Adam, Eve, and human population genetics: addressing critics—Poythress, chimpanzees, and DNA identity (Part 1) | The BioLogos Forum


(system) #1

Note: In this series, we explore the genetic evidence that indicates humans became a separate species as a substantial population, rather than descending uniquely from an ancestral pair.

In the previous posts in this series, we’ve examined several of the converging lines of evidence that support the conclusion that our lineage became human as a population – one that has not numbered below about 10,000 individuals over the last 18 million years or more. Not surprisingly, this conclusion is one that many Christians find difficult to accept, since it is commonly held that this scientific finding is incompatible with the Genesis narratives (though as we have discussed, there is good reason not to think so, given the limits of what science can say). As population genetics information and its implications for interpreting Genesis have become more widely known among evangelical Christians, some apologetically-minded organizations and scholars have attempted to cast doubt on these lines of evidence.

One such individual is the Rev. Dr. Vern S. Poythress, professor of New Testament Interpretation at Westminster Theological Seminary. In 2013 Poythress authored a lengthy article on human population genetics that has subsequently been adapted into a short book, Did Adam Exist?, in the series Christian Answers to Hard Questions. Here's a short video of Dr. Poythress introducing Did Adam Exist?:

Christian Answers to Hard Questions: Did Adam Exist? from Westminster Theological Seminary on Vimeo.

In both the article and the book, Poythress argues against the ideas that humans and other forms of life share common ancestors, and that humans descend from a population, rather than a pair. Since Poythress is one of the few leading evangelical scholars to address these issues, and to do so from a scientific, rather than an exclusively theological perspective, we will take the time in this series to carefully examine his arguments.

Poythress’s two main scientific arguments can be summarized as follows:

1. Reports of human – chimpanzee DNA comparisons overstate the identity between our two genomes because they selectively focus on areas where high DNA identity is to be expected because of functional constraint. The true overall identity value is lower, and is difficult to explain if common ancestry is true.

2. Population genetics estimates of ancestral human population sizes can only report on long-term population size averages, and thus could not detect a bottleneck of two individuals.

These two arguments are not disconnected as they might seem at first glance. Poythress correctly understands that some methods used to measure human ancestral population sizes use the DNA of species closely related to humans (such as gorillas and chimpanzees) in their analyses. As such, for some methods – such as incomplete lineage sorting, as we have examined – knowing the correct pattern of species relatedness is important for the analysis.

From these arguments, Poythress concludes that what he sees as the “biblical view of human origins” – that Adam was created directly from dust, that Eve was created directly from his side, and that Adam and Eve are the sole genetic progenitors of the entire human race – remains scientifically credible. However, as we will see, these arguments do not hold up to scientific scrutiny. As such, Poythress does not have scientific support for his preferred interpretation of the Genesis narratives.

Common ancestry and human-chimpanzee DNA identity

Poythress’s first line of argument is to call into question the commonly-reported values for human-chimpanzee genome identity – values on the order of 96-99%, depending on how the analysis is done. As we heard in the video linked above, Poythress claims that these values are overinflated:

“For instance, the percentages go down to something like 70% if you actually take all the DNA, and not just the part that codes into proteins… And what about the 30% that doesn’t agree? Well, that’s problematic of where did that come from? That’s an awful lot when you think about it, to be different, if indeed there is common ancestry.”

In Did Adam Exist? the argument runs along similar lines (pp. 7-8):

“If the comparison focuses only on substitutions within aligned protein-coding regions, the match is 99 percent. Indels constitute roughly a 3 percent difference in addition to the 1 percent for substitutions, leading to the figure of 96 percent offered by the NIH… But we have only begun. The 96 percent figure deals only with DNA regions for which an alignment or partially matching sequence can be found. It turns out that not all the regions of human DNA align with chimp DNA. A technical article in 2002 reported that 28 percent of the total DNA had to be excluded because of alignment problems, and that “for 7% of the chimpanzee sequences, no region with similarity could be detected in the human genome.”

Even when there is alignment, the alignment with other primate DNA may be closer than the alignment with chimp DNA: “For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions.” The study in question analyzed similarities with orangutan, gorilla, and rhesus monkey, and found cases where human DNA aligns better with one of them than with chimpanzees.

At this point in the book, Poythress includes two questions for reflection, since the book is intended for use in small-group discussions:

What new issue have we discovered about the 96% “identical” genetic codes? How does this change the situation?

Does human DNA always align best with chimp DNA? How might this change your attitude to the first statistic given?

