Tag: Ancient DNA

Answering Scientific Questions on Neanderthal-Human Interbreeding

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By Fazale Rana – August 5, 2020

So don’t ask me no questions
And I won’t tell you no lies
And don’t ask me about my business
And I won’t tell you good-bye

“Don’t Ask Me No Questions”

—Ronnie Van Zandt and Gary Robert Rossington

One of my favorite rock bands of all time is Lynyrd Skynyrd. (That’s right…Skynyrd, baby!) I know their musical catalog forward and backwards. I don’t know if it is a good thing or not, but I am conversant with the history of most of the songs recorded by the band’s original lineup.

“Don’t Ask Me No Questions” was the first single released from their second studio album, Second Helping. The album also included “Sweet Home Alabama.” When juxtaposed with the success of “Sweet Home Alabama,” it’s ironic that “Don’t Ask Me No Questions” never even broke the charts.

An admonition to family and friends not to pry into their personal affairs, this song describes the exhaustion the band members felt after spending months on tour. All they want is peace and respite when they return home. Instead, they find themselves continuously confronted by unrelenting and inappropriate questions about the rock ‘n’ roll lifestyle.

As a Christian apologist, people ask me questions all the time. Yet, rarely do I find the questions annoying and inappropriate. I am happy to do my best to answer most of the questions asked of me—even the snarky ones posed by internet trolls. As of late, one topic that comes up often is interbreeding between modern humans and Neanderthals:

  • Is it true that modern humans and Neanderthals interbred?
  • If interbreeding took place, what does that mean for the credibility of the biblical account of human origins?
  • Did the children resulting from these interbreeding events have a soul? Did they bear the image of God?

Recently, an international team of investigators looking to catalog Neanderthal genetic contributions, surveyed a large sampling of Icelander genomes. This work generated new and unexpected insights about interbreeding between hominins and modern humans.1

No lie.

It came as little surprise to me when the headlines announcing this discovery triggered another round of questions about interbreeding between modern humans and Neanderthals. I will address the first two questions above in this article and the third one in a future post.

RTB’s Human Origins Model in 2005

To tell the truth, for a number of years I resisted the idea that modern humans interbred with Neanderthals and Denisovans. When Hugh Ross and I published the first edition of our book, Who Was Adam? (2005), there was no real evidence that modern humans and Neanderthals interbred. We took this absence of evidence as support for the RTB human origins model.

According to our model, Neanderthals have no evolutionary connection to modern humans. The RTB model posits that the hominins, such as Neanderthals and Denisovans, were creatures made by God that existed for a time and went extinct. These creatures had intelligence and emotional capacity (like most mammals), which enabled them to establish a culture. However, unlike modern humans, these creatures lacked the image of God. Accordingly, they were cognitively inferior to modern humans. In this sense, the RTB human origins model regards the hominins in the same vein as the great apes: intelligent, fascinating creatures in their own right that share some biological and behavioral attributes with modern humans (reflecting common design). Yet, no one would confuse a great ape and a modern human because of key biological distinctions and, more importantly, because of profound cognitive and behavioral differences.

When we initially proposed our model, we predicted that the biological differences between modern humans and Neanderthals would have made interbreeding unlikely. And if they did interbreed, then these differences would have prohibited the production of viable, fertile offspring.

Did Humans and Neanderthals Interbreed?

In 2010, researchers produced a rough draft sequence of the Neanderthal genome and compared it to modern human genomes. They discovered a closer statistical association of the Neanderthal genome with those from European and Asian people groups than with genomes from African people groups.2 The researchers maintained that this effect could be readily explained if a limited number of interbreeding events took place between humans and Neanderthals in the eastern portion of the Middle East, roughly 45,000 to 80,000 years ago, just as humans began to migrate around the world. This would explain why non-African populations display what appears to be a 1 to 4 percent genetic contribution from Neanderthals while African people groups have no contribution whatsoever.

At that time, I wasn’t entirely convinced that modern humans and Neanderthals interbred because there were other ways to explain the statistical association. Additionally, studies of Neanderthal genomes indicate that these hominins lived in small insular groups. At that time, I argued that the low population densities of Neanderthals would have greatly reduced the likelihood of encounters with modern humans migrating in small populations. It seemed to me that it was unlikely that interbreeding occurred.

Other studies demonstrated that Neanderthals most likely were extinct before modern humans made their way into Europe. Once again, I argued that the earlier extinction of Neanderthals makes it impossible for them to have interbred with humans in Europe. Extinction also raises questions about whether the two species interbred at all.

The Case for Interbreeding

Despite these concerns, in the last few years I have become largely convinced that modern humans and Neanderthals interbred. Studies such as the one cataloging the Neanderthal contribution to the genomes of Icelanders leave me little choice in the matter.

Thanks to the deCODE project, the genome sequences for nearly half the Icelandic population have been determined. An international team of collaborators made use of this data set, analyzing over 27,500 Icelander genomes for Neanderthal contribution using a newly developed algorithm. They detected over 14.4 million fragments of Neanderthal DNA in their data set. Of these, 112,709 were unique sequences that collectively constituted 48 percent of the Neanderthal genome.

This finding has important implications. Even though individual Icelanders have about a 1 to 4 percent Neanderthal contribution to their genomes, the precise contribution differs from person to person. And when these individual contributions are combined it yields Neanderthal DNA sequences that cover nearly 50 percent of the Neanderthal genome. This finding aligns with previous studies which demonstrate that, collectively, across the human population Neanderthal sequences are distributed throughout 20 percent of the human genome. And 40 percent of the Neanderthal genome can be reconstructed from Neanderthal sequences found in a sampling of Eurasian genomes.3

Adding to this evidence for interbreeding are studies that characterized ancient DNA recovered from several modern human fossil remains unearthed in Europe, dating between about 35,000 and 45,000 years in age. The genomes of these ancient modern humans contain much longer stretches of Neanderthal DNA than what’s found in contemporary modern humans, which is exactly what would be expected if modern humans interbred with these hominins.4

As I see it, interbreeding is the only way to make sense of these results.

