This talk was presented at the God of Wonder NZCIS conference 2017 by Graeme Finlay

For further reading on evolution and creation see the multiple resources at Biologos

The relationship between biblical creation and biological evolution is often misconstrued. I provide two reasons why Christians may accept evolutionary biology and two reasons why they must do so. (1) People often regard creation and evolution as being opposing ideas. This is erroneous because these terms mean different things. Creation means the gift of existence; evolution refers to change within created (existent) reality. There is no inconsistency in believing that the created universe has an unfolding evolving history. (2) People often assume that the creation stories of Genesis and the mechanistic accounts of evolutionary biologists are incompatible. However, Genesis uses stock stories and metaphors of the ancient world to proclaim the supremacy and goodness of Israel’s God. Genesis provides no data for science, but describes a God of wisdom and faithfulness, who creates a good universe. This radically new understanding of reality facilitated the development of science. (3) Since the late 1990s, DNA sequencing has made it possible to compare the genomes of multiple species. Comparative genomics provides unprecedented and compelling evidence for evolutionary change. (4) Biblical faith is an interpretation of history. Evolutionary biology is a form of history. Inevitably, we interpret history. An interpretation of evolution as a part of God’s purposive plan for creation is highly congenial to biblical thought. 

Science developed as an expression of Christian worship.[1] Scientific research reveals a wonderful world. Cell and molecular biology have always fascinated me. The wonders of DNA and its four-letter code (A, C, G, T) were part of this fascination, and I became a cancer cell biologist. Familiarity with cancer genetics took me, by surprise, into evolutionary genetics.

1          Creation and evolution

One of the wonders disclosed by science is the unfolding (evolutionary) history of the cosmos and of organisms. There is a widespread perception that creation and evolution are incompatible ideas. These words, however, have different meanings. Appreciation of those meanings removes all scope for conflict.

Creation indicates the gift of existence, of being. St Paul writes that God’s ‘command brings into being what did not exist’, and ‘… all things were created by him and all things exist through him and for him’.[1] Theologian David Hart has stated that God is that reality ‘upon which all else depends; otherwise nothing could exist at all’.[2] The idea of creation is a fundamental aspect of a Christian world view, one that we accept (or reject) as an act of faith. That there should be a universe of exquisite order and potentiality for life, mind and beauty is compatible with divine creation.

Evolution is change within an ordered creation. A static universe, one that does not undergo change with time, would be a very boring place (if in fact it is conceivable – apart from being frozen in the blackness of absolute zero). Cosmic and biological evolution are descriptions of that change, and may be understood, in all consistency, as aspects of a created universe. It is entirely consistent to accept as true both biblical creation and biological evolution. God’s world has an unfolding (evolving) history. God is creator of evolution.

To put it another way: we may in all rationality accept both creation and evolution as being true. But we may not rationally regard them as mutually exclusive.

2          Genesis and phylogenesis

The relation between Scripture – especially the creation stories in the earliest chapters of Genesis – and evolutionary accounts of the world has occasioned controversy. The ongoing debate is framed in terms of whether we believe the account given by Genesis or that given by science. Again, it is important to recognise the genre and purpose of these narratives.  Archaeological research over the last century has discovered many creation stories and myths from the Ancient Near East (ANE) that circulated over a period of 2,000 years. These include the Gilgamesh Epic, the Atrahasis Epic and the Sumerian King List (Figure 1). The Genesis stories share many motifs with these.[3]

     
Figure 1. Creation stories (the Gilgamesh and Atrahasis epics) and Sumerian King list from the Ancient near East. Wikipedia, public domain.

Scholars agree that the author(s) of Genesis made use of literary motifs that were endemic to the ANE, but adapted them to proclaim a revolutionary new understanding of God, humanity and the world. Genesis is not primitive tribal legend, but an artfully constructed, highly subversive expression of Israel’s faith. It is sophisticated polemic against the organismic universe. It incorporated familiar forms used in the ancient myths, but filled them with unfamiliar content.[4] Genesis displaced the crude gods of the ANE by the one peerless Creator God of Israel. Table 1 shows examples of the different views of reality portrayed.

