Dr. Stewart's DNA Paper...

[Jan]

I noticed that Dr. David Stewart's DNA presentation from this year's FAIR conference is already up.

I know a lot of you (e.g., The Dude) were waiting for it ...

DNA and the Book of Mormon by David G. Stewart Jr, M.D.

It's doesn't look as long on-line as the 15 page single-spaced document he distributed but the headings all look right so I think it's all there.

[Great King Peter]

OK

I just tried to read the paper.

Am I the only one who needs a readers digest version written in english?

Great King Peter

[MorningStar]

When is someone going to write "DNA and The Book of Mormon for Dummies"?

[Jerubaal]

Methinks I see El Duderino viewing the thread...

[The Dude]

Martin Tanner explains:

"The idea [that] haplogroup X has been in the Americas for 10 to 35 thousand years is based solely upon the assumptions of the Hardy-Weinberg equilibrium, which include: (1) completely neutral variants, (2) no mutation, (3) no migration, (4) constant near infinite population size, and (5) completely random mate choice. In the Book of Mormon account, most of the Hardy-Weinberg equilibrium assumptions are inapplicable. The wilderness journey, the ocean voyage, and the colonization of the New World, result in patterns of genetic selection and DNA migration different from that found in Lehi's home environment. Closely related individuals married and we are dealing with [initially] a very small group, not a nearly infinite population which would dramatically alter DNA marker distribution and inheritance over time. If we take these assumptions about haplogroup X instead of the Hardy-Weinberg assumptions, haplogroup X could have been introduced into the Americas as recently as one to two thousand years ago, far less than the ten to thirty-five thousand years under the Hardy-Weinberg assumptions."

Stewart disputes consensus science on the dating of haplogroup X (arrived in America 10,000-20,000 years ago) based on "personal communication" from Martin S. Tanner. Who is this Tanner person? Well, he's a lawyer and radio talk show host who has authored a few book reviews for FARMS. Here's his bio on the FARMS website:

Martin S. Tanner J.D., is a founding partner in the law firm of Howe & Tanner. He hosted a radio talk show, "Religion on the Line," on KTKK Radio, 1989-94; he currently hosts a new program, "Religion Today," on KSL Radio. He contributed an article on "Schismatic Groups" to the Encyclopedia of Mormonism.

That is Stewart's source for disputing the dating of haplogroup X. I believe it is a serious misstep.

Here is what the medical doctor (?) Stewart says, quoting the lawyer/radio-host Tanner:

"The idea [that] haplogroup X has been in the Americas for 10 to 35 thousand years is based solely upon the assumptions of the Hardy-Weinberg equilibrium...

The dating is not based solely on assumptions. I have read these papers and I can tell you that they are based on a careful examination of the DNA sequences within the population that composes haplogroup X. I covered this in a very involved thread started by PacMan back in May, so if anyone wants to see how the dating is determined go here.

Oh, Hardy-Weinberg equilibrium is assumed, to be sure, but that is not the sole basis of the dating. That statement is just a strawman set-up for Tanner to knock down. His knocking down is in reality a precarious stumble for Limited Genetics Theory:

...which include: (1) completely neutral variants, (2) no mutation, (3) no migration, (4) constant near infinite population size, and (5) completely random mate choice. In the Book of Mormon account, most of the Hardy-Weinberg equilibrium assumptions are inapplicable.

What???? He is saying that once the 30 or so Lehites arrived in the New World and quickly merged with the native populations, the relevant population didn't exhibit those five characteristics?

(1) completely neutral variants -- the identifying mtDNA sequences are neutral in an evolutionary sense. That is, they do not give a selective advantage/disadvantage to those who carry them. There is every reason to assume this, or else all population genetics using mtDNA is flawed.

(2) no mutation -- actually, some mutation is observed and this is a necessary part of the dating method. See my explanation in PacMan's thread (page 5 and later).

(3) no migration -- see Tanner's elaboration:

The wilderness journey, the ocean voyage, and the colonization of the New World, result in patterns of genetic selection and DNA migration different from that found in Lehi's home environment.

Yes, there was a migration to get the Lehites to America... so what? Once they arrived in "Mesoamerica" or wherever you think it was, it is claimed by Limited Genetics Theory (LGT) that they melded into the indigenous populations. That is the point at which Hardy-Weinberg assumptions come into play, not the relatively short period of the Lehite migration.

