Neanderthal Gene Deserts Provide Oasis for RTB’s Creation Model

My two-year-old grandson’s favorite book is Yummy Yucky by Leslie Patricelli. This work helps little ones learn which things they should put in their mouths (yummy things) and which things they shouldn’t (yucky things).  

Spoiler alert!

Blueberries are yummy; blue crayons are yucky

Spaghetti is yummy; worms are yucky

Burgers are yummy; boogers are yucky

For now, my grandson has two categories he uses to organize the world: yummy and yucky. He seems to be much more interested in things that are yucky than yummy. He loves to point them out, talk about them, and even smell them when they’re stinky. 

In my experience as a Christian apologist who barters in the science-faith arena, if there’s one thing that most Christians find yucky—disturbing and disgusting—it is the fact that modern humans and Neanderthals interbred and produced modern human-Neanderthal hybrid offspring. Yet, it’s also a topic that Christians love to discuss.

There’s a good reason for this interest. The prospect of human-Neanderthal interbreeding raises a plethora of questions, such as:

  • If interbreeding took place, what does that mean for the credibility of the biblical account of human origins?
  • Are humans truly exceptional? 
  • Are we truly made in God’s image?
  • Did the children resulting from these interbreeding events have a soul? Did they bear the image of God?

I have addressed these questions in two articles: “Answering Scientific Questions on Human-Neanderthal Interbreeding, Part 1,” and “Answering Theological Questions on Human-Neanderthal Interbreeding.” 

The interbreeding between modern humans and Neanderthals is particularly problematic for our (RTB) human origins creation model (presented in detail in Who Was Adam?). On the surface, it appears to falsify several key predictions of our model. 

Yet, new work by investigators from the University of Barcelona helps address this significant challenge to our model.In fact, their work on “gene deserts”—large regions in the human genome where no Neanderthal DNA exists—can be marshaled to make a case that modern humans are exceptional and made in God’s image! That which is yucky has become, in a manner of speaking, yummy.

RTB’s Human Origins Model on Neanderthals
Our model holds that Adam and Eve were the first two humans, created in God’s image through his direct and personal actions. We maintain that Adam and Eve were modern humans and gave rise to all people alive today and all people who have lived throughout human prehistory and history. We affirm that Adam and Eve were created and we deny the notion that Adam and Eve were the products of a God-guided evolutionary process. 

As for the hominins such as Neanderthals, we don’t see them as evolutionary predecessors to modern humans. Instead, we regard them as animals created by God that lived for a period, then went extinct. 

According to our model, these creatures were intelligent and led emotionally rich lives. They had their own technology and culture. Yet we take the view that these creatures were not made in God’s image. That status is exclusive to Adam and Eve and their descendants, modern humans. 

Based on our view of the hominins, we would predict both biological similarities (because humans and animals were made from the same stuff—the dust of the earth) and biological differences. We also predict significant behavioral differences between modern humans (who bear God’s image), and hominins (who lack God’s image).

But What if Modern Humans and Neanderthals Interbred?
Along with the “yuck” factor, several more questions come to mind:

  • Doesn’t interbreeding between modern humans and Neanderthals invalidate the RTB model?
  • Doesn’t it mean that Neanderthals and modern humans really are the same species? 
  • Doesn’t this discovery mean that Neanderthals were just like us?

Not necessarily. There’s plenty of evidence to suggest that modern humans and Neanderthals were distinct species. There’s also plenty of evidence that indicates modern humans were cognitively superior to Neanderthals, as evidenced by genetic differences and differences in brain structure.  (See Resources.) Finally, there’s a plethora of evidence that members of distinct species can interbreed to produce healthy, viable offspring. (See Resources.) So, why wouldn’t the same be true for modern humans and Neanderthals?

According to the RTB human origins model, interbreeding between modern humans and Neanderthals is possible because of the shared biological designs between the two species. This interpretation may explain the evidence scientifically, but it still doesn’t answer troubling theological questions. 

Did Modern Human-Neanderthal Hybrids Have the Image of God?
If Neanderthals lacked the image of God, then what are we to make of the offspring that resulted from the interbreeding between modern humans and Neanderthals? Did these creatures have a soul? Did they bear God’s image?

Even though—according to our model—Neanderthals lacked God’s image, I hold the view that the modern human-Neanderthal hybrids bore God’s image. I offer a detailed explanation for why I embrace this view in the Resources section. 

Briefly, it’s possible to conceive of scenarios in which a human-hominin hybrid receives a soul. For example, one could envision God creating a soul in the human-Neanderthal hybrid at the time of conception, honoring the fact that at least one of the parents is an image-bearer and knowing that the hybrid would likely interbreed with other humans. Alternatively, as long as one of the parents is an image-bearer, then the offspring should also possess God’s image. In effect, the image of God is indivisible. Either a being has the image of God or it doesn’t. It makes no sense to think of a creature having only half of the image of God.