Table 1. Ancient epics and Genesis: same form, contrasting message

Babylonian epics Genesis
divinity many gods

fractious

one God

holy

sun, moon, stars gods creatures
sea monsters represent chaos creatures
humanity an afterthought

made from the blood of a god

progressing

the climax of creation

made from earth

sinful

temple tower of Babel ‘Gate of God’ ‘confusion’

It is a huge mistake to treat Genesis and the historical sciences as competing accounts of history. Correctly understood, they are complementary. Genesis describes a rational and good God who is the source of an ordered and good creation. Science seeks to describe that order. Genesis presents a concept of creation in which there are only two ultimate realities: God and his creation. There are no spirits or gods lurking in the stars, trees or animals – nature is de-deified. This means that scientists are free to investigate the world around them. It follows that the history of life and its record in the DNA of every living organism is wholly open to our perusal.

3          Comparative genomics

Genome sequencing has revolutionised biology. The means by which we may discover histories, inscribed in DNA, will be exemplified by research on snakes (how they lost their legs), birds (how they lost their teeth), and humans (how they relate to the other primates). And the evidence is so compelling that it requires our acceptance of evolutionary history.

Snakes don’t have legs, but are descendants of creatures that did. During the embryonic development of most reptiles, birds and mammals, limb buds form in response to signals carried by a molecule called sonic hedgehog (seriously!). The gene encoding sonic hedgehog (SHH) is turned on when a short DNA sequence known as an enhancer binds one or more gene-activating proteins. Enhancers are so important that their sequences tend to be similar for distantly related species. (Such sequences are said to be conserved.) Figure 2 depicts enhancer sequences that drive SHH expression in multiple species. Strikingly, a stretch of 16 bases has been deleted from the enhancer DNA of all species of snakes investigated. Experimental introduction of this mutation into the SHH enhancer of mice produces pups without legs.[5]

We conclude two things. First, that snakes lost their ability to form limbs when a deletion knocked out the SHH enhancer. Perhaps by that time, snakes were developing new modes of locomotion and the loss of legs was no hindrance to them. Second, the deletion is the same in all snake species and, as complex mutations occur randomly and uniquely, all snake species must be descended from one ancestor – the ancestor in which that mutation occurred. These snake species are monophyletic.

Figure 2. Enhancer sequences that activate the SHH gene, with a 16-base deletion in snakes. Invariant bases are shown in bold type. The binding site for a gene-activating protein is highlighted (ref. 6).  

Birds are toothless wonders. The surface of teeth is composed of enamel, the hardest substance made by vertebrates.  Extant birds all lack teeth. Several genes that are dedicated to the production of enamel have been found in their genomes – but in highly degenerated forms. An example of a mutation in the gene encoding ameloblastin is depicted in Figure 3. The mutation is a ten-base deletion, as compared with sequences from two species of alligator (which retain teeth) and a turtle (which lacks teeth, and possesses alternative inactivating mutations). We conclude that this tooth-forming gene was inactivated by mutations including a ten-base deletion and that finches, ducks and chickens are descended from the one individual (indeed the one unique cell) in which this mutation occurred.[6]

Figure 3. Sequences from the ameloblastin (AMBN) gene, with a ten-base deletion (del 515-524) in birds (ref. 7).

Human evolutionary history has been disclosed by many genomic markers, and will be illustrated by a cunning type of virus. Retroviruses cause some significant diseases. One species of retrovirus causes an aggressive form of leukaemia. Another species, HIV, causes the acquired immunodeficiency syndrome, AIDS. When a retrovirus infects a cell, it inserts its piece of DNA into the DNA of the cell, at some randomly chosen, unique site. In this way, the viral DNA becomes a part of the cell’s genome and is transmitted to every descendant cell.

Figure 4 depicts a unique HIV insertion site in the DNA of a patient’s lymphocytes. The viral enzymes have selected, at random, a site in the cell’s genome, CCTTG, and have cut the DNA at this point. The HIV DNA, which is about 10,000 bases long, has been spliced into the genome in such a way that it is bracketed by duplications of the target site.[7]  Any cell that possesses the HIV genome at this point, marked by the characteristic target site duplications, is a descendent of the original cell in which the insertion occurred.

