Discussions of Mormons and Mormon life, Book of Mormon issues and evidences, and other Latter-day Saint (LDS) topics.

Saturday, January 15, 2005

When DNA Evidence is Ignored: Systematic Bias Against Non-Asian Origins of Ancient Americans

One of several issues that I raise in my essay on DNA and the Book of Mormon is the tendency for scientists to ignore DNA evidence that might point to non-Asian origins for Native Americans. Non-Asian DNA types found in living Native Americans is almost universally assumed to be from European admixture (often a reasonable assumption, of course), and non-Asian DNA types found in ancient DNA (from, say, pre-Columbian remains) is often assumed to be due to modern contamination (again, this is a correct conclusion in many cases), even when there is no apparent source to explain the alleged contamination. Such discarding of non-Asian genetic links, in my opinion, may sometimes be made not so much because it is truly demanded by a sound scientific analysis of the data, but because it is demanded by the paradigm of the "established" Asia-only origin of Native Americans.

It is wrong to say that there has been no DNA evidence pointing to non-Asian (e.g., European or Middle East) origins of ancient Native Americans. But some of the possible evidence has routinely been discarded and ignored. Here is an excerpt from my essay on DNA and the Book of Mormon:
The problem in applying DNA analysis to the Book of Mormon goes beyond the likelihood of discarding the most relevant evidence. There is also the possibility of attributing evidence of pre-Columbian migrations to recent admixture. Worse, there is the possibility of missing the date of entry of the most relevant genes, and thus eliminating them from the scope of the Book of Mormon, as we shall discuss below.

All this is compounded by the fact that researchers are understandably interested in explaining the dominant genetic origins of Native Americans, which will likely correspond to the dominant population groups that were already on the continent when Lehi's little boatload of people landed. There is typically little interest in understanding or even studying the origins of unusual haplotypes in Native Americans. For example, Bonatto and Salzano (1997), in concluding that the four major mtDNA haplotypes likely derived from a single Asian migration, felt that other less common haplotypes could be safely ignored:
We agree that some additional founding haplogroups (such as group X from Forster et al. 1996; also see Bailliet et al. 1994; Merriwether and Ferrell 1996) might exist, besides the four major ones studied here. However, they constitute only ~10% of the sequences now found in the Americas and, because of their very small sample size, could not be analyzed in the study. Since we analyzed each haplogroup separately, and since the number of haplogroups was not a relevant parameter, including these putatively additional founding haplogroups should not significantly change the results presented here.
Salzano (2002) lists 7 biallelic haplotypes for Y chromosomes in Native Americans in his Table 9. He states that haplotypes 5 through 7 "occur in low frequencies, and since they present high prevalences in European or African populations, may be due to interethnic gene flow." But these haplotypes occur in Eskimos, Na-Denes, and Amerinds of North American, as well as in natives of Central America and South America. Can we safely ignore them because they are also characteristic of Old World peoples outside of Asia?

As a further characteristic example of the exclusion of "other" DNA types, Malhi et al. (2002) investigated the mtDNA haplogroup identities of 1,612 Native Americans. They state that:

Individuals whose mtDNAs did not belong to one of the five Native American haplogroups were not included in this analysis. Although it is possible that one or more of these individuals possess previously undocumented founding Native American mtDNA types, previous studies indicate that the frequency of "other" mtDNA types is very low and that most--or all--of these result from recent admixture (Torroni et al. 1993b, 1994; Huoponen et al. 1997; Smith et al. 1999).
An excellent discussion of the very real problem of contamination of ancient DNA samples is provided by Kolman and Tuross (2000), who also provide an interesting example in which pre-Columbian genetic material from a Native American appears to provide reproducible evidence of European origins. In spite of numerous efforts to exclude contamination, this result, identically reproduced in multiple careful trials, is presented as a case of "obvious" contamination because it was non-Asian:

The data presented here can be used to illustrate the dangers of imprudent inclusion of data. The DNA sequence identified in sample 5 had never been detected in our laboratory or in New World indigenous populations. All associated extraction and PCR controls were negative. Multiple extractions resulted in the same RFLP/deletion haplotype. Therefore, it could be proposed that this haplotype represents a new founding lineage for the New World. However, the fact that this haplotype is found at high frequency in European populations (17%, Richards et al., 1996) and is not found in presumably ancestral Asian populations argues against this interpretation and against the inclusion of this sequence in a NewWorld database.