Are Humans and Neanderthals the Same Species?

Because the biological species concept (BSC) defines a species as an interbreeding population, some people argue that modern humans and Neanderthals must belong to the same species. This perspective is common among young-earth creationists who see Neanderthals as a subset of humanity.

This argument fails to take into account the limitations of the BSC, one being the phenomenon of hybridization. Mammals that belong to separate species have been known to interbreed and produce viable—even fertile—offspring called hybrids. For example, lions and tigers in captivity have interbred successfully—yet both parent animals remain considered separate species. I would argue that the concept of hybridization applies to the interbreeding that took place between modern humans and Neanderthals.

Even though it appears that modern humans and Neanderthals interbred, other lines of evidence indicate that these two hominins were distinct species. Significant anatomical differences exist between the two. The most profound difference is skull anatomy and, consequently, brain structure

blog__inline--answering-scientific-questions-on-neanderthal-human-interbreeding-part-1Anatomical Differences between Human and
Neanderthal Skulls. Image credit: Wikipedia.

Additionally, Neanderthals possessed a hyper-polar body design, consisting of a stout, barrel-shaped body with shortened limbs to help with heat retention. Neanderthals and modern humans display significant developmental differences as well. Neanderthals, for example, spent a minimal time in adolescence compared to modern humans. The two hominins also exhibit significant genetic differences (which includes differences in gene expression patterns), most notably for genes that play a role in cognition and cognitive development. Most critically, modern humans and Neanderthals display significant behavioral differences that stem from substantial differences in cognitive capacity.

Along these lines, it is important to note that researchers believe that the resulting human-Neanderthal hybrids lacked fecundity.5 As geneticist David Reich notes, “Modern humans and Neanderthals were at the edge of biological compatibility.”6

In other words, even though modern humans and Neanderthals interbred, they displayed sufficient biological differences that are extensive enough to justify classing the two as distinct species, just as the RTB model predicts. The extensive behavioral differences also validate the view that modern humans are exceptional and unique in ways that align with the image of God—again, in accord with RTB model predictions.

Is the RTB Human Origins Model Invalid?

It is safe to say that most paleoanthropologists view modern humans and Neanderthals as distinct species (or at least distinct populations that were isolated from one another for over 500,000 to 600,000 years). From an evolutionary perspective, modern humans and Neanderthals share a common evolutionary ancestor, perhaps Homo heidelbergensis, and arose as separate species as the two lineages diverged from this ancestral population. In the evolutionary framework, the capacity of Neanderthals and modern humans to interbreed reflects their shared evolutionary heritage. For this reason, some critics have pointed to the interbreeding between modern humans and other hominins as a devastating blow to the RTB model and as clear-cut evidence for human evolution.

In light of this concern, it is important to recognize that the RTB human origins model readily accommodates the evidence for interbreeding between modern humans and Neanderthals. Instead of reflecting a shared evolutionary ancestry, within a creation model framework, the capacity for interbreeding is a consequence of the biological designs shared by modern humans and Neanderthals.

The RTB model’s stance that shared biological features represent common design taps into a rich tradition within the history of biology. Prior to Charles Darwin, life scientists such as the preeminent biologist Sir Richard Owen, routinely viewed homologous systems as manifestations of archetypal designs that resided in the Mind of the First Cause. The RTB human origins model co-opts Owen’s ideas and applies them to the biological features modern humans share with other creatures, including the hominins.

Without question, the discovery that modern humans interbred with other hominins, stands as a failed prediction of the initial version of the RTB human origins model. However, this discovery can be accommodated by revising the model–as is often done in science. Of course, this leads to the next set of questions.

  • Is there biblical warrant to think that modern humans interbred with other creatures?
  • Did the modern human-Neanderthal hybrid have a soul? Did it bear God’s image?

I will take on these questions in the next article. And I am telling you no lie.

Resources

Biological Differences between Humans and Neanderthals

Archetype Biology

Endnotes
  1. Laurits Skov et al., “The Nature of Neanderthal Introgression Revealed by 27,566 Icelandic Genomes,” Nature (published online April 22, 2020), doi:10.1038/s49586-020-2225-9.
  2. Fazale Rana with Hugh Ross, Who Was Adam? A Creation Model Approach to the Origin of Humanity, 10-Year Update (Covina, CA: RTB Press, 2015), 301–12.
  3. Sriram Sankararaman et al., “The Genomic Landscape of Neanderthal Ancestry in Present-Day Humans,” Nature 507 (2014): 354–57, doi:10.1038/nature12961; Benjamin Vernot and Joshua M. Akey, “Resurrecting Surviving Neandertal Lineages from Modern Human Genomes,” Science 343 (2014): 1017–21, doi: 10.1126/science.1245938.
  4. Rana with Ross, Who Was Adam?, 304–5.
  5. Sankararaman et al., “Genomic Landscape,” 354–57, Vernot and Akey, “Resurrecting Surviving Neandertal Lineages,” 1017–21.
  6. Ewen Callaway, “Modern Human Genomes Reveal Our Inner Neanderthal,” Nature News (January 29, 2014), https://www.nature.com/news/modern-human-genomes-reveal-our-inner-neanderthal-1.14615.

