“Species” based on mtDNA phylogenies? As far as the topic of …

Comment on Dr. Geraty clarifies his “Challenge” to literal 6-day creationism by Sean Pitman.

“Species” based on mtDNA phylogenies?

As far as the topic of human ethnic groups compared to various “species” definitions for animals, consider the case of the Neanderthal. Many scientists consider Neanderthals to have been a separate “species” of human – not just a unique ethnic variation. This is due to several unique morphologic features of Neanderthals compared to modern humans – as well as to unique DNA sequences and average numbers of mutational differences.

According to a 1997 study by Pääbo et. al., on certain mtDNA sequences of Neanderthals compared to modern humans, Neanderthals would seem to qualify as a unique “species” – and not just a “cryptic species” due to their prominent morphologic differences.

“The Neandertal sequence was compared to 994 contemporary human mitochondrial lineages, i.e., distinct sequences occurring in one or more individuals, found in 478 Africans, 510 Europeans, 494 Asians, 167 Native Americans and 20 individuals from Australia and Oceania. Whereas these modern human sequences differ among themselves by an average of 8.0 (range 1-24) substitutions, the difference between the humans and the Neandertal sequence is 27.2 (range 22-36) substitutions. Thus, the largest difference observed between any two human sequences was two substitutions larger than the smallest difference between a human and the Neandertal…

The Neandertal mtDNA sequence thus supports a scenario in which modern humans arose recently in Africa as a distinct species and replaced Neandertals with little or no interbreeding.”

If mtDNA was in fact isolated from the Neanderthal bones, these conclusions might seem reasonable until one considers a few more facts. The Cell article itself noted that the range of sequence differences for modern human mtDNA goes from 1 to 24 with an average of 8 substitutions. The mtDNA sequence differences between modern humans and the single Neanderthal fossil range from 22 to 36 substitutions, with the average being 27. In other words, the two most different humans analyzed in this study, as far as mtDNA substitutions are concerned, are different by 24 substitutions. The closest that any human in this study was to the single specimen of Neanderthal mtDNA was 22 substitutions. This means that there are some people living today that are closer to Neanderthals in their mtDNA sequencing than they are to some other modern human beings. Someone might be found to be only 22 substitutions away from our Neanderthal, but 24 substitutions away from his own next-door neighbor. Interesting isn’t it? If Neanderthals are classed as separate species because of these differences, which one of our modern human volunteers should be classify as a separate species? Perhaps the one who was only 22 substitutions different from the Neanderthal? Or, maybe his next-door neighbor who is 24 substitutions away from his neighbor as well as 22 substitutions away from our Neanderthal friend? I mean, some of us might have neighbors that look like Neanderthals (or maybe we might look like Neanderthals compared to our neighbors), but can a different species really be assumed based on a difference of 20-some substitutions in a particular hypervariable region of DNA?

That means that there are a few modern humans who differ by 24 substitutions from a few other modern humans—two substitutions more than the Neanderthal individual. Would not logic demand that those few modern humans living today should also be placed in a separate species? To state the question is to reveal the absurdity of using such differences as a measure of species distinctions.

Lubenow, Marvin (1998), “Recovery of Neandertal mtDNA: An Evaluation,” CEN Technical Journal, 12[1]:87-97.

A subsequent paper published by Pääbo and his team in May of 1999, show that the range (1-81) for chimp/bonobo substitutions (in certain regions of mtDNA) are even wider than previously thought. In other words, if one chose a chimp at random, this chimp might be as many as 81 substitutions different from the chimp swinging on the branches right next to him. This is interesting because this same chimp might be only 78 substitutions different from a given modern human. This more recent paper also points out that the range between humans (1-35) is also wider than was reported in the first paper. The range between humans and the Neanderthal sequence was also altered in the updated paper to (29-43).

This second paper seems to make it even more clear that substitution differences in a given variable region cannot be used to absolutely measure the boundary between different species. In fact, using this method of reason, it seems like some chimps might be more closely related to certain humans than to certain chimps within their own species. Since this clearly is not the case, this logic seems flawed. Evolutionary conclusions therefore cannot be effectively supported using this these methods.

Of course, there is an additional problem that some humans from certain ethic groups are more closely “related” to Neanderthals than they are to certain other living humans from other groups. The question remains as to who should be classed as a separate species?