While the text of Did Adam Exist? left these questions somewhat open, the intent of the arguments (and the questions themselves) seems clear when considered alongside Poythress’s summary statement in the video above. Poythress is advancing an argument that the overall DNA identity between humans and chimpanzees is much less than the commonly-agreed value of 96-99%. His view, it would appear, is that around 30% of our genome has no similarity to chimpanzees – lowering the overall identity value to about 70%.

This is of course, mistaken – but it will take some effort to explain exactly why this is the case.

It’s also not exactly clear what the basis is for the argument—is it the 28% that had “alignment problems” in the 2002 study? The 7% in that same study that had “no region of similarity” to match to? The 23% of our genome that “share(s) no immediate genetic ancestry with … the chimpanzee”? While Poythress does not divulge exactly how he is calculating the ~30% dissimilar figure, these are the only sources he cites to this end. As such, it appears that he views these statements as the technical support for his argument.

These scientific statements—while accurate—do not support the conclusion that the human and chimpanzee genomes are only 70% identical, however. We will begin to unpack why this is the case in the next post in this series tomorrow.

Further reading on the scientific and theological issues related to Adam and Eve:

Note: this list is mostly drawn from my BioLogos colleague Ted Davis's current series, found here.


This is a companion discussion topic for the original entry at https://biologos.org/blog/adam-eve-and-human-population-genetics-addressing-criticspoythress-chimpanz

Feedback on Discourse System (Please Respond)
#4

I think what needs to be answered is why the 99% similarity was ever reported in the first place. What is it about the bias in the minds of the geneticist that caused this false report to happen? Why was the dissimilarity not reported instead?

The other question that needs to be answered is what the significance of the differences is. A large difference in the genome might be surmountable, while a small difference might be insurmountable; it depends on which genes we are looking at and what they control. We know that some genes control at least three different functions simultaneously, while others apparently do not. Some control elements of growth such as size or metabolism, while others are specific to organ formation and brain growth. This means that all numerical differences are not created equal.


(Dennis Venema) #5

Hi John,

The 99% value is perfectly fine in some cases - and the media does not do a good job of carefully explaining how the various percentages are calculated. If you read first post in the “ID and common ancestry” series - in the “for further reading” section, I explain how the various numbers are calculated.

Poythress is correct that restricting the analysis to coding sequences returns a value of 99% identical - but he’s incorrect that the genome-wide value is ~70%. Tomorrow’s post will get into the details of why Poythress is mistaken.


(Albert Leo) #6

This debate is interesting from a scientific point of view, but theologically it may be beside the point, since Christians want to know if it is foolish to believe that we, as present day humans are unique in God’s eyes–are we really made in His image? That comes down to human behavior, not human physiology. Modern anthropology supports the scenario that Homo sapiens, after following a lifestyle almost identical to their contemporary Neaderthal ‘cousins’ for over 100,00 yrs., suddenly started to behave as we modern humans do. They buried their dead with items for an afterlife; they became skilled artists; they invented music; they invented language and conversed with each other in ways that encouraged large social groups. As yet, no scientific explanation can be offered for this Great Leap Forward, but it apparently was not genetic–not some magical mutation. It was as if the Homo sapien brain, which was an obvious exaptation (having a much greater potential than was necessary for survival in the stone age), was suddenly ‘programmed’. Once programmed, a single Homo sapiens, or a couple (if you wish to retain a belief in a historical Adam & Eve) could program their neighbor’s brains via a taught language. Personally, I believe that Darwinian evolution brought my ancestors to the point, some 40 thousand years ago, when some epigenetic change equipped their brains to have a relationship with their Creator. They acquired a conscience and could be considered, potentially, God’s image bearers.


(Dan Ippolito) #7

Albert,

You raise an interesting point in your last two sentences. I have been wondering for a long time at what point, along the evolutionary continuum, human beings (defined as God’s image bearers) appear on the scene. There seems to be no way to draw a definite line based on the fossil evidence. If one falls back on the notion of “ensoulment” (i.e., God supernaturally confers a soul on a pair or a small group of hominids), then one is left with the troubling implication that ensouled human beings were born of soulless hominids. I have never heard anyone address this issue satisfactorily. Any thoughts out there?


#8

Dennis, you are right that the media often portrays things inaccurately… the National Geographic headline “War on Science” is a perfect example. But media does not deserve all the blame. Geneticists and fossil hunters also live for the sensational, and understandably so. Nevertheless, as scientists, they need to communicate in an unbiased fashion, or shall we say in an unenthusiastic fashion when they are speculating. The headline for ape-human similarity could have just as well said that so far, only 87% or less of the genome is similar. Or, based on percentage of genome compared, it is only the compared % x 96% similar. When scientists report in an unscientific fashion, then of course media will get it wrong. How often do scientists point out that mitochondrial dna is only about 0.0005 % of the total human genome?