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design

How Can DNA Survive for 75 Million Years? Implications for the Age of the Earth

 
By Fazale Rana – April 15, 2020

My family’s TV viewing habits have changed quite a bit over the years. It doesn’t seem that long ago that we would gather around the TV, each week at the exact same time, to watch an episode of our favorite show, broadcast live by one of the TV networks. In those days, we had no choice but to wait another week for the next installment in the series.

Now, thanks to the availability of streaming services, my wife and I find ourselves binge-watching our favorite TV programs from beginning to end, in one sitting. I’m almost embarrassed to admit this, but we rarely sit down to watch TV with the idea that we are going to binge watch an entire season at a time. Usually, we just intend to take a break and watch a single episode of our favorite program before we get back to our day. Inevitably, however, we find ourselves so caught up with the show we are watching that we end up viewing one episode after another, after another, as the hours of our day melt away.

One program we couldn’t stop watching was Money Heist (available through Netflix). This Spanish TV series is a crime drama that was originally intended to span two seasons. (Because of its popularity, Netflix ordered two more seasons.) Money Heist revolves around a group of robbers led by a brilliant strategist called the Professor. The Professor and his brother nicknamed Berlin devise an ambitious, audacious plan to take control of the Royal Mint of Spain in order to print and then escape with 2.5 billion euros.

Because their plan is so elaborate, it takes the team of robbers five months to prepare for their multi-day takeover of the Royal Mint. As you might imagine, their scheme consists of a sequence of ingenious, well-timed, and difficult-to-execute steps requiring everything to come together in the just-right way for their plan to succeed and for the robbers to make it out of the mint with a treasure trove of cash.

Recently a team of paleontologists uncovered their own treasure trove—a haul of soft tissue materials from the 75-million-year-old fossilized skull fragments of a juvenile duck-billed dinosaur (Hypacrosaurus stebingeri).1 Included in this cache of soft tissue materials were the remnants of the dinosaur’s original DNA—the ultimate paleontological treasure. What a steal!

This surprising discovery has people asking: How is possible that DNA could survive for that long a period of time?

Common wisdom states that DNA shouldn’t survive for more than 1 million years, much less 75 million. Thus, young-earth creationists (YECs) claim that this soft-tissue discovery provides the most compelling reason to think that the earth is young and that the fossil record resulted from a catastrophic global deluge (Noah’s flood).

But is their claim valid?

Hardly. The team that made the soft-tissue discovery propose a set of mechanisms and processes that could enable DNA to survive for 75 million years. All it takes is the just-right set of conditions and a sequence of well-timed, just-right events all coming together in the just-right way and DNA will persist in fossil remains.

Baby Dinosaur Discovery

The team of paleontologists who made this discovery—co-led by Mary Schweitzer at North Carolina State University and Alida M. Bailleul of the Chinese Academy of Sciences—unwittingly stumbled upon these DNA remnants as part of another study. They were investigating pieces of fossilized skull and leg fragments of a juvenile Hypacrosaurus recovered from a nesting site. Because of the dinosaur’s young age, the researchers hoped to extend the current understanding of dinosaur growth by carrying out a detailed microscopic characterization of these fossil pieces. In one of the skull fragments they observed well-defined and well-preserved calcified cartilage that was part of a growth plate when the juvenile was alive.

A growth plate is a region in a growing skeleton where bone replaces cartilage. At this chondro-osseous junction, chondrocytes (cells found in cartilage) can be found within lacunae (spaces in the matrix of bone tissues). Here, chondrocyte cells secrete an extracellular matrix made up of type II collagen and glucosamine glycans. These cells rapidly divide and grow (a condition called hypertrophy). Eventually, the cells die, leaving the lacunae empty. Afterwards, bone fills in the cavities.

The team of paleontologists detected lacunae in the translucent, well-preserved cartilage of the dinosaur skull fragment. A more careful examination of the spaces revealed several cell-like structures sharing the same lacunae. The team interpreted these cell-like structures as the remnants of chondrocytes. In some instances, the cell-like structures appeared to be doublets, presumably resulting from the final stages of cell division. In the doublets, they observed darker regions that appeared to be the remnants of nuclei and, within the nuclei, dark colored materials that were elongated and aligned to mirror each other. They interpreted these features as the leftover remnants of chromosomes, which would form condensed structure during the later stages of cell division.

Given the remarkable degree of preservation, the investigators wondered if any biomolecular remnants persisted within these microscopic structures. To test this idea, they exposed a piece of the fossil to Alcian blue, a dye that stains cartilage of extant animals. The fact that the fossilized cartilage picked up the stain indicated to the research team that soft tissue materials still persisted in the fossils.

Using an antibody binding assay (an analytic test), the research team detected the remnants of collagen II in the lacunae. Moreover, as a scientific first, the researchers isolated the cell-like remnants of the original chondrocytes. Exposing the chondrocyte remnants to two different dyes (PI and DAPI) produced staining in the cell interior near the nuclei. These two dyes both intercalate between the base pairs that form DNA’s interior region. This step indicated the presence of DNA remnants in the fossils, specifically in the dark regions that appear to be the nuclei.

Implications of This Find

This discovery adds to the excitement of previous studies that describe soft tissue remnants in fossils. These types of finds are money for paleontologists because they open up new windows into the biology of extinct life. According to Bailleul:

“These exciting results add to growing evidence that cells and some of their biomolecules can persist in deep-time. They suggest DNA can preserve for tens of millions of years, and we hope that this study will encourage scientists working on ancient DNA to push current limits and to use new methodology in order to reveal all the unknown molecular secrets that ancient tissues have.”2

Those molecular secrets are even more exciting and surprising for paleontologists because kinetic and modeling studies indicate that DNA should have completely degraded within the span of 1 million years.