Figure 4. The insertion site of a retrovirus (HIV) in lymphocytes from a patient with AIDS.

The sequences are from HIV (top), normal human DNA (below) and a clone of the patient’s cells (centre). The target site CCTTG, and its duplications on each side of the viral inserted DNA are in bold and highlighted (ref. 8).

 

But we encounter retroviral DNA inserts in another context. Eight percent of the genome that each of us has inherited is composed of DNA sequence derived from retroviruses. Approximately 400,000 segments of retroviral DNA lie interspersed through each set of our chromosomal DNA. Each of these lengths of retroviral DNA infected a germ (reproductive) cell of one of our ancestors. These inherited retroviruses are known as endogenous retroviruses, ERVs. But when did they become domiciled in the genome?

Some ERVs of the ERV-K subtype entered the human germ-line in relatively recent human history: they are found in only a proportion of the human population. The rest of the human population (and other primate species) retain the uninterrupted target site. Figure 5 depicts the insertion site of an ERV-K found only in some humans. Anyone who possesses this particular insert must be descended from the same ancestor as the Neanderthal individual, who also possessed it.[8] An older insert is shared by all the great apes (but not by gibbons or monkeys). It follows that the insert arose in an ancestor of all the great apes (Figure 6).[9] Computer searches through multiple genomes for a selection of ERV-K inserts have resolved the phylogenetic relationships of all the higher primates (Figure 7). Eight inserts are shared by all the apes and by macaques (representing Old World Monkeys). This means that apes and macaques share common ancestors. Another eight inserts are shared by the apes but not by the macaques. These ERVs must have appeared in an ape ancestor, after the macaque lineage had branched off as part of the Old World Monkey group of species.[10]

 Figure 5. The insertion site of an endogenous retrovirus (of the ERV-K type) in some human genomes.

The sequences are from ERV-K (top), the uninterrupted DNA from some humans and from other apes (below) and ERV-interrupted DNA of a proportion of humans, including archaic humans (centre). The target site CTGGTC and its duplications on each side of the viral inserted DNA are in bold and highlighted (ref. 9).

 
Figure 6. The insertion site of an endogenous retrovirus (of the ERV-K type) in great ape genomes.

The sequences are from ERV-K (top), the uninterrupted DNA from gibbons, Old and New World Monkeys (below) and ERV-K-interrupted DNA of humans and other great apes (centre). The target site and its duplications on each side of the viral inserted DNA are in bold and highlighted (ref. 10).

 
Figure 7.  A phylogenetic tree, demonstrating the relationships of higher primates, based on the presence of particular ERV-K inserts (ref. 11).  

The distribution of other subtypes of ERVs leads to the same conclusion. A member of the ERV-W subtype is shared by all the ape species, including the lesser apes (gibbons), but not by the New World Monkeys, which retain the uninterrupted target site (Figure 8).[11] This example is particularly interesting: ERV genes usually decay, but the envelope gene of this retrovirus retains its protein-coding functionality, and now serves an essential role in the formation of the placenta. Viral envelop proteins enable virus particles to stick to cells; this domesticated protein enables cells to stick to each other and form the syncytiotrophoblast, the outermost layer of the placenta. A gene belonging to a pathogenic virus now functions as a gene that is essential for our foetal development.

As with ERV-K, the distribution of 212 members of the ERV-W subtype in primate species discloses our phylogenetic relationships (Figure 9).[12] An astonishing 129 individual inserts establish that macaques and apes are issue of the same ancestors.

Figure 8. The insertion site of an endogenous retrovirus (of the ERV-W type) in ape genomes.

The sequences are of the uninterrupted DNA from New World Monkeys (below) and ERV-W-interrupted DNA of humans, and other apes (above). The target site CAAC and its duplications on each side of the viral inserted DNA are in bold and highlighted (ref. 12).

 
Figure 9.  A phylogenetic tree, demonstrating the relationships of higher primates, based on the presence of particular ERV-W inserts (ref. 13).  

One more example will suffice. ERV9/LTR12C is another subtype of retrovirus that has invaded primate genomes. Figure 10 depicts a particular instance. This retrovirus inserted itself into the germline of an ancestor of the African great apes.[13] It is of interest because it appears to contribute to the control of the nearby RAE1 gene. This gene encodes a protein that exports messenger RNAs out of the nucleus.