Furthermore, a comparison to "Lehi's home environment" is irrelevant to the issue of dating the x haplogroup because the dating figures arise from comparison of variants within haplogroup x in the New World.

(4) constant near infinite population size -- see Tanner's elaboration:

Closely related individuals married and we are dealing with [initially] a very small group, not a nearly infinite population which would dramatically alter DNA marker distribution and inheritance over time.

Tanner makes the same misapplication as he did for point 3. The point at which Hardy-Weinberg assumptions come into effect is when (according to LGT) the Lehites joined with the Asian/Natives, and together they composed a near infinite population size (in genetic terms... obviously the population of the entire New World is not literally infinite).

(5) completely random mate choice -- this is assumed. Tanner gives no explanation for why we should not make this assumption. However I have argued in the past that the BoM gives reasons against random mate choice, for example, when it is said that Nephites did not intermarry with the "dark" Lamanites/Natives. Ironically, if you take this to the point where it violates Hardy-Weinberg assumptions, the segregated marriages of the BoM actually work against the utility of LGT in salvaging the BoM from the negative DNA evidence!

"There's no way that negative evidence on [DNA] hurts the Book of Mormon whatsoever once you believe in a limited geography. If you believe in a global geography, you're basically done, toasted, game over." -- BYU archaeologist John Clark. The unspoken conundrum raised in this article is that LGT doesn't work anymore without Hardy-Weinberg assumptions.

So do these scientific assumptions apply to the BoM or don't they? (To be completely honest with ourselves, we should decide this based solely on the BoM story, and not consider what we will gain by opportunistically embracing Haplogroup X as Lehi's DNA signature)

I think Tanner and Stewart need to reconsider their approach and it would be wise for them to consult some of the actual geneticists and scientists who have written for FARMS and for the Church. From what I have seen, the LDS professionals do not dispute Hardy-Weinberg assumptions for any of the Native American mtDNA groups, because, I think, they see how necessary they are for LGT to explain away the negative DNA evidence.

If we take these assumptions about haplogroup X instead of the Hardy-Weinberg assumptions, haplogroup X could have been introduced into the Americas as recently as one to two thousand years ago, far less than the ten to thirty-five thousand years under the Hardy-Weinberg assumptions."

Calculations please?

And after what I just explained, are we sure about throwing out Hardy-Weinberg assumptions, along with the Limited Genetics Theory that depends on it? Do we now realize that Tanner/Stewart are saying that there should be genetic evidence for the Israelite heritage of Native Americans? Or more precisely, they imply that there is such evidence, and it is Haplogroup X.

http://en.wikipedia.org/wiki/Haplogroup_X_(mtDNA)

Edit to add intact quote at the top of the post.

[The Dude]

Who is David G. Stewart Jr.? Has he ever written anything else for FARMS/FAIR, and what is his background as an MD?

He is willing to cite any dubious source he can lay his hands on, or fragments of credible sources, as long as they support his view that Native Americans have a recent history in the New World and a single source originating overwhelmingly from Book of Mormon people. With selective sources, he is advocating a Hemispheric genetic influence of Book of Mormon people. It is pseudoscience. Under Y chromosome DNA:

Although critics have claimed that Native Americans and modern Jews share no relevant Y-chromosome affinities, recent data have proven such statements resoundingly false. Douglas Forbes points out that Y-chromosome SNP biallelic marker Q-P36 (also known by the mutation marker M-242), postulated by Behar and colleagues to be a founding lineage among Ashkenazi Jewish populations,15 is also found in Iranian and Iraqi Jews,16,17 and is a founding lineage group18 present in 31% of self-identified Native Americans in the U.S.19 A branch of the Q-P36 lineage (M-323) is also found in Yemenite Jews. The Q-P36 lineage is ancestral to the Q-M3 mutation group. The Q-P36 and Q-M3 lineages together (haplogroup Q) are found in over 76% of Native Americans.20 Douglas Forbes writes, "We find M242 scattered all over central Eurasia and concentrated in Turkistan just north of Iran.21 The ten tribes including Manasseh were taken captive to Media (northwest Iran). So M242 is found scattered just where you would expect it would be if legends of the 10 tribes escaping captivity by going north are true."22 While the ethnohistory behind these variations remains to be elucidated, these intriguing findings produce considerable difficulty for critics' arguments.  The finding of two dominant Y-chromosome lineages in Amerindian populations is harmonious with traditional LDS view of Lehi and Ishmael representing the principal male ancestors of Native Americans, with Zoram and the Mulekites contributing minor lineages. The discovery of a founding Y chromosome lineage prevalent at a very high frequency among Native Americans corresponding to a founding lineage present in world Jewish populations demonstrates remarkable consistency with the Book of Mormon account.