The YEC Response

The surprising persistence of DNA in the dinosaur fossil remains is like bars of gold for YECs and they don’t want to hoard these treasure for themselves. YECs assert that this find is the “last straw” for the notion of deep time (the view that Earth is 4.5 billion years old and life has existed on it for upwards of 3.8 billion years). For example, YEC author David Coppedge insists that “something has to give. Either DNA can last that long, or dinosaur bones are not that old.”3 He goes on to remind us that “creation research has shown that there are strict upper limits on the survival of DNA. It cannot be tens of millions of years old.”4 For YECs, this type of discovery becomes prima facia evidence that the fossil record must be the result of a global flood that occurred only a few thousand years ago.

Yet, in my book Dinosaur Blood and the Age of the Earth, I explain why there is absolutely no reason to think that the radiometric dating techniques used to determine the ages of geological formations and fossils are unreliable. The certainty of radiometric dating methods means that there must be mechanisms that work together to promote DNA’s survival in fossil remains. Fortunately, we don’t have to wait for the next season of our favorite program to be released by Netflix to learn what those mechanisms and processes might be.

blog__inline--how-can-dna-survive-for-75-million-years-2

Preservation Mechanisms for Soft Tissues in Fossils

Even though common wisdom says that DNA can’t survive for tens of millions of years, a word of caution is in order. When I worked in R&D for a Fortune 500 company, I participated in a number of stability studies. I quickly learned an important lesson: the stability of chemical compounds can’t be predicted. The stability profile for a material only applies to the specific set of conditions used in the study. Under a different set of conditions chemical stability can vary quite extensively, even if the conditions differ only slightly from the ones employed in the study.

So, even though researchers have performed kinetic and modeling studies on DNA during fossilization, it’s best to exercise caution before we apply them to the Hypacrosaurus fossils. To say it differently, the only way to know what the DNA stability profile should be in the Hypacrosaurus fragments is to study it under the precise set of taphonomic (burial, decay, preservation) conditions that led to fossilization. And, of course, this type of study isn’t realistic.

This limitation doesn’t mean that we can’t produce a plausible explanation for DNA’s survival for 75 million years in the Hypacrosaurus fossil fragments. Here are some clues as to why and how DNA persisted in the young dinosaur’s remains:

  • These fossilized cartilage and chondrocytes appear to be exceptionally well-preserved. For this reason, it makes sense to think that soft tissue material could persist in these remains. So, while we don’t know the taphonomic conditions that contributed to the fossilization process, it is safe to assume that these conditions came together in the just-right way to preserve remnants of the biomolecules that make up the soft tissues, including DNA.
  • Soft tissue material is much more likely to survive in cartilage than in bone. The extracellular matrix that makes up cartilage has no vascularization (channels). This property makes it less porous and reduces the surface area compared to bone. Both properties inhibit groundwater and microorganisms from gaining access to the bulk of the soft tissue materials in the cartilage. At the growth plate, cartilage actually has a higher mineral to organic ratio than bone. Minerals inhibit the activity of environmental enzymes and microorganisms. Minerals also protect the biomolecules that make up the organic portion of cartilage because they serve as an adsorption site stabilizing even fragile molecules. Also, minerals can form cross-links with biomolecules. Cross-linking slows down the degradation of biopolymers. Because the chondrocytes in the cartilage lacunae were undergoing rapid cell division at the time of the creature’s death, they consumed most of the available oxygen in their local environment. This consumption would have created a localized hypoxia (oxygen deficiency) that would have minimized oxidative damage to the tissue in the lacunae.
  • The preserved biomolecules are not the original, unaltered materials, but are fragmented remnants that have undergone chemical alteration. Even with the molecules in this altered, fragmented state, many of the assays designed to detect the original, unaltered materials will produce positive results. For example, the antibody binding assays the research team used to detect collagen II could easily detect small fragmented pieces of collagen. These assays depend upon the binding of antibodies to the target molecule. The antibody binding site consists of a relatively small region of the molecular target. This feature of antibody binding means that the antibodies designed to target collagen II will also bind to small peptide fragments of only a few amino acids in length—as long as they are derived from collagen II.

The dyes used to detect DNA can bind to double-stranded regions of DNA that are only six base pairs in length. Again, this feature means that the dye molecules will as readily intercalate between the bases of intact DNA molecules as relatively small fragments derived from the original material.

  • The biochemical properties of collagen II and condensed chromosomes explain the persistence of this protein and DNA. Collagen is a heavily cross-linked material. Cross-linking imparts a high degree of stability to proteins, accounting for their long-term durability in fossil remains.
In the later stage of cell division, chromosomes (which consist of DNA and proteins) exist in a highly compact, condensed phase. In this phase, chromosomal DNA would be protected and much more resistant to chemical breakdown than if the chromosomes existed in a more diffuse state, as is the case in other stages of the cell cycle.

In other words, a confluence of factors worked together to promote a set of conditions that allows small pieces of collagen II and DNA to survive long enough for these materials to become entombed within a mineral encasement. At this point in the preservation process, the materials can survive for indefinite periods of time.

More Historical Heists to Come

Nevertheless, some people find it easier to believe that a team of robbers could walk out of the Royal Mint of Spain with 2.5 billion euros than to think that DNA could persist in 75-million-year-old fossils. Their disbelief causes them to question the concept of deep time. Yet, it is possible to devise a scientifically plausible scheme to explain DNA’s survival for tens of millions of years, if several factors all work together in the just-right way. This appears to be the case for the duck-billed dinosaur specimen characterized by Schweitzer and Bailleul’s team.