The phylogeny obtained by computational analysis is the same as that that found with the other virus subtypes (Figure 11).[14] In this case, 31 inserts appeared in ancestors of macaques and apes, 81 in ancestors of the great apes, and 17 in ancestors of the African great apes. No new instances of the ERV9 subtype have appeared in our genome since then. Like the ERV-W viruses, this subtype seems to have died out – we hope!

Figure 10. The insertion site of an endogenous retrovirus (of the ERV-9/LTR12C type) in great ape genomes.

The sequences are from ERV9 (top), the uninterrupted DNA from orangutans, gibbons and monkeys (below) and ERV9-interrupted DNA of African great apes (centre). The target site ACAT and its duplications on each side of the viral inserted DNA are in bold and highlighted (ref. 14).

 

 

 
Figure 11.  A phylogenetic tree, demonstrating the relationships of higher primates, based on the presence of particular ERV9 inserts (ref. 15).  

This small selection of genome markers demonstrates that humans are descended from ancestors that we share with chimps, and (a little further back) with gorillas, and (a little further back) with orangutans, and gibbons and Old World Monkeys. The history extends far beyond this into deep time.[15]  The history inscribed in our DNA connects us indissolubly with ancient ancestors shared with other species. We are an evolved species. Christians must take that fact on board.

4          History and the purposes of God

Which brings us to the final point. Christian faith is based on events in history. Christians must think historically because they believe that God has revealed himself in the earthiness of history. The insight that we have arisen through a vast historical process is richly congruent with Christian thought.

The study of human history identifies patterns that appear also in biological history. A former Professor of History at Cambridge, Herbert Butterfield, argued that human history may be investigated in terms of its subtle processes. It is chancy and yet structured. There is catastrophe and yet progress. Ultimately, humans interpret what it might mean (Table 2).[16]

Table 2. Features shared by human and biological histories.

human history (Butterfield, ref. 17) biological history
process (78, 90, 92, 96, 110, ch 5) organisms acting out their given capacities
chanciness (93-95) chance (happenstance, contingency)
structure, pattern (68-70; 108-111, 123) necessity (lawfulness)
catastrophe (11, 78, ch 4 esp 113, 116) disease, suffering, and in humans, sin
progress (127-129) culmination in creatures that bear God’s image
interpretation (114-115, 148, 165-166) interpretation

Human and biological histories are characterised by process. Historians, including those who peruse DNA, are free to investigate every aspect of the interacting mechanisms that operate in history. Just as Butterfield saw both chanciness and structure in human history, biologists speak of the interacting polarities of chance (randomness) and necessity (lawfulness, predictability) as underlying evolutionary development. Christians see this interplay as God’s two gifts of freedom and reliability or order.[17]

Histories are messy. There is catastrophe. Evolution includes extinctions, the rise of pathogens, and the retrograde evolution of cancers, because it is an authentic, and therefore free, historical process. And yet the narrative from simple cells to complex brains inspires wonder. A materialist may dismiss this history as brute fact, and make the metaphysical leap of faith that dogmatises evolutionary history as being non-progressive, the random walk of a drunk. A Christian sees the cells-to-cerebra grand narrative as part of an overarching plan. The physical world is so structured that worshiping creatures would emerge. Perhaps evolution is a search engine, a motor, by which physical creatures may discover ‘the deeper realities of the universe.’[18] Chance and necessity so interact that at least one creature would discover the noetic, spiritual dimension in which it could hear God’s address.