Who is Douglas Forbes? A software engineer with a blog!

http://dougsaythis.blogspot.com/2005/09/lamanites.html

Sure, if you go back far enough, you will find affinities between Native Americans, Iranians, Jews... everybody has a relationship. Forbes and Stewart express no understanding that these affinities are hierarchical, or that there are time scales involved that do not harmonize with the Book of Mormon.

[katherine the great]

I didn't have to get very far down the page to find a glaring mistake. He mentioned Asenath being the ancestral mother of the Ephraimites. That really isn't accurate from a genetic standpoint since mitochondrial dna passes through the generations only through the female line. Asenath (whom we presume was Egyptian, but she really could have been from anywhere) passed her mtdna to her sons, but they could NOT pass it down to their descendants. Only her daughters (if she had any) could have continued to pass it down. Ephraim and Manassah's wives would be the ones who's mtdna haplogroups would be passed down to their direct descendants. I'm not sure it changes the argument (unless the scriptures specifically mention the genetic profile of their wives), but it seems like a pretty big misunderstanding of basic deep ancestry dna.

[Homestar Runner]

When is someone going to write "DNA and The Book of Mormon for Dummies"?

It's been written countless hundreds of times already. Here it is again:

* Show me a critic advancing a DNA-themed criticism of BoM claims, and I'll show you a critic who is ignorant of either 1) BoM claims, or 2) what DNA can or can't do.

* There is no such thing as a DNA scientist performing DNA research in order to prove the BoM wrong.  There are a handful of fairly smart people who are not DNA scientists, taking someone else's DNA research, and trying unsuccessfully to make it say something bad about BoM claims.

* LDS are winning this battle, in most part because critics refuse to interact with our responses to their original criticisms.  The arguments go like this:

Critic: All dogs have 4 legs!

Mormon: Here is a list of reasons why some dogs can have less than 4 legs, from congenital defects to bear traps.  Also, here is a picture of Lucky, a 4 legged dog. 

Critic: FARMS is full of biased mormons!  I won't read them!

[a week later]

Critic: All dogs have 4 legs!

The problem with "DNA and the BoM for Dummies" book, is that it was produced by a mormon, and therefore no critic will read it.

HSR

[The Dude]

I would write the DNA for Dummies book like this:

*Critics who know what the BoM claims and what DNA can/can't do have argued successfully that DNA evidence disproves traditional claims about Lamanites and the BoM. LDS scientists agree.

*Upon interacting with the response by LDS scientists the critics reluctantly conceded that DNA can't disprove all interpretations of the BoM. Versions of Limited Genetic Theory are beyond the power of genetics.

Appendix I) Stewart departs from the other LDS DNA apologists, who are professional scientists, essentially saying that not only the critics but also the scientists doing the original DNA research, who don't even know about the BoM, are wrong. He claims the traditional Hemispheric Genetics Theory is just fine.

[awyatt]

The Dude said:  Who is David G. Stewart Jr.? Has he ever written anything else for FARMS/FAIR, and what is his background as an MD?

You can find info on Dr. Stewart at this URL.

-Allen

[katherine the great]

The Dude said:

[The Dude]

He sounds very well qualified to write on this topic.

It doesn't show in his sources.

[katherine the great]

He sounds very well qualified to write on this topic.

It doesn't show in his sources.

Maybe not, but he did study Molecular Biology.

[Who Knows]

The Dude - can you sum up your thoughts on the paper in 1 paragraph? I read through it, and it seems like you disagree with just about everything in it. Was it sloppy scholarship? Do you just have a difference of opinion with Stewart? Could any of this have any hope of passing some sort of scientific peer review?

I'm just curious what your real thoughts on this paper are.

[Kevin Barney]

I don't know whether it constitutes a BoM and DNA for dummies, but the piece I wrote for Anthropology News is pretty straightforward and doesn't require an advanced degree in molecular biology to follow:

http://www.fairlds.org/Book_of_Mormon/Brie...ileo_Event.html

(It is along the lines of what the Dude wrote above.)

[Jan]

He sounds very well qualified to write on this topic. I am frankly mystified though that he doesn't know that mtdna will not show up in a woman's descendants who come through her sons.