As this latest study demonstrates, if the just-right sequence of events occurs in the just-right way with the just-right timing, scientists have the opportunity to walk out of the fossil record vault with the paleontological steal of the century.

It is exciting to think that more discoveries of this type are just around the corner. Stay tuned!

Resources

Responding to Young Earth Critics

Mechanism of Soft Tissue Preservation

Recovery of a Wide Range of Soft Tissue Materials in Fossils

Detection of Carbon-14 in Fossils

Endnotes
  1. Alida M. Bailleul et al., “Evidence of Proteins, Chromosomes and Chemical Markers for DNA in Exceptionally Preserved Dinosaur Cartilage,” National Science Review, nwz206 (January 12, 2020), doi:10.1093/nsr/nwz206, https://academic.oup.com/nsr/advance-article/doi/10.1093/nsr/nwz206/5762999.
  2. Science China Press, “Cartilage Cells, Chromosomes and DNA Preserved in 75 Million-Year-Old Baby Duck-Billed Dinosaur,” Phys.org, posted February 28, 2020, https://phys.org/news/2020-02-cartilage-cells-chromosomes-dna-million-year-old.html.
  3. David F. Coppedge, “Dinosaur DNA Found!”, Creation-Evolution Headlines (website), posted February 28, 2020, https://crev.info/2020/02/dinosaur-dna-found/.
  4. Coppedge, “Dinosaur DNA Found.”

Reprinted with permission by the author

Original article at:
https://reasons.org/explore/blogs/the-cells-design

New Genetic Evidence Affirms Human Uniqueness

By Fazale Rana – March 4, 2020

It’s a remarkable discovery—and a bit gruesome, too.

It is worth learning a bit about some of its unseemly details because this find may have far-reaching implications that shed light on our origins as a species.

In 2018, a group of locals discovered the remains of a two-year-old male puppy in the frozen mud (permafrost) in the eastern part of Siberia. The remains date to 18,000 years in age. Remarkably, the skeleton, teeth, head, fur, lashes, and whiskers of the specimen are still intact.

Of Dogs and People

The Russian scientists studying this find (affectionately dubbed Dogor) are excited by the discovery. They think Dogor can shed light on the domestication of wolves into dogs. Biologists believe that this transition occurred around 15,000 years ago. Is Dogor a wolf? A dog? Or a transitional form? To answer these questions, the researchers have isolated DNA from one of Dogor’s ribs, which they think will provide them with genetic clues about Dogor’s identity—and clues concerning the domestication process.

Biologists study the domestication of animals because this process played a role in helping to establish human civilization. But biologists are also interested in animal domestication for another reason. They think this insight will tell us something about our identity as human beings.

In fact, in a separate study, a team of researchers from the University of Milan in Italy used insights about the genetic changes associated with the domestication of dogs, cats, sheep, and cattle to identify genetic features that make human beings (modern humans) stand apart from Neanderthals and Denisovans.1 They conclude that modern humans share some of the same genetic characteristics as domesticated animals, accounting for our unique and distinct facial features (compared to other hominins). They also conclude that our high level of cooperativeness and lack of aggression can be explained by these same genetic factors.

This work in comparative genomics demonstrates that significant anatomical and behavioral differences exist between humans and hominins, supporting the concept of human exceptionalism. Though the University of Milan researchers carried out their work from an evolutionary perspective, I believe their insights can be recast as scientific evidence for the biblical conception of human nature; namely, creatures uniquely made in God’s image.

Biological Changes that Led to Animal Domestication

Biologists believe that during the domestication process, many of the same biological changes took place in dogs, cats, sheep, and cattle. For example, they think that during domestication, mild deficits in neural crest cells resulted. In other words, once animals are domesticated, they produce fewer, less active neural crest cells. These stem cells play a role in neural development; thus, neural crest cell defects tend to make animals friendlier and less aggressive. This deficit also impacts physical features, yielding smaller skulls and teeth, floppy ears, and shorter, curlier tails.

Life scientists studying the domestication process have identified several genes of interest. One of these is BAZ1B. This gene plays a role in the maintenance of neural crest cells and controls their migration during embryological development. Presumably, changes in the expression of BAZ1B played a role in the domestication process.

Neural Crest Deficits and Williams Syndrome

As it turns out, there are two genetic disorders in modern humans that involve neural crest cells: Williams-Beuren syndrome (also called Williams syndrome) and Williams-Beuren region duplication syndrome. These genetic disorders involve the deletion or duplication, respectively, of a region of chromosome 7 (7q11.23). This chromosomal region harbors 28 genes. Craniofacial defects and altered cognitive and behavioral traits characterize these disorders. Specifically, people with these syndromes have cognitive limitations, smaller skulls, and elf-like faces, and they display excessive friendliness.

Among the 28 genes impacted by the two disorders is the human version of BAZ1B. This gene codes for a type of protein called a transcription factor. (Transcription factors play a role in regulating gene expression.)

The Role of BAZ1B in Neural Crest Cell Biology

To gain insight into the role BAZ1B plays in neural crest cell biology, the European research team developed induced pluripotent stem cell lines from (1) four patients with Williams syndrome, (2) three patients with Williams-Beuren region duplication syndrome, and (3) four people without either disorder. Then, they coaxed these cells in the laboratory to develop into neural crest cells.