Based on the biblical texts (again, see the Resources section), it appears that God would have been displeased with the interbreeding between modern humans—Adam and Eve’s descendants— and Neanderthals. Interbreeding isn’t what God intended, though he appears to have used the yucky behavior for good purposes. 

Protective Measures
It appears that God put in place protective measures to limit the impact of interbreeding once it took place, as evinced by the discovery of Neanderthal gene deserts in the human genome. The discovery of Neanderthal gene deserts is a bit surprising because Neanderthal DNA sequences are distributed throughout the modern human genome. For example, people of Eurasian descent have about 1–4% Neanderthal DNA in their genomes. These sequences aren’t concentrated in one location. The DNA sequences are found nearly everywhere. 

Neanderthal gene deserts must exist because it would have been a disadvantage for the descendants of the hybrids to have the Neanderthal version of the genes in the desert regions. In other words, over time, the forces of natural selection would have eliminated the Neanderthal version of the genes in these regions of the genome (negative selection). Alternatively, it could have been that the modern human version of these genes was so advantageous for the hybrid’s descendants that they were preserved (positive selection). Yet, for other regions of the modern human genome outside the Neanderthal gene deserts, replacing the modern human version of genes with Neanderthal versions must have had minimal impact or may have even been beneficial.2

As it turns out, a catalog of the genes found in four of the largest Neanderthal gene deserts includes genes that play a central role in language trait development, such as FOXP2ROBO1ROBO2, and EPHA3, and it explains why Neanderthal versions of these genes were eliminated from the modern human genome via natural selection. Modern human versions of genes in Neanderthal gene deserts also appear to be expressed at high levels in the developing cerebral cortex. By the same token, the expression of Neanderthal versions of genes is suppressed in modern human brain regions.3

Building off these earlier insights, the research team from Spain wanted to probe more deeply the role played by genes in Neanderthal gene deserts. The team identified genes in four of the largest Neanderthal gene deserts that were under positive selection. Using Allen Brain Atlas (a database that seeks to combine genomics with neuroanatomy) data, they also analyzed the gene expression profile of these genes in different brain regions at different developmental stages. 

Compared to random regions of the genome (of comparable size to the four Neanderthal gene deserts), they discovered that key genes that play a role in neuronal growth and brain development (such as CADPS2ROBO2, and SYT6) were under positive selection and were expressed at high levels in three brain regions: 

  • The striatum, which integrates different areas of the brain, plays a role in coordinating motor functions, action planning, decision making, motivation reinforcement, and reward perception;
  • The thalamus, which serves as a hub in the brain for the exchange of information and for relaying sensory information to the cerebral cortex. The thalamus also regulates consciousness, alertness, and sleep; and 
  • The cerebellum, which plays an integrator’s role by coordinating motor activities. It also plays a role in language, regulates emotions, and controls attention.

Collectively, these observations suggest that:

  • Neanderthals and modern humans are, indeed, distinctive species. 
  • A species barrier exists between the two groups of hominins, preventing them from merging into a single species. 
  • Cognitive differences exist between modern humans and Neanderthals. 

The final observation (cognitive differences) in the list finds affirmation from other independent lines of evidence. For example, the shape of the modern human skull appears to be unusual and distinct compared to the skulls of hominins such as Neanderthals, H. heidelbergensis, and H. erectus. The skull shape of these hominins was more elongated along the anterior-posterior axis. But the skull shape of modern humans is globular, with bulging and enlarged parietal and cerebral areas. Additionally, in the modern human skull, the face is retracted and relatively small. 

The difference in skull shape and facial structure impacts the shape of the modern human brain and the relative sizes of different brain regions. The chief difference between human and Neanderthal brains is the size and shape of the cerebellum. The cerebellar hemisphere is projected more toward the interior in the modern human brain than it is in the Neanderthal brain and the volume of the modern human cerebellum is larger. The right side of the Neanderthal cerebellum is significantly smaller than the left side—a phenomenon called volumetric laterality. This discrepancy doesn’t exist in the modern human brain. The parietal regions in the modern human brain were also larger than those regions in Neanderthals’ brains.4

Genome-wide comparisons of the Neanderthal and modern human genomes have identified different versions of genes that play a role in skull morphology (shape) and cognitive development.5 Molecular anthropologists studying neurological and neuropsychiatric disorders in modern humans have also inferred differences in the expression of genes in coding regions of the Neanderthal and modern human genomes. They’ve also detected differences in expression patterns for genes that play a role in facial and vocal tract development.6

While these genetic differences suggest disparities in cognitive capacities between modern and archaic humans, the evidence is circumstantial. Recently, however, researchers have developed experimental approaches to directly assess the impact of these genetic differences on brain development and function. 