#9

God could have confered a soul (image of God) on an animal if he wanted to. He also could have easily said so in Genesis… ie. “…then on the sixth day, god took one of the land animals he had made and breathed his spirit into it, and it became a man, and it began to walk upright on two feet, and it had communion with God…” But God did not so inform us.

To date, while genetic similarities exist between man and animals such as chimps and mice (it would be surprising if they didn’t given the similarity of so many biological functions), it is not possible to eliminate/explain the differences between them by relying solely on evolutionary explanations.


(Dennis Venema) #10

Hi John,

In my experience, scientists report things accurately, especially in the scientific literature. The fault here, alas, is generally with Christians who want the value to be lower than it is.


(David Hume (nom de plume)) #11

Poythress is wrong, and qualified biologists can see this at a glance. I have no survey data, but would be willing to wager that 8 out of 10 biologists would identify his claims as so far afield that they would assume him to be an untrained and poorly informed layperson. If one were to then reveal that the writer is a theologian at a seminary, I surmise that this would reduce the respectability of theologians in the eyes of those scientists. But I could be wrong. Perhaps it would be more like 9 out of 10.

I’m keen to see Prof. Venema’s explanation, but couldn’t resist posting a link (below) to a recent review that provides details and accurate estimates of what we know (and don’t know) about genomic change in primate lineages.

My biggest question, though, is why it is thought important to answer an uninformed unqualified theologian’s claims about genomics. I think I know the answer (I’m a former evangelical), but my biased opinion is that this is more important to understand than genomics itself.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4097811/


(Dennis Venema) #12

Hi David,

Perceptive comments - as to your main question, unfortunately many evangelicals look to authority figures (such as Poythress) for answers. Poythress’s book is in a series called “Christian Answers to Hard Questions” even. These readers deserve to know that Poythress has not properly understood the science he is commenting on, and that his arguments - that many will accept uncritically - are fatally flawed.


(David Hume (nom de plume)) #13

I agree that people “deserve to know” when they are being misinformed. I just want people to consider one more question: “why would an intelligent person ask a theologian about genomics?” But thanks for the response, and I shall sleep restlessly as I await your next post. :sleeping:


#14

Dennis, I agree that generally scientists report things accurately in the scientific literature. I rely on the scientific literature in my work. But that’s not the issue. The issue is how scientists talk to the media. I’m also not sure that you can blame Christians for the comparative analysis, or how the analysis is portrayed, regardless of what their motivation or perspective is on the value. If scientists and/or media report a 99% similarity, how is that the fault of christians?


(Dennis Venema) #15

John, I’m not sure I follow. In certain contexts it is absolutely valid to say that the human and chimpanzee genomes are 99% identical (if indels are excluded). If indels are included, the value drops to ~95-96%. I discuss all of this in the series linked above.

If Poythress was to argue that the value should not be stated as 99%, but rather 95%, he would be saying nothing incorrect, but voicing a preference for including indels in the analysis. But he’s not saying that - he’s saying the value is ~70%, and that’s just plain wrong.


(Roger A. Sawtelle) #16

@aleo, @Daniel, and @johnZ

The soul, Greek “psyche,” is often associated with the spirit, but for the Greeks it was generally associated with the mind. Most people recognize that a spiritual being must also be a rational being.

I believe that that saying that humans are created in the Image of God, is the same thing as saying that God gave humans rational and spiritual beings.

Some say that humans are not special, not different from other hominids, because God could not give humans souls through evolution, but only breathing the Spirit into them. The problem with this as I have hinted is that this would apply to a rational mind also.

God created humans in such a way that they were able to think and with the ability to think, they had the ability to act morally. This happened through a gradual process, but at a certain time and place humans deliberately rebelled against their Maker and the Fall took place.


#17

Dennis, I am waiting for your post tomorrow… but the problem is this, why would one exclude indels if they are different? They can have a disastrous effect on protein formation. Secondly, it is not only indels, but also genome size that is different. My understanding is that it is about 8% different in size. Thirdly, while similarities are large, it is somewhat deceiving (not intentionally, but…) to say merely 95% or 87% similar, when the differences are in the hundreds of thousands of base pairs that are different. In fact, a 10% difference would seem to be about 300 million base pairs… or is that not right? In addition, numerical differences do not capture the significance of the differences, in that multiple genes are required to perform a combined result, and alternatively, that some genes perform more than one function (more than one protein or more than one regulatory function). My comments are not directly relating to Poythress, but rather to the numbers and the way they are often presented. So I agree with what you are saying about what he said, but why is 99% w/o indels more significant than the 96% with indels? And why ignore the difference in genomes sizes? (I have heard the 70% number before as well, but not sure where… it may related to unanalyzed portions, or different locations/orders, or portions considered to be junk DNA, but I’m not sure about that.)