I think he is aware of that so we'd want to know his response to this.

[The Dude]

The Dude - can you sum up your thoughts on the paper in 1 paragraph?

[Who Knows]

Of course this isn't the kind of thing you would even submit for peer review. The intended audience was FAIR conference attendees, not scientific peers. He does frequently say that the jury is still out on this or that, but then he offers up some very fringe opinion, based on sloppy scholarship, and gives false hope...

Ok, thanks. I just see it too often here - people taking these apologetic presentations/papers as solid scholarly work.

Thanks!

[The Dude]

Of course this isn't the kind of thing you would even submit for peer review.  The intended audience was FAIR conference attendees, not scientific peers.  He does frequently say that the jury is still out on this or that, but then he offers up some very fringe opinion, based on sloppy scholarship, and gives false hope...

Ok, thanks. I just see it too often here - people taking these apologetic presentations/papers as solid scholarly work.

Thanks!

To clarify, Dr. Stewart couldn't possibly have meant it for peer review, so your question is off base.

[David Stewart]

There is certainly more heat than light here.

I don't have the time or interest to engage in a lengthy discussion, but want to briefly address some of the more egregious mis-statements of some of the posters.

"katherine the great" wrote:

"I am frankly mystified though that he doesn't know that mtdna will not show up in a woman's descendants who come through her sons."

I am perfectly aware of this. The problem seems to be with the reader's comprehension rather than my writing. I wrote:

"Joseph's wife Asenath, daughter of Potipherah priest of On, is the ancestral mother of the tribes of Ephraim and Manasseh (Genesis 46:20). While her genealogy is unknown, there is no reason to believe that her mitochondrial lineage or that of her descendants, including the Lehites, would have matched that of the tribe of Judah. The presence of mtDNA types in Native Americans that do not match those found in modern Jewish groups is fully consistent with both Book of Mormon and Bible accounts."

If you read this more carefully, you will see that I do not suggest that being the "ancestral mother" in a genealogical sense necessarily implies that all descendants carry her mtDNA, nor that all Lehites shared Asenath's mtDNA. My point is that the female mitochondrial lineage is unknown and that expectations that Lehite mtDNA should match that of the tribe of Judah are unfounded. I had additional comments on mtDNA that I removed from the talk in the interest of time.

My statement is correct as written, and I stand by it.

"The Dude" wrote:

"it would be wise for them to consult some of the actual geneticists and scientists who have written for FARMS and for the Church."

The fact that I cite a source does not imply that I agree with every point in it. That is the purpose of attribution. Unlike Tanner, I do not in any way see haplogroup X as a "Lehite signature." I simply cited his quote as is because of his concise summary of some (although by far not all) of the dating difficulties. One would have to be dishonest not to acknowledge that the Lehite dynamics in the critical early years differ substantially from the Hardy-Weinberg assumptions, your strained critique notwithstanding.

The vast range of dates cited by Mr. Murphy himself for entry into the America (7,000-50,000 years ago) and several other scientific sources I cite about discrepancies in timing should give you cause to ponder. I am fully aware of the manner in which mtDNA dating is done. I am also acutely aware of the wide discrepancies in results, the limitations and assumptions of this technique, the considerable disagreement among scientists, and the lack of definite consensus. The references I have cited demonstrate this, and your efforts to reduce the whole issue to your disagreement with Mr. Tanner miss the point.

Second, you criticize me for citing Douglas Forbes, yet are unable to rebut his conclusions. You ignore the careful and extensive citations I have made from published genetic literature to rigorously support Forbes' conclusion. You yourself acknowledge his point: "sure, if you go back far enough, you will find affinities between Native Americans, Iranians, Jews." But somehow he is still wrong, or these concusions are unimportant, because he is a software engineer? And you turn this around by insulting us that we "express no understanding that these affinities are hierarchical?" I am not the one here who expresses "no understanding."

Third, you grossly misrepresent my work stating that I am "willing to cite any dubious source he can lay his hands on" and home in on my citations of two non-scientists (Forbes and Tanner), while ignoring the dozens of scientific works that I have studied and meticulously cited during the paper. Most of the references are primary research in genetic journals. My points are carefully researched and supported, your insinuations notwithstanding. Your efforts to characterize my entire talk based on brief references to Forbes and Tanner are nonsensical.