Using a technique called RNA interference, they down-regulated BAZ1B in all three types of neural crest cells. By doing this, the researchers learned that changes in the expression of this gene altered the migration rates of the neural crest cells. Specifically, they discovered that neural crest cells developed from patients with Williams-Beuren region duplication syndrome migrated more slowly than control cells (generated from test subjects without either syndrome) and neural crest cells derived from patients with Williams syndrome migrated more rapidly than control cells.

The discovery that the BAZ1B gene influences neural crest cell migration is significant because these cells have to migrate to precise locations in the developing embryo to give rise to distinct cell types and tissues, including those that form craniofacial features.

Because BAZ1B encodes for a transcription factor, when its expression is altered, it alters the expression of genes under its control. The team discovered that 448 genes were impacted by down-regulating BAZ1B. They learned that many of these impacted genes play a role in craniofacial development. By querying databases of genes that correlate with genetic disorders, researchers also learned that, when defective, some of the impacted genes are known to cause disorders that involve altered facial development and intellectual disabilities.

Lastly, the researchers determined that the BAZ1B protein (again, a transcription factor) targets genes that influence dendrite and axon development (which are structures found in neurons that play a role in transmissions between nerve cells).

BAZ1B Gene Expression in Modern and Archaic Humans

With these findings in place, the researchers wondered if differences in BAZ1B gene expression could account for anatomical and cognitive differences between modern humans and archaic humans—hominins such as Neanderthals and Denisovans. To carry out this query, the researchers compared the genomes of modern humans to Neanderthals and Denisovans, paying close attention to DNA sequence differences in genes under the influence of BAZ1B.

This comparison uncovered differences in the regulatory region of genes targeted by the BAZ1B transcription factor, including genes that control neural crest cell activities and craniofacial anatomy. In other words, the researchers discovered significant genetic differences in gene expression among modern humans and Neanderthals and Denisovans. And these differences strongly suggest that anatomical and cognitive differences existed between modern humans and Neanderthals and Denisovans.

Did Humans Domesticate Themselves?

The researchers interpret their findings as evidence for the self-domestication hypothesis—the idea that we domesticated ourselves after the evolutionary lineage that led to modern humans split from the Neanderthal/Denisovan line (around 600,000 years ago). In other words, just as modern humans domesticated dogs, cats, cattle, and sheep, we domesticated ourselves, leading to changes in our anatomical features that parallel changes (such as friendlier faces) in the features of animals we domesticated. Along with these anatomical changes, our self-domestication led to the high levels of cooperativeness characteristic of modern humans.

On one hand, this is an interesting account that does seem to have some experimental support. But on the other, it is hard to escape the feeling that the idea of self-domestication as the explanation for the origin of modern humans is little more than an evolutionary just-so story.

It is worth noting that some evolutionary biologists find this account unconvincing. One is William Tecumseh Fitch III—an evolutionary biologist at the University of Vienna. He is skeptical of the precise parallels between animal domestication and human self-domestication. He states, “These are processes with both similarities and differences. I also don’t think that mutations in one or a few genes will ever make a good model for the many, many genes involved in domestication.”2

Adding to this skepticism is the fact that nobody has anything beyond a speculative explanation for why humans would domesticate themselves in the first place.

Genetic Differences Support the Idea of Human Exceptionalism

Regardless of the mechanism that produced the genetic differences between modern and archaic humans, this work can be enlisted in support of human uniqueness and exceptionalism.

Though the claim of human exceptionalism is controversial, a minority of scientists operating within the scientific mainstream embrace the idea that modern humans stand apart from all other extant and extinct creatures, including Neanderthals and Denisovans. These anthropologists argue that the following suite of capacities uniquely possessed by modern humans accounts for our exceptional nature:

  • symbolism
  • open-ended generative capacity
  • theory of mind
  • capacity to form complex social systems

As human beings, we effortlessly represent the world with discrete symbols. We denote abstract concepts with symbols. And our ability to represent the world symbolically has interesting consequences when coupled with our abilities to combine and recombine those symbols in a countless number of ways to create alternate possibilities. Our capacity for symbolism manifests in the form of language, art, music, and even body ornamentation. And we desire to communicate the scenarios we construct in our minds with other human beings.

But there is more to our interactions with other human beings than a desire to communicate. We want to link our minds together. And we can do this because we possess a theory of mind. In other words, we recognize that other people have minds just like ours, allowing us to understand what others are thinking and feeling. We also have the brain capacity to organize people we meet and know into hierarchical categories, allowing us to form and engage in complex social networks. Forming these relationships requires friendliness and cooperativeness.

In effect, these qualities could be viewed as scientific descriptors of the image of God, if one adopts a resemblance view for the image of God.

This study demonstrates that, at a genetic level, modern humans appear to be uniquely designed to be friendlier, more cooperative, and less aggressive than other hominins—in part accounting for our capacity to form complex hierarchical social structures.

To put it differently, the unique capability of modern humans to form complex, social hierarchies no longer needs to be inferred from the fossil and archaeological records. It has been robustly established by comparative genomics in combination with laboratory studies.

A Creation Model Perspective on Human Origins

This study not only supports human exceptionalism but also affirms RTB’s human origins model.

RTB’s biblical creation model identifies hominins such as Neanderthals and the Denisovans as animals created by God. These extraordinary creatures possessed enough intelligence to assemble crude tools and even adopt some level of “culture.” However, the RTB model maintains that these hominids were not spiritual creatures. They were not made in God’s image. RTB’s model reserves this status exclusively for Adam and Eve and their descendants (modern humans).

Our model predicts many biological similarities will be found between the hominins and modern humans, but so too will significant differences. The greatest distinction will be observed in cognitive capacity, behavioral patterns, technological development, and culture—especially artistic and religious expression.