(Dennis Venema) #18

Hi John - thanks for the good questions. Have you read that first post in the “ID and common ancestry” series? It gets into the details in a way that I don’t have time to replicate here at the moment.

A few quick comments - the gene sequences for humans and chimps are over 99% identical. Indels don’t really figure into that because indels that occur in gene sequences are weeded out if they have a negative effect on gene function.

Let me illustrate some of the issues: compare the two following sentences: how identical are they?

The gene sequences for humans and chimps are over 99% identical.
The gene sequences for humans and chimps are over 99% identical identical.

See the issues?


(Preston Garrison) #19

There’s a crack from the physicists that theologians were driven out of cosmology by a “straightforward application of tensor calculus.” It seems that they can be driven out of biology by a “straightforward application of alignment software and genome browsers” which are actually a lot easier to understand than tensor calculus. It’s a mystery why a theologian would attempt this in the first place, and even more mysterious why he wouldn’t seek the help of a trained molecular biologist who agrees with him on the issue at hand. Todd Wood agrees with Poythress in rejecting common descent, but he would have told him that arguing about overall percentage identities is about the weakest approach that he could have chosen. With many of the usual culture warriors, I would suspect that there was a calculation that the intended audience wouldn’t know the difference, but I wouldn’t expect such cynicism from Poythress, so why he did this and did it this way is something of a mystery.

What percentage identity is the cut-off for common descent? How would you pick one? As Dennis knows there are far better forms of evidence in genomes for common descent than percentage identities. Dennis has written about quite a few of them here.

The reason for the initial statements of 99% is in the early stages they were looking at the easiest regions to align. 3 billion base pairs is a lot of sequence to analyze and no one had done that much before. Naturally they started with the stuff that was known to be functional or aligned with sequences in other organisms that were known to be functional. They were still developing software to deal with such large amounts of sequence. There’s not much point in looking at those papers from a year or two after the draft human sequence was finished. They were just getting started on the analysis. The papers from after the completion of the chimp sequence are much more informative. In addition to the initial publication, there were a number of papers looking at various aspects of the two sequences, and the realization, at least for me, that you have to have multiple sequences from each species to know what is a fixed difference and what is polymorphic (present in 2 or more variant forms within the population.)


(Dennis Venema) #20

Preston, you’re prescient - as you’ll see in tomorrow’s post, I cite Todd Wood, and cite him (as usual) favorably.

I agree that Poythress would not likely be cynical as you suggest. It seems he doesn’t realize that he is in error. The journal that his article appeared in is a theological journal, and thus it is unlikely that it was reviewed by anyone with expertise in biology. Todd would have made an excellent reviewer for the paper.


(Dan Ippolito) #21

JohnZ,

Your choice of the word “inform” in the sentence “…then on the sixth day, god took one of the land animals he had made and breathed his spirit into it, and it became a man, and it began to walk upright on two feet, and it had communion with God…” But God did not so inform us." clarifies for me the real point of our discussion. You seem to view the first chapters of Genesis as “information” - like what we would find in a textbook. Many Old Testament scholars view those chapters as poetic myth that explains deep truths (there is one God, He is the Creator, we are creatures meant to be in relationship with him, etc) rather than as straightforward propositions. I try to interpret Genesis in light of the best available scholarship, both Biblical and scientific, and I am inclined to read it as divinely inspired poetry that encapsulates fundamental truths rather than as dry statement of facts. Note that I did not say that human scholarship should “judge” God’s word, but rather that God’s word is understood more fully in light of good scholarship. Daniel Harlow has provided as good a case as any I’ve come across for so interpreting Genesis in http://www.asa3.org/ASA/PSCF/2010/PSCF9-10Harlow.pdf.



#22

Daniel, while you think your approach is rational, I do not. Most scholars agree that the first chapters of Genesis are NOT poetic myth by any normal standards of hebrew writing. In addition, you have not explained why such a myth was necessary if it was so inaccurate. My example clearly shows that it would not be difficult to write a different poem/narrative that could be easily understood. Without giving a rationale for such poetry, your inclination is no more valid than anyone else’s and just takes us back to the idea that anyone can interpret anything in whatever way they choose. I do not read Genesis as mere information, but certainly the information in it is important to the message.

If someone tells you that they love their girlfriend because they bought her some flowers and a ring, and sit waiting at the phone for hours to talk, and then you discover that no flowers were given, no ring exists, and the person doesn’t have a phone, will you still believe the message about love?