Finally, this bizarre little quote of "The Dude" deserves a place in the hall of bad logic:

"Stewart departs from the other LDS DNA apologists, who are professional scientists, essentially saying that not only the critics but also the scientists doing the original DNA research, who don't even know about the BoM, are wrong."

It is evident that you don't understand what my points are, and therefore your attempts to critique them are misdirected. The criticisms you have offered here amount to mere polemics, insinuations, and dismissive hand-waving without the substance or data to back them up.

I am not interested in polemics, nor do I have any interest in attempting to educate the unreasonable. The poor "signal to noise" ratio demonstrates why I rarely if ever come by the boards here. There is adequate data for those who want to understand to understand, while those with hostile agendas will always be able to contrive rationalizations to explain away any evidence not to their liking.

[juliann]

Of course this isn't the kind of thing you would even submit for peer review.  The intended audience was FAIR conference attendees, not scientific peers.  He does frequently say that the jury is still out on this or that, but then he offers up some very fringe opinion, based on sloppy scholarship, and gives false hope.  Instead of going with the solid "genetic science can't rule out limited genetics models" I see him suggesting that genetic science may yet validate a traditional BoM interpretation.

And where is the scientific peer review on the countermopologists ever changing accusations? They are the one setting the standard....they are the one who need to come up the goods.

To my knowledge, critics to date have not been able to generate a single peer-reviewed publication in a scientific journal on Book of Mormon DNA issues. Although validation of study controls is critical to the testing of any scientific hypothesis, Mr. Murphy and other critics have accepted without validation the assumption that modern Jewish populations represent a comprehensive control of ancient Israelite genetics.

Are you aware of a peer-reviewed publication which validates the "DNA proves the BOM wrong" nonsense? Aren't you somewhat knowledgable about this kind of thing, Dude? How about adding something to the discussion? I don't see what I heard about Dr. Stewart in his bio. He is beyond qualified for this topic and probably has more hands-on experience than anyone yet.

[Tarski]

Of course this isn't the kind of thing you would even submit for peer review.

[Pahoran]

Of course this isn't the kind of thing you would even submit for peer review.

[Tarski]

For once, Tarski, I agree with you. For scientific inquiry, The Book of Mormon is largely out of scope.

Regards,

Pahoran

Not quite. Neither druid aliens nor BoM historicity are "out of scope" in principle. Proponents of the BoM do not get a free pass and neither do the those promoting any other fringe claim.

Its just that there are so many such claims and no reason to take them seriously at this time. So, scientists have better things to do. We have a good picture of ancient american orgins and it doesn't include the main points of what we find in the BoM. On the other hand, if the belief in such things becomes wide spread then I suppose scientists will have to do more than a casual rebuttal.

Notice that we don't find serious scientific journals publishing arguments explaining why the earth isn't 7000 years old. Nevertheless, scientists can give reasons if push comes to shove. Same with the BoM etc.

[katherine the great]

There is certainly more heat than light here.

I don't have the time or interest to engage in a lengthy discussion, but want to briefly address some of the more egregious mis-statements of some of the posters.

"katherine the great" wrote:

"I am frankly mystified though that he doesn't know that mtdna will not show up in a woman's descendants who come through her sons."

I am perfectly aware of this. The problem seems to be with the reader's comprehension rather than my writing. I wrote:

"Joseph's wife Asenath, daughter of Potipherah priest of On, is the ancestral mother of the tribes of Ephraim and Manasseh (Genesis 46:20). While her genealogy is unknown, there is no reason to believe that her mitochondrial lineage or that of her descendants, including the Lehites, would have matched that of the tribe of Judah. The presence of mtDNA types in Native Americans that do not match those found in modern Jewish groups is fully consistent with both Book of Mormon and Bible accounts."

If you read this more carefully, you will see that I do not suggest that being the "ancestral mother" in a genealogical sense necessarily implies that all descendants carry her mtDNA, nor that all Lehites shared Asenath's mtDNA. My point is that the female mitochondrial lineage is unknown and that expectations that Lehite mtDNA should match that of the tribe of Judah are unfounded. I had additional comments on mtDNA that I removed from the talk in the interest of time.

My statement is correct as written, and I stand by it.

Thank you for replying! I don't think I misread you. Maybe some of the material you deleted due to length would have clarified this. To the ordinary person, this reads: Lehites would belong to the same Mtdna haplogroup as Asenath. I think it would be better stated that Lehite mtdna would have come from Sarah and Ishmael's wife.