In total, seven different non-New World sequences were identified in the current study. They are most likely all European in origin and may represent a minimum of seven independent sources of contamination. . . .

In sum, there is no easy, objective method of identifying contaminating sequences other than to painstakingly analyze them within the genetic framework of the ancient population under study.

The conclusion is understandable, if one is constrained by the paradigm that all ancient Native Americans must have DNA originating from Asia. But when an ancient human's DNA comes up as European, in trial after trial with great precautions taken to prevent contamination, and then that data is simply excluded as a fine example of the dangers of contamination because it is not Asian, what chance do we have to find non-Asian genes in ancient human samples from the Americas? Ancient DNA that does not fit the out-of-Asia paradigm is repeatedly discarded from consideration because of "obvious" contamination.

There is no evidence in the paper by Kolman and Tuross that any of the other samples discarded for "contamination" had contamination from any of the researchers conducting the study. The approach appears to be that anything unexpected will be discarded as due to contamination. Is it any surprise that this approach - apparently a common approach - consistently suppresses surprises, surprises like the presence of non-Asian groups in ancient America?

Further work with the typically neglected outliers still needs to be done, and done without instantly assuming that modern contamination or admixture is the source of genes that appear to have a non-Asian origin. While contamination can be a serious problem, it is still possible to get good results with ancient DNA if proper procedures are followed, as shown by Gilbert et al. (2003). More recently, Matthew Spencer and Christopher J. Howe (Spencer and Rowe, 2004) have established statistical tools and recommended procedures to help researchers determine the probability that an amplified DNA sequence from an ancient sample actually corresponds to ancient DNA or modern contamination. Their discussion of the problem of contamination is also helpful.
References cited above:
Bailliet, G., et al., "Founder Mitochondrial Haplotypes in Amerindian Populations," American Journal of Human Genetics, 55(1): 27-33 (July 1994). (Available online.)

Bonatto, S.L. and Salzano, F.M., "Diversity and Age of the Four Major mtDNA Haplogroups, and their Implications for the Peopling of the New World", American Journal of Human Genetics, 61:1413-1423 (1997a). (Available online.)

Forster, P., Hardin, R., Torroni, A., and Bandelt, H.-J., "Origin and Evolution of Native American mtDNA Variation: A Reappraisal," American Journal of Human Genetics, 59: 935-954 (1996).

Gilbert, M.T.P., Willerslev, E., Hansen, A.J., Barnes, I., Rudleck, L., Lynnerup, N., and Cooper, A., "Distribution Patterns of Postmortem Damage in Human Mitochondrial DNA," American Journal of Human Genetics, 72:32-47 (2003). (Available online.)

Huoponen, K., Torroni, A., Wickman, P.R., Sellitto, D., Gurley, D.S., Scozzari, R., and Wallace, D.C., "Mitochondrial DNA and Y Chromosome-specific Polymorphisms in the Seminole of South Florida," European Journal of Human Genetics, 5:25-34 (1997), as cited by Malhi et al., 2000.

Kolman, C.J., and Tuross, N., "Ancient DNA Analysis of Human Populations," American Journal of Physical Anthropology, 111: 5-23 (2000). (Available online.)

Malhi, R.S., et al., "The Structure of Diversity within New World Mitochondrial DNA Haplogroups: Implications for the Prehistory of North America," American Journal of Human Genetics, 70(4): 905-919 (April 2002). (Available online.)

Merriwether D.A., and Ferrell, R.E., "The Four Founding Lineage Hypothesis for the New World: A Critical Reevaluation. Mol. Phylogenet. Evol., 5:241-246 (1996), as cited by Bonatto and Salzano (1997a). (Abstract available online.)