Maryellen Ruvolo (Harvard University) points out that the genetic variation between the modern human and Neanderthal sequences is within the range of other single species of primates. She goes on to say: “there isn’t a yardstick for genetic difference upon which you can define a species.”

Further confusion comes from the comments in the Cell article that seem to indicate that Neanderthals are more closely related to the ancestral “chimpanzee” than modern humans are. This might not have been the actual intention of the authors, but one could easily get confused by the wording of the article. The fact of the matter is that the single specimen of Neanderthal mtDNA was actually farther away from chimp mtDNA than humans are from chimp mtDNA substitutions. Clearly then, Neanderthal DNA is no closer “related” to chimp DNA than human DNA is.

Add to all of this the fact that the popular notion that mtDNA mutations can be used as a molecular clock has been called into question by the journal Science. As it turns out, former ideas about the timing of this clock might be in error by as much as “20-fold” – (or even 100 fold based on other studies). The famous “Mitochondrial Eve” once thought to be around 100,000 to 200,000 years old, might now have to be revised to as young as “6,000” years old.

D. Melnick and G. Hoelzer (Columbia University) tested the assumptions of mtDNA based phylogenic relationships and concluded:

“Our results suggest serious problems with use of mtDNA to estimate ‘true’ population genetic structure, to date cladogenic events, and in some cases, to construct phylogenies.”

If that isn’t an understatement of the problem I don’t know what is?

Jonathan Marks (Yale University) declared mtDNA determined relationships to be highly biased:

“Most analysis of mitochondrial DNA are so equivocal as to render a clear solution impossible, the preferred phylogeny relying critically on the choice of outgroup and clustering technique.”

In August of 2002, Gabriel Guitierrez et al., from the Universidad de Sevilla, Spain, published a paper in the well known journal, Molecular Biology and Evolution entitled, “A Reanalysis of the Ancient Mitochondrial DNA Sequences Recovered from Neandertal Bones.” Consider some of their conclusions:

Recent reports analyzing mitochondrial DNA sequences from Neandertal bones have claimed that Neadnertals and modern humans are different species. The phylogenetic analyses carried out in these articles did not take into account the high substitution rate variation among sites observed in the human mitochondrial D-loop region and also lack an estimation of the parameters of the nucleotide substitution model…

The computation of pairwise distances between 171 randomly selected sequences and the Neandertals rendered 1.6% of human-human comparisons larger than the smallest difference between Neandertals and humans. Likewise, 27% of the comparisons are lower than the largest human-human difference. This result suggests that Neandertals sequences are not so different from those of extant humans, in contrast to the NSG claims…

The main conclusion can be extracted from our analyses: the phylogenetic position of the ancient DNA sequences recovered from Neandertal bones is sensitive to the phylogenetic methods employed. It depends on the model of nucleotide substitution, the branch support method, and the set of data used.

In fact, Guitierrez et. al. went on to show that depending upon the mtDNA region(s) chosen Neaderthals could be clustered with modern humans while certain ethnic groups could be isolated out as separate “species” groups. This only highlights the subjective nature and definition of “species” using mtDNA-based phylogenies.

Although the molecular data appears to be very objective and precise, John Marcus states that the interpretation of the molecular data is just as subjective as is the interpretation of the fossils. Not only is the molecular evidence unfalsifiable, but

‘… the scientist must always choose which piece(s) of DNA he is going to use to do his comparisons. Very often a particular piece of DNA will not give the “right” answer and so it is dismissed as a poor indicator of the evolutionary process’.

Kenneth A.R. Kennedy (Cornell University) comments:

‘This practice of forcing the paleontological and archaeological data to conform to the evolutionary and genetic models continues in reinterpretations of dates based upon the molecular clock of mitochondrial DNA as well as radiometric samples… .’

The misinterpretation of the mtDNA data is seen in the work of Pääbo and his associates in that the Neandertal fossil evidence contradicts their interpretation of the mtDNA evidence.


These same problems are not likely to be restricted to the determination of hominid “species” and phylogenetic relationships but are likely to affect the determination of different animal species as well – to include the numerous “cryptic species” that are being discovered today…

For further discussion of this topic see:


Sean Pitman

Sean Pitman Also Commented

Dr. Geraty clarifies his “Challenge” to literal 6-day creationism
@Ron Nielsen:

Sean, it seems to me that if you admit ANY functional change in the DNA the creation/evolution debate is lost in favor of evolution. All the rest, however you define species is just a matter of time and quantity.