The results of this study fulfill these two predictions. Or, to put it another way, the RTB model’s interpretation of the hominins and their relationship to modern humans aligns with “mainstream” science.

But what about the similarities between the genetic fingerprint of modern humans and the genetic changes responsible for animal domestication that involve BAZ1B and genes under its influence?

Instead of viewing these features as traits that emerged through parallel and independent evolutionary histories, the RTB human origins model regards the shared traits as reflecting shared designs. In this case, through the process of domestication, modern humans stumbled upon the means (breeding through artificial selection) to effect genetic changes in wild animals that resemble some of the designed features of our genome that contribute to our unique and exceptional capacity for cooperation and friendliness.

It is true: studying the domestication process does, indeed, tell us something exceptionally important about who we are.

Resources

Endnotes
  1. Matteo Zanella et al., “Dosage Analysis of the 7q11.23 Williams Region Identifies BAZ1B as a Major Human Gene Patterning the Modern Human Face and Underlying Self-Domestication,” Science Advances 5, no. 12 (December 4, 2019): eaaw7908, doi:10.1126/sciadv.aaw7908.
  2. Michael Price, “Early Humans Domesticated Themselves, New Genetic Evidence Suggests,” Science (December 4, 2019), doi:10.1126/science.aba4534.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design

Ancient DNA Indicates Modern Humans Are One-of-a-Kind

By Fazale Rana – February 19, 2020

The wonderful thing about tiggers
Is tiggers are wonderful things!
Their tops are made out of rubber
Their bottoms are made out of springs!
They’re bouncy, trouncy, flouncy, pouncy
Fun, fun, fun, fun, fun!
But the most wonderful thing about tiggers is
I’m the only one!1

With eight grandchildren and counting (number nine will be born toward the end of February), I have become reacquainted with children’s stories. Some of the stories my grandchildren want to hear are new, but many of them are classics. It is fun to see my grandchildren experiencing the same stories and characters I enjoyed as a little kid.

Perhaps my favorite children’s book of all time is A. A. Milne’s (1882–1956) Winnie-the-Pooh. And of all the characters that populated Pooh Corner, my favorite character is the ineffable Tigger—the self-declared one-of-a-kind.

blog__inline--ancient-dna-indicates-modern-humans-1
A. A. Milne. Credit: Wikipedia

For many people (such as me), human beings are like Tigger. We are one-of-a-kind among creation. As a Christian, I take the view that we are unique and exceptional because we alone have been created in God’s image.

For many others, the Christian perspective on human nature is unpopular and offensive. Who are we to claim some type of special status? They insist that humans aren’t truly unique and exceptional. We are not fundamentally different from other creatures. If anything, we differ only in degree, not kind. Naturalists and others assert that there is no evidence that human beings bear God’s image. In fact, some would go so far as to claim that creatures such as Neanderthals were quite a bit like us. They maintain that these hominins were “exceptional,” just like us. Accordingly, if we are one-of-a-kind it is because, like Tigger, we have arrogantly declared ourselves to be so, when in reality we are no different from any of the other characters who make their home at Pooh Corner.

Despite this pervasive and popular challenge to human exceptionalism (and the image-of-God concept), there is mounting evidence that human beings stand apart from all extant creatures (such as the great apes) and extinct creatures (such as Neanderthals). This growing evidence can be marshaled to make a scientific case that as human beings we, indeed, are image bearers.

As a case in point, many archeological studies affirm human uniqueness and exceptionalism. (See the Resources section for a sampling of some of this work.) These studies indicate that human beings alone possess a suite of characteristics that distinguish us from all other hominins. I regard these qualities as scientific descriptors of the image of God:

  • Capacity for symbolism
  • Ability for open-ended manipulation of symbols
  • Theory of mind
  • Capacity to form complex, hierarchical social structures

Other studies have identified key differences between the brains of modern humans and Neanderthals. (For a sample of this evidence see the Resources section.) One key difference relates to skull shape. Neanderthals (and other hominins) possessed an elongated skull. In contradistinction, our skull shape is globular. The globularity allows for the expansion of the parietal lobe. This is significant because an expanded parietal lobe explains a number of unique human characteristics:

  • Perception of stimuli
  • Sensorimotor transformation (which plays a role in planning)
  • Visuospatial integration (which provides hand-eye coordination)
  • Imagery
  • Self-awareness
  • Working and long-term memory

Again, I connect these scientific qualities to the image of God.

Now, two recent studies add to the case for human exceptionalism. They involve genetic comparisons of modern humans with both Neanderthals and Denisovans. Through the recovery and sequencing of ancient DNA, we have high quality genomes for these hominins that we can analyze and compare to the genomes of modern humans.

While the DNA sequences of protein-coding genes in modern human genomes and the genomes of these two extant hominins is quite similar, both studies demonstrate that the gene expression is dramatically different. That difference accounts for anatomical differences between humans and these two hominins and suggests that significant cognitive differences exist as well.

Differences in Gene Regulation

To characterize gene expression patterns in Neanderthals and Denisovans and compare them to modern humans, researchers from Vanderbilt University (VU) used statistical methods to develop a mathematical model that would predict gene expression profiles from the DNA sequences of genomes.2 They built their model using DNA sequences and gene expression data (measured from RNA produced by transcription) for a set of human genomes. To ensure that their model could be used to assess gene expression for Neanderthals and Denisovans, the researchers paid close attention to the gene expression pattern for genes in the human genome that were introduced when modern humans and Neanderthals presumably interbred and compared their expression to human genes that were not of Neanderthal origin.

blog__inline--ancient-dna-indicates-modern-humans-2The Process of Gene
Expression.
Credit: Shutterstock

With their model in hand, the researchers analyzed the expression profile for nearly 17,000 genes from the Altai Neanderthal. Their model predicts that 766 genes in the Neanderthal genome had a different expression profile than the corresponding genes in modern humans. As it turns out, the differentially expressed genes in the Neanderthal genomes failed to be incorporated into the human genome after interbreeding took place, suggesting to the researchers that these genes are responsible for key anatomical and physiological differences between modern humans and Neanderthals.