Richards, M., Corte-Real, H., Forster, P., Macaulay, V., Wilkinson-Herbots, H., Demaine, A., Papiha, S., Hedges, R., Bandelt, H.-J., Sykes, B., "Paleolithic and Neolithic Lineages in the European Mitochondrial Gene Pool," American Journal of Human Genetics, 59:185-203 (1996), as cited by Kolman and Tuross (2000).

Salzano, F.M., "Molecular Variability in Amerindians: Widespread but Uneven Information," Anais de Academia Brasileira de Ciencias, 74(2): 223-263 (2002). (Available online.)

Smith, D.G., Malhi, R.S., Eshleman, J., Lorenz, J.G., Kaestle, F.A., "Distribution of mtDNA Haplogroup X among Native North Americans," American Journal of Physical Anthropology, 110: 271-284 (1999).

Spencer, M. and Rowe, C.J., "Authenticity of Ancient-DNA Results: A Statistical Approach," American Journal of Human Genetics, 75(2): 240-250 (Aug. 2004). (Available online.)

Torroni, A., et al. "Asian Affinities and Continental Radiation of the Four Founding Native American mtDNAs," American Journal of Human Genetics, 53: 563-590 (1993b).

Torroni, A., Neel, J.V., Barrantes, R., Schurr, T.G., Wallace, D.C., "Mitochondrial DNA "Clock" for the Amerinds and Its Implications for Timing Their Entry into North America," Proceedings of the National Academy of Science USA, 91: 1158-1162 (1994). (Available online.)

11 comments:

Anonymous said...

Silly scientists! You can't throw out evidence just because it doesn't fit your preconceived notions. That's not the scientific method at all. And now the preconceived notion of North American aborigines coming across a land bridge from Asia and moving south is starting to be seriously questioned. A recent study of bison bones and other evidence indicates that western Canada was populated by a migration from the SOUTH - Oops, so much for the Bering Straits story that we all heard in school. Archaeologists will probably be fighting this battle for a few years yet, but, in the meantime, no one should be dumping any DNA evidence that doesn't fit their pre-existing and likely incorrect understanding of American population origins. For more information, see http://www.news-leader.com/today/1118-Discoveryp-229184.html, http://www.mytelus.com/news/article.do?pageID=bc_home&articleID=1806114, http://www.washingtonpost.com/wp-srv/inatl/americas/feb/17/artifact.htm, and http://www.edenseve.net/discovery_casts_doubt_on_bering_.htm.

Anonymous said...

Wow. Jeff Lindsay gives the genetics community a huge slap in the face here. To assert that a man is flipantly discarding credible evidence that does not fit his preconceived notions is to insult his status as a scientist and to reduce him to the level of the pseudo-scientists, like the creationists or the UFO abductionists, who themselves routinely ignore evidence that does not fit their preconceived notions of how the universe is (or should be). The given quotes were all from ancient literature, from a scientific perspective (1993, 1996, 1999). And he picks out a handful of quotes, presents them out of context (or, worse, with his own contrived context), then makes the assumption that the entire genetics community is misbehaving. The strongest theory Jeff manages to put forth is that geneticists are uncertain as to the exact dates at which the European genetic markers found their way into the Native American DNA. He ignores the broad and extensive DNA analysis from pre-Columbian Native American remains taking place, which directly addresses that issue.

The convergence of such studies have revealed 100% Northeastern and North Central Asian origin. In general, Jeff's approach flies in the face of the scientific paradigm of consilience of inductions. He points to a fluke in one study by Kolman and Tuross, implies that this fluke is reproducing itself all over the map, and then before we know it, the sky is falling and the entire study of genetics is in collective denial. This preposterous suggestion is inspired by a desperate attempt by an apologist to validate the historicity of one popular interpretation of a religious text. Jeff Lindsay demonstrates in this article that he does not understand how science works, or at least, he has little respect for the scientific community.

Scientists set themselves apart by making surprising new discoveries. Every geneticist out there would love to present convincing proof that shatters previously held convictions by the scientific community. This is why everyone is trying to prove that P=NP and that Einstein was wrong! A successful scientist is the one that teaches us something that we had previously not known, or that we had previously had misconceptions about. The scientist who breaks new ground is heralded as the example for other scientists to follow.