Hardly. The vast majority of functional mutations are detrimental – based on a loss of qualitatively unique pre-established functionality. Most of the rare mutations that are functionally beneficial do not produce something that is qualitatively new within the gene pool of options, but produce only an increase or decrease in activity of the same type of functionality that was already there to begin with. And, the very rare beneficial mutations that actually produce something qualitatively unique as well as functionally beneficial never produce anything that requires a minimum of more than 1000 specifically arranged amino acid residues to work – not even close.

The reason for this is that evolution beyond this very low level of functional complexity would require trillions upon trillions of years to achieve – – on average.

This is why the constant demonstration of low-level examples of “evolution in action” do not remotely explain how higher levels of evolution are therefore reasonable – even given a few billion years. The extrapolation is not at all reasonable because of the exponential decline in evolutionary potential with each step up the ladder of functional complexity.

You say, “it’s just a matter of time and quantity”. What you don’t understanding is that the time required is simply not reasonable. The time required to get beyond even the 1000aa level is in the multiple trillions of years. Do you not see that as a problem?

That is why I think it is so dangerous to state that evolution is incompatible with belief in God and creation, because no one, not even you are willing to deny that that the mechanisms for evolution are in place.

The mechanism for evolution is not “in place” beyond extremely low levels of functional complexity. That’s the problem.

It’s similar to saying that because natural processes are known which can produce roughly cube shape granite blocks that obviously such mindless natural mechanisms could explain a highly symmetrical polished granite cube measuring exactly one meter on each side. Such a conclusion does not rationally follow since the higher level illustration requires exponentially more time for the natural mechanism to achieve relative to the lower level demonstration that does not require the same level of constraints…

Except out of wanton ignorance, it is not possible to deny evolution in this day of DNA mapping. If you insist on making evolution and belief in God mutually exclusive you will have to declare every single educated person in the church to be athiests and drive them out of the church. Your stance just isn’t reasonable.

Anyone who wishes to worship in our Church is welcome – even if he/she is an “atheists”. I would not drive anyone who wants to come out of our Church. However, this does not mean that such a one should ever expect to get a paycheck from the SDA Church for promoting his/her atheistic ideas from pulpit or classroom.

You see, attendance is not the same thing as paid representation. A paid representative must be held to a higher standard in any organization.

Sean Pitman

Dr. Geraty clarifies his “Challenge” to literal 6-day creationism
@Michael Prewitt:

I agree with this general line of reasoning…

Sean Pitman

Dr. Geraty clarifies his “Challenge” to literal 6-day creationism
@Geanna Dane:

In other words, you’d believe in the existence and love of God despite all physical evidence to the contrary? That is very similar to the faith of some LDS friends of mine. I suppose it works for some people, but my own relationship with God is based on the evidence that I think He has given me of His own existence and the reliability of his Word combined with personal experiences with answers to prayer, etc.

Now, I agree with you that theistic evolutionists can be saved even if they got the whole origins thing all wrong. God loves everyone and will save all who earnestly seek after Him and love Him in the person of “the least of these…” Salvation itself is not based on correct doctrinal knowledge, but on living according to the Royal Law of Love. However, correct doctrinal knowledge is not therefore worthless. It is very valuable in that it has the power to give us a clearer picture of God here and now and to provide a solid basis of hope here in now in the reality of God and of a bright and glorious future.

I’m sorry, but without correct doctrinal knowledge, without the Bible, you may have some sort of vague idea of God’s existence and maybe even His love for you through the features of nature, but you would have very little else upon which to base a solid hope in such notions. It is the evidence that the Bible is reliable in those things which can be tested and evaluated that gives solid confidence in those metaphysical statements that cannot be directed evaluated – at least for me.

This is why when you argue so strongly for the idea that science works against SDA doctrinal positions and offer nothing up but blind faith that the Bible is true that you undermine the basis of many people’s hope in the reality of the Good News. Your seeming suggestion is that science is quite clearly contrary to some very plain biblical statements and that the only way to overcome such evidence is through blind faith. That simply doesn’t do it for many many people. It certainly doesn’t do it for me.

I hope this helps you to at least understand why your ideas and comments are so strongly opposed by those who actually consider it important that the Bible be consistent with the physical evidence in order for its metaphysical statements to be considered trustworthy…

Sean Pitman

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