The VU investigators determined that these 766 deferentially expressed genes play roles in reproduction, forming skeletal structures, and the functioning of cardiovascular and immune systems.

Then, the researchers expanded their analysis to include two other Neanderthal genomes (from the Vindija and Croatian specimens) and the Denisovan genome. The researchers learned that the gene expression profiles of the three Neanderthal genomes were more similar to one another than they were to either the gene expression patterns of modern human and Denisovan genomes.

This study clearly demonstrates that significant differences existed in the regulation of gene expression in modern humans, Neanderthals, and Denisovans and that these differences account for biological distinctives between the three hominin species.

Differences in DNA Methylation

In another study, researchers from Israel compared gene expression profiles in modern human genomes with those from and Neanderthals and Denisovans using a different technique. This method assesses DNA methylation.3 (Methylation of DNA downregulates gene expression, turning genes off.)

Methylation of DNA influences the degradation process for this biomolecule. Because of this influence, researchers can determine the DNA methylation pattern in ancient DNA by characterizing the damage to the DNA fragments isolated from fossil remains.

Using this technique, the researchers measured the methylation pattern for genomes of two Neanderthals (Altai and Vindija) and a Denisovan and compared these patterns with genomes recovered from the remains of three modern humans, dating to 45,000 years in age, 8,000 years in age, and 7,000 years in age, respectively. They discovered 588 genes in modern human genomes with a unique DNA methylation pattern, indicating that these genes are expressed differently in modern humans than in Neanderthals and Denisovans. Among the 588 genes, researchers discovered some that influence the structure of the pelvis, facial morphology, and the larynx.

The researchers think that differences in gene expression may explain the anatomical differences between modern humans and Neanderthals. They also think that this result indicates that Neanderthals lacked the capacity for speech.

What Is the Relationship between Modern Humans and Neanderthals?

These two genetic studies add to the extensive body of evidence from the fossil record, which indicates that Neanderthals are biologically distinct from modern humans. For a variety of reasons, some Christian apologists and Intelligent Design proponents classify Neanderthals and modern humans into a single group, arguing that the two are equivalent. But these two studies comparing gene regulation profiles make it difficult to maintain that perspective.

Modern Humans, Neanderthals, and the RTB Human Origins Model

RTB’s human origins model regards Neanderthals (and other hominins) as creatures made by God, without any evolutionary connection to modern humans. These extraordinary creatures walked erect and possessed some level of intelligence, which allowed them to cobble together tools and even adopt some level of “culture.” However, our model maintains that the hominins were not spiritual beings made in God’s image. RTB’s model reserves this status exclusively for modern humans.

Based on our view, we predict that biological similarities will exist among the hominins and modern humans to varying degrees. In this regard, we consider the biological similarities to reflect shared designs, not a shared evolutionary ancestry. We also expect biological differences because, according to our model, the hominins would belong to different biological groups from modern humans.

We also predict that significant cognitive differences would exist between modern humans and the other hominins. These differences would be reflected in brain anatomy and behavior (inferred from the archeological record). According to our model, these differences reflect the absence of God’s image in the hominins.

The results of these two studies affirm both sets of predictions that flow from the RTB human origins model. The differences in gene regulation between modern human and Neanderthals is precisely what our model predicts. These differences seem to account for the observed anatomical differences between Neanderthals and modern humans observed from fossil remains.

The difference in the regulation of genes affecting the larynx is also significant for our model and the idea of human exceptionalism. One of the controversies surrounding Neanderthals relates to their capacity for speech and language. Yet, it is difficult to ascertain from fossil remains if Neanderthals had the anatomical structures needed for the vocalization range required for speech. The differences in the expression profiles for genes that control the development and structure of the larynx in modern humans and Neanderthals suggests that Neanderthals lacked the capacity for speech. This result dovetails nicely with the differences in modern human and Neanderthal brain structure, which suggest that Neanderthals also lacked the neural capacity for language and speech. And, of course, it is significant that there is no conclusive evidence for Neanderthal symbolism in the archeological record.

With these two innovative genetic studies, the scientific support for human exceptionalism continues to mount. And the wonderful thing about this insight is that it supports the notion that as human beings we are the only ones who bear God’s image and can form a relationship with our Creator.

Resources

Behavioral Differences between Humans and Neanderthals

Biological Differences between Humans and Neanderthals

Endnotes
  1. Richard M. Sherman and Robert B. Sherman, composers, “The Wonderful Thing about Tiggers” (song), released December 1968.
  2. Laura L. Colbran et al., “Inferred Divergent Gene Regulation in Archaic Hominins Reveals Potential Phenotypic Differences,” Nature Evolution and Ecology 3 (November 2019): 1598-606, doi:10.1038/s41559-019-0996-x.
  3. David Gokhman et al., “Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan,” Science 344, no. 6183 (May 2, 2014): 523–27, doi:1126/science.1250368; David Gokhman et al., “Extensive Regulatory Changes in Genes Affecting Vocal and Facial Anatomy Separate Modern from Archaic Humans,” bioRxiv, preprint (October 2017), doi:10.1101/106955.

Reprinted with permission by the author

Original article at:

https://reasons.org/explore/blogs/the-cells-design