Researchers have generated and characterized brain organoids produced from modern human stem cells and have compared them with “Neanderthalized” brain organoids generated with gene-editing techniques. To date, four independent studies have identified physiological differences between modern human and “Neanderthalized” brain organoids. They observed the differences when the modern human versions of the genes TKTL1, NOVA1, Adenylosuccinate LyaseKIF18A, KNL1, and SPAG5 were gene-edited to the Neanderthal versions. These distinctions all indicate that the genetic differences in these genes (which all play a role in neural development) are significant and that Neanderthals were cognitively inferior to modern humans.7

Yummy or Yucky?
From a biblical perspective, the quality that makes modern humans unique and exceptional is the image of God. While theologians debate the nature of God’s image in human beings, it’s reasonable to think that the image of God refers to capabilities that modern humans alone possess, such as the capacity for symbolism, which manifests in language, music, and art. This quality most likely involves an immaterial aspect of our nature as human beings, but it’s also reasonable to think that there must be brain structures and neurochemical processes that support the expression of the image of God. This expectation is being fulfilled before our eyes as life scientists produce mounting evidence for the uniqueness of the human brain. Along with it, they’re providing evidence that modern humans display a distinct type of advanced cognition that separates us from the other hominins, including Neanderthals.

The discovery of Neanderthal gene deserts in the modern human genome adds to the case for human exceptionalism. These gene deserts point to the existence of a species barrier between modern humans and Neanderthals—a barrier that ensures the brain structures that grant modern humans the capacity for advanced cognition remain undisturbed, even when we interbred with Neanderthals. 

From a theological standpoint, it appears that God put in place a protective mechanism that ensures that the image of God was not lost when modern humans interbred with Neanderthals. Ironically, when the scientific consequences of interbreeding between modern humans and Neanderthals are studied in detail, instead of undermining the case for human exceptionalism, interbreeding affirms it. 

Now, I find that affirmation to be delicious.


Responding to Questions about Human-Neanderthal Interbreeding

Brain Structure Differences between Modern Humans and Neanderthals

Brain Organoid Studies

Genetic Differences between Modern Humans and Neanderthals


  1. Raül Buisan et al., “A Brain Region-Specific Expression Profile for Genes within Large Introgression Deserts and Under Positive Selection in Homo sapiens,” Frontiers in Cell and Developmental Biology 10 (April 26, 2022): 824740, doi:10.3389/fcell.2022.824740.
  2. Buisan et al., “A Brain Region-Specific Expression Profile,” 824740. 
  3. Buisan et al., 824740.
  4. Takanori Kochiyama et al., “Reconstructing the Neanderthal Brain Using Computational Anatomy,” Science Reports 8 (April 26, 2018): 6296, doi:10.1038/s41598-018-24331-0.
  5. Richard E. Green et al., “A Draft Sequence of the Neandertal Genome,” Science 328, no. 5979 (May 7, 2010): 710–722, doi:10.1126/science.1188021.
  6. For example, see Laura L. Colbran et al., “Inferred Divergent Gene Regulation in Archaic Hominins Reveals Potential Phenotypic Differences,” Nature Ecology and Evolution 3 (November 2019): 1598–1606, doi:10.1038/s41559-019-0996-x; David Gokhman et al., “Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan,” Science 344, no. 6183 (May 2, 2014): 523–527, doi:10.1126/science.1250368; David Gokhman et al., “Differential DNA Methylation of Vocal and Facial Anatomy Genes in Modern Humans,” Nature Communications 11 (March 4, 2020): 1189, doi:10.1038/s41467-020-15020-6.
  7. Cleber A. Trujillo et al., “Reintroduction of the Archaic Variant of NOVA1 in Cortical Organoids Alters Neurodevelopment,” Science 371, no. 6530 (February 12, 2021): eaax2537, doi:10.1126/science.aax2537; Vita Stepanova et al., “Reduced Purine Biosynthesis in Humans after Their Divergence from Neandertals,” eLife 10 (May 4, 2021): e58741, doi:10.7554/eLife.58741; Felipe Mora-Bermúdez et al., “Longer Metaphase and Fewer Chromosome Segregation Errors in Modern Human Than Neanderthal Brain Development,” Science Advances 8, no. 30 (July 29, 2022): eabn7702, doi:10.1126/sciadv.abn7702; Anneline Pinson et al., “Human TKTL1 Implies Greater Neurogenesis in Frontal Neocortex of Modern Humans Than Neanderthals,” Science 377, no. 6611 (September 9, 2022): doi:10.1126/science.abl6422.