensive and said something about an email that had really annoyed him. Soon after I was released as bishop I had written an email to several life science researchers at BYU about the DNA problem, asking if any had managed to resolve the issue satisfactorily. I assumed that was the email that had annoyed Scott and I apologised if that had caused him any problems. It was only when Perego accused me of altering Scott's emails to me in the 2009 FAIR hit piece, that the penny dropped for me. I suspect Woodward assumed that I had deliberately tried to hurt his career and Perego has probably embellished the story to suite his apologetic agenda.

By the time I visited Scott he was already an apologist. He hinted that they were on the verge of publishing amazing data that would support the Book of Mormon. Of course nothing has appeared.

Unfortunately for Perego, his descent into the Mormon apologetic swamp has probably come at a significant cost to his scientific career. His early career publication record was outstanding. This is largely because he was working in a DNA lab that had far more money than any other lab in the world. In the mid 1990's Scott's lab had sequenced mitochondrial DNA from at least 6,000 Native Americans. Only 2,000 had been published by the entire world by 1998 when I stumbled on the research. If you have piles of DNA data you can write piles of papers. And other labs want to collaborate with you. Normally, someone with Perego's CV would easily secure a university position. But he is languishing at a community college somewhere. I guess when you write dodgy apologetics that contradicts your research, its not a good look to a panel reviewing your application for an academic position. It reflects poorly on the applicant and it would be too big a risk for the university if they hired him.

[canpakes]

The figure below … shows how the percentage of ancestors who contributed DNA to you starts to drop off beyond 6 generations and by the 10th generation only about 50% contribute DNA.

It’s worth noting that Perego was writing for a layman, Mormon audience, not presenting a paper to a geneticist convention. Of course he will dumb it down. His main point that Lamanite DNA might have disappeared from today’s population on the basis that 100% of some ancestors DNA drops out of today’s populations DNA is accurate. It is also accurate, within that context, to say that the number of ancestors whose DNA drops out of your own record increases the further back you look. 10 ancestors is, what, a 250 year timespan? Lamanite ancestors would be what 1,500 years ago. Looking over that timespan, many of your ancestors DNA traces would be completely missing. (I think this paragraph is arguably to strongest argument in defence of Perego’s statement).

Its not just Lamanite DNA that has miraculously vanished off the face of the Western Hemisphere. Jaredite DNA and Mulekite DNA has also vanished as well. All three Book of Mormon civilisations were very large. There must have been significant admixture from all three groups. Autosomal DNA would easily pick it up. Its harder to pick up admixture with mtDNA.

Yes but <dons apologist hat> they were many generations earlier and so have had longer to disappear. Especially if they didn’t interbreed with indigenous populations.

Simon, I’m asking this as a person who knows pretty much nothing about this subject, so I apologize for ignorance and incorrect word use:

For the chart above, is the implication that this shows the effect of (say) Group A’s detectable DNA dropping out of a population that used to contain both Group A and Group B, but after the point at which all individuals that were purely Group A were completely, suddenly and/or definitively removed from that population?

Or can the same eventual drop out occur via genetic drift given enough time, if Group A is merely significantly reduced but generationally continues to reproduce along with the larger group, creating a traceable line that could be (theoretically) documented like a family tree, but not verifiable via DNA?

[simon southerton]

The figure below … shows how the percentage of ancestors who contributed DNA to you starts to drop off beyond 6 generations and by the 10th generation only about 50% contribute DNA.




Simon, I’m asking this as a person who knows pretty much nothing about this subject, so I apologize for ignorance and incorrect word use:

For the chart above, is the implication that this shows the effect of (say) Group A’s detectable DNA dropping out of a population that used to contain both Group A and Group B, but after the point at which all individuals that were purely Group A were completely, suddenly and/or definitively removed from that population?

The graph shows the probability (Y axis) that you carry DNA from all of your ancestors at particular generations. For generations 1 through to 6 the probability is 1.0 (or 100%). You almost certainly carry DNA from all of your ancestors in those generations, including the 64 of your 6th generation ancestors. But beyond 6 generations some ancestors start to drop out. Those people are still your ancestors but you don't carry any of their DNA.

The reason Perego claimed you only carry DNA from 12% of your 10th generation ancestors is to make it look like autosomal DNA is prone to being lost. Look!! You have lost DNA from almost 90% of your 10th generation ancestors!! How useless is autosomal DNA! He knows his readers will then dismiss autosomal DNA. But the true figure is close to 50%. Meanwhile, he forgets to mention, you only carry mitochondrial DNA from 0.1% of your 10th generation ancestors.

Or can the same eventual drop out occur via genetic drift given enough time, if Group A is merely significantly reduced but generationally continues to reproduce along with the larger group, creating a traceable line that could be (theoretically) documented like a family tree, but not verifiable via DNA?

The problem the church has is that Lehite DNA has vanished. So they hammer this line that genetic drift has caused the extinction of Lehi's DNA. But genetic drift generally does not lead to extinction. It leads to changes in allele or mtDNA frequencies.

If Lehi's group grew to 1 or 2% of say the Mayan population, then we would expect to see 1-2% of Maya mtDNA or autosomal DNA to be Middle Eastern. Mitochondrial DNA is more prone to extinction so maybe the apologists can argue that is whats happened. But that excuse doesn't fly at all with autosomal DNA. If just 1% of the Mayan population were descended from Lehi then we would have seen Middle Eastern DNA already. With autosomal DNA you can detect small fractions of a percent of admixture. They have already done whole genome studies on hundreds of Maya, including about 80 ancient individuals. There is no sign of Middle Eastern autosomal DNA.

One of the best examples of the capacity of autosomal DNA to detect ancient admixture is the recent discovery of Native American DNA in several islands in eastern Polynesia. It arrived there a few hundred years BEFORE Columbus reached the Americas. https://www.nature.com/articles/s41586-020-2487-2. I've looked at the supplementary data for this paper. In some islands the scientists detected 0.1% Native American DNA. In some islands it was closer to 4%. If you came back and tested these populations in 1000 or 10,000 years time the Native American DNA will still be there at about the same level. Extinction of autosomal DNA is far less likely than mtDNA.

[canpakes]

Thank you, Simon. Your response is helping to make some things understandable to me.

Or can the same eventual drop out occur via genetic drift given enough time, if Group A is merely significantly reduced but generationally continues to reproduce along with the larger group, creating a traceable line that could be (theoretically) documented like a family tree, but not verifiable via DNA?

The problem the church has is that Lehite DNA has vanished. So they hammer this line that genetic drift has caused the extinction of Lehi's DNA. But genetic drift generally does not lead to extinction. It leads to changes in allele or mtDNA frequencies.

And this is what brought me to ask this question. If DNA is being ‘replaced’, what does that process look like? I assumed that this was the action of reproducing within a large enough pool of individuals to end up seeing DNA from any given individual eventually being booted, for lack of a better way to put it. Which means that the Church presumably claims that all of the 3 early Mormon civilizations were so completely extinguished as to not be able to keep adding any DNA to the population pool. Hence the switch years ago regarding the origination claim about Native Americans, and Perego’s bind of trying to make this DNA question work somehow.

I can’t imagine how heartbreaking these fruitless searches for evidence were to folks like Woodward and Ferguson.

Perhaps the early Book of Mormon settlers had really strict marriage practices, and only grew their own population by intermarrying without intermixing with the natives … which would seem to have introduced its own set of issues, given the size of the initial 3 groups …
; )

Again, thanks. Looks like I need to do some self-study on DNA to catch up with the great data in this thread.