If geneticists were to come across viable evidence of non-Asian DNA mixing in pre-Columbian American societies, such a finding would be featured a major genetics journal and would be a hot topic of debate among the scientists. Every self-respecting geneticist would jump at the opportunity to present credible evidence of such a thing. As it now stands, however, there exists no evidence for European ancestry in pre-Columbian Native American populations that the genetics community judges worthy of consideration.

Jeff's article is, at the core, an ad-hominem attack and is alarmist in nature.

Anonymous said...

But by the same token can't your argument be reduced to an "Ad Hominem" as well? I mean really the structure for the reduction is the same: both provide a clean analysis of the faults inherent in the methodology of the argument. His can be construed to say that the scientists are sloppy in their experimentation (which I suppose if you consider sloppy to be a insult could be perceived as being an attack on the person himself) while your attack on his methodology has the distinct undertone of comparing Mr. Lindsay to one who believes in UFOs or Creationism (whom, it's quite clear, you regard with a fair amount of derision and contempt...) This brings up an interesting question: so what? So what if you call Mr. Linday a bafoon, and he calls a scientist sloppy? I suppose calling Mr. Lindsay a bafoon doesn't really say much about his argument, and calling a scientist sloppy does have the possibility of affecting his results, but in reality, we're at the same place we started. Nobody is really saying anything worthwhile.

At any rate: since no one has performed actual experimentation to determine if any of the various theories of Book of Mormon geography are plausible genetically (c.f. http://farms.byu.edu/display.php?table=jbms&id=311) I think we can safely say that most of this argument is... well... kind of fruitless. You can both argue at each other until the end of time, but it'll still be true that most Native American DNA that has been examined appears to be mostly Asian in origin. Which still proves nothing about the Book of Mormon or its veracity.

Anonymous said...

His can be construed to say that the scientists are sloppy in their experimentation (which I suppose if you consider sloppy to be a insult could be perceived as being an attack on the person himself)It was more insidious than that. Jeff said that they outright ignored evidence that did not fit their preconceived notions, which is about as insulting as you could get to someone who considers himself a scientist.

but in reality, we're at the same place we started. Nobody is really saying anything worthwhile.

At any rate: since no one has performed actual experimentation to determine if any of the various theories of Book of Mormon geography are plausible genetically (c.f. http://farms.byu.edu/display.php?table=jbms&id=311) I think we can safely say that most of this argument is... well... kind of fruitless.
Thank you for pulling us back into limbo. Done in the true spirit of FARMS. I was afraid for a minute there that we might actually arrive at a conclusion.

Anonymous said...

But wasn't that my point? There are no good conclusions that can be reached from this data because there is no proposition that can be tested.
You can ad hominem FARMS all you want, too, but it still doesn't make them wrong. That's the beauty about an ad hominem attack: you don't have to defend against the actual claims because you just tear down the person...

At any rate, I must say that your (forgive the pun) blind faith in science is quite startling: scientists and scholars have a long standing tradition of being quite myopic when things don't fit into their preconceived models/notions of how the world works. The greatest modern example of this is the deciphering of the Mayan Language. One scientist (Eric Thompson) intellectually dominated the field, and he insisted that the engravings in southern Mexico were not phonetic in any way shape or form. He ridiculed those who thought otherwise (with, as you can imagine, the typical ad hominem attacks) and single-handedly held the entire field of Mayan studies back about 30-40 years. ("Breaking the May Code" by Michael Coe, who is not Mormon nor a supporter of Mormons in any way shape or form is a great treatise on this subject). It turns out Thompson (along with the majority of the Mayanists of his time) was quite simply wrong: the Mayan script is phonetic, and a Russian had done some break-through deciphering work back in the cold war era that aided the eventual decipherment in the 80s and 90s.