Our evolutionary history is part of the wonder of a human-friendly universe. Why should such a universe even exist? It seems to point to a Creator. But there are no knockdown arguments that point to (or away from) God. Butterfield’s interpretation of history came from his conviction that the Creator had revealed himself in Jesus. ‘I am unable to see how a man can find the hand of God in secular history, unless he has first found that he has an assurance of it in his personal experience.’[19]

To Christians, the history of Jesus of Nazareth provides the hermeneutic key to interpreting history. As Wright states, it is only ‘the radically new thing that God did in the middle of history’ that gives ‘the meaning which that history would otherwise lack.[20] The advent of Jesus, including his death, resurrection and moral challenge, sets the seal on phylogenetic history as a part of the plan for the cosmos. We come back to St Paul, who wrote of the ‘secret plan which God will complete when the time is right … to bring all creation together, everything in heaven and on earth with Christ as head.’[21]

References

[1] Rom 4:17; 11:36; Acts 17:28; 1 Cor 11:12; Rev 4:11, GNB

[2] Hart DB. The Experience of God (New Haven: Yale University Press, 2013), 105-106

[3] Wagner R and Briggs A. The Penultimate Curiosity: How Science Swims in the Slipstream of Ultimate Questions (Oxford: Oxford University Press, 2016)

[4] Walton J. The Lost World of Genesis One (Downers Grove: IVP, 2009)

[5] Kvon EZ, Kamneva OK, Melo US et al (2016). Progressive loss of function

in a limb enhancer during snake evolution. Cell 167, 633; Leal F and Cohn MJ (2016). Loss and re-emergence of legs in snakes by modular evolution of sonic hedgehog and HOXD enhancers. Current Biology 26, 2966

[6] Meredith RW, Gatesy J and Springer MS (2013). Molecular decay of enamel matrix protein genes in turtles and other edentulous amniotes. BMC Evol Biol 13, 20

[7] Shao W, Shan J, Kearney MF et al (2016) Retrovirus integration database (RID): a public database for retroviral insertion sites into host genomes. Retrovirology 13, 47; the HIV-1 sequences are from O’Neil PK et al (2002) Mutational analysis of HIV-1 long terminal repeats… J Biol Chem 277, 38053

[8] Marchi E, Kanapin A, Byott M et al (2013) Neanderthal and Denisovan retroviruses in modern humans. Current Biology 23, R994; chimp, bonobo, gorilla, orang and gibbon sequences, NCBI database by BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi)

[9] Kahyo T, Yamada H, Tao H et al (2017). Insertionally polymorphic sites of human endogenous retrovirus-K (HML-2) with long target site duplications. BMC Genomics 18, 487; bonobo, gorilla, baboon, crab-eating macaque, green monkey, marmoset and squirrel monkey sequences were recovered by BLAST.

[10] Gemmell P, Hein J and Katzourakis J (2016). Phylogenetic analysis reveals that ERVs ‘die young’ but HERV-H is unusually conserved. PLoS Computational Biology 12, e1004964

[11] Bonnaud B, Beliaeff J, Bouton O et al (2005). Natural history of the ERVWE1 endogenous retroviral locus. Retrovirology 2, 57; bonobo and capuchin sequences were added by BLAST search (https://blast.ncbi.nlm.nih.gov/Blast.cgi)

[12] Grandi N, Cadeddu M, Blomberg J and Tramontano E (2016). Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes. Retrovirology 13, 67

[13] Jung Y-D, Lee H-E, Jo A et al (2017). Activity analysis of LTR12C as an effective regulatory element of the RAE1 gene. Gene 634, 22; primate sequences were from NCBI by BLAST; LTR12C consensus was from http://dfam.org/entry/DF0000402/model

[14] Gemmell et al (2016). PLoS Computational Biology 12, 52

[15] As described in my book, Human Evolution: Genes, Genealogies and Phylogenies (Cambridge: Cambridge University Press, 2013)

[16] Butterfield H. Christianity and History (Fontana, 1949)

[17] Polkinghorne J. Science and Creation (London: SPCK, 1988), 48; Science and Christian Belief (London: SPCK, 1994)

[18] Conway Morris S. The Deep Structure of Biology (West Conshohocken: Templeton Foundation Press, 2008), 62

[19] Butterfield, 140-141

[20] Wright NT. Paul and the Faithfulness of God (London: SPCK, 2013), 1211

[21] Ephesians 1:10

[1] Hannam J. God’s Philosophers: How the Medieval World Laid the Foundations of Modern Science (London: Icon Books, 2009); Wagner R and Briggs A. The Penultimate Curiosity: How Science Swims in the Slipstream of Ultimate Questions (Oxford: Oxford University Press, 2016)

The wonder of our inscribed history

Leave a Reply

Your email address will not be published.