The bottom line is that paradigm shifts, even tiny ones, require the leaving behind of carefully constructed (and incredibly useful) taxonomies of knowledge. If you've spent your entire life building a model that fairly accurately describes a phenomenon you tend to get fairly attached to it. That means that you tend to defend it vigorously, and you tend to throw out evidence which you think you can discount, because you don't want to admit that much of your work has been for naught. Saying that a scientist would biased towards his own theory seems to be to go without saying; and therefore still doesn't seem to be much of an ad hominem attack to me. I believe my point still stands: your ad hominem attack on Mr. Lindsay still does nothing to bring anything to a conclusion: nobody has even devised a decent experiment that would prove or disprove anything about any Book of Mormon claim, and therefore, we're all just blowing a bunch of hot air... :)

J B Lopez said...

On the subject of DNA, Should the modern population of the Brittish Isles share the same DNA as those from Asia? I would have thought so seeing as they have a the same progenitor i.e. Noah. Perhaps I am wrong. Let me know.

Anonymous said...

This is of interest here:

http://www.sciencedaily.com/releases/2007/10/071018145955.htm

Note the second to last paragraph which says:

The AncestryByDNA test also reads certain markers found in people from the Middle East, India and the Mediterranean region to be diagnostic of Native American ancestry, for which there is no historical, archeological or genetic evidence, according to the study.

Anonymous said...

You find what you look for...

seven7up said...

Naked Science: Prehistoric Americans

"Who were the first Americans? NGC sheds new light on the discoveries that challenge our earliest chapters of our history, long before Columbus landed. No longer is it universally accepted that the first Americans were hunters, who came over the Bering land bridge around 13,500 years ago. Using high-tech forensic science, see why some scientists believe that early pioneers, with a sophisticated understanding of engineering, arrived thousands of years earlier than we previously believed."

Now, what this synopsis does not explain, but is very well presented (in the televised program by top scientists in the field) is that there were "many 'First Americans'". The ancient Americans mentioned above are not related to modern Native Americans. Many different groups arrived at different times throughout history and by many different means (ice bridge, land bridge, boats, etc were all mentioned). Some came from around the Pacific Rim, others deeper in Asia, others from Europe, etc.

In other words, the old "science" of the Americas having been populated ONLY by one group of people crossing the land bridge at limited points in history has been blown out of the water, "the picture is much more complicated than that" , "America has been the 'melting pot' for the last 20,000 years".

Large groups being wiped out by warfare between different groups was also discussed.

-7up

Anonymous said...

Leaving DNA aside for a minute, why does the introduction to the Book of Mormon still claim that "After thousands of years, all were destroyed except the Lamanites, and they are the principal ancestors of the American Indians."??? Isn't use of the term "principal ancestors" a bit of a stretch?

id said...

Alright, Anonymous. The one who posted the link:

http://www.sciencedaily.com/releases/2007/10/071018145955.htm
.

Whoever said "you find what you look for" is right, only you found solely what you were looking for.

How many times have I heard a Mormon tell me "it's out of context" when I show them a quote from a General Authority? EVERY. SINGLE. ONE.

And yet here we are, reading tidbits of articles that are completely out of context.

Review 2nd to last paragraph:
"The AncestryByDNA test also reads certain markers found in people from the Middle East, India and the Mediterranean region to be diagnostic of Native American ancestry, for which there is no historical, archeological or genetic evidence, according to the study."

However, THE ENTIRE ARTICLE is about how UNRELIABLE these types of tests are.

Even in the last paragraph, we see:
"Indeed, the article gives very little credence to these tests, which it concludes "cannot pinpoint the place of origin or social affiliation of even one ancestor with exact certainty.""

That's the final paragraph out of very many.

So, is "this is of interest here"?
Well, if you consider "Systematic Bias" to include absolutely no supporting data whatsoever to base a claim on, which is why the AncestryByDNA test can be rejected. And by supporting data, I mean "no historical, archeological or genetic evidence, according to the study."

Looks more like a Mormon bias grasping for evidence, just as Creationists and UFO abductionists love to do. I think it's safe to add conspiracy theorists to that list as well.

And yes, I understand not all Mormons are like this.