Recombination happens often in bats that carry many viruses known to infect humans. The SARS-CoV-2 virus shares 96% of its RNA genetic material with a virus found in a bat in a cave in Yunnan, China, which suggests--although it does not prove--that this virus or some immediately ancestral virus came from bats. The SARS-CoV-2 virus differs in one critical respect from this similar virus found in the rat. The spike proteins of coronaviruses have a receptor-binding domain (RBD) that connects to the membrane of the host cell and allows the virus to enter the cell. This is the key that unlocks the cell so that the virus can invade the cell and then hijack its metabolic machinery for reproducing new viruses that then break out of the cell for transmission to other host cells. The SARS-CoV-2 virus has a particularly efficient binding domain adapted for entering human cells. This binding domain differs in important ways from the binding domain of the Yunnan bat virus, which seems to be unable to infect humans.
A scaly anteater called the pangolin carries a coronavirus that has a receptor-binding domain almost identical to the RBD of the SARS-CoV-2 virus. But the rest of this coronavirus in the pangolin is only 90% genetically similar to SARS-CoV-2. So there is debate among virologists over whether the pangolin could have been the intermediary animal between bats and humans for the evolution of SARS-CoV-2.
So the SARS-CoV-2 virus might have evolved by natural selection in an animal host (a bat or a pangolin) before it jumped into a human. Or an ancestor of this virus might have jumped into humans, and then it might have evolved into SARS-CoV-2 through adaptation to its human host cells.
It is unlikely that SARS-CoV-2 was designed in a lab by genetic engineering because its genome does not show any of the standard genetic tools used by genetic engineering scientists (Andersen et al. 2020).
Although it cannot be proven one way or the other, one can infer from this that the most plausible explanation for the SARS-CoV-2 virus is that it emerged not by human genetic engineering but by evolution through natural selection.
On his popular blog, P. Z. Myers--a self-described "godless liberal" who fervently defends Darwinian evolution against creationists and intelligent design proponents--has concluded: "Sorry, conspiracy theorists. The best explanation is evolution and natural selection, not Evil Intelligent Design."
Michael Egnor, an advocate of intelligent design theory affiliated with the Discovery Institute, responded to Myers' blog post by agreeing with him that evolution by natural selection can explain the origin of SARS-CoV-2. But he also insisted that this shows the failure of Darwinian evolution as an explanation for the origin of living species. He wrote: "There is another lesson about design and evolution to be learned from scientific research on this virus. Natural selection, if understood as undirected variation and differential reproductive success, is a destructive process. Natural selection destroys biological functional complexity--it produces diseases, cancer, and pandemics. It weakens and kills. Natural selection does to living organisms what rust does to a machine. Natural selection corrodes and destroys life, and plays no role in creating it."
Myers responded by claiming that Egnor was wrong about this: "Not for the virus, it wasn't a destructive process. What was undergoing natural selection here was the virus, not us, and it has acquired attributes that make it wildly successful--it is now colonizing vast fields of billions of human beings, producing uncountable numbers of progeny, infecting more people at an accelerating rate. The virus is stronger and thriving thanks to those features, and doing very well thank you very much." It is also possible, he observed, that natural selection could be working through the viral pandemic attack on human beings to make the human species more resistant to SARS-CoV-19, which would be a constructive process in improving the functional complexity of the human immune system.
Egnor responded by claiming that Myers fails to see how the evolution of SARS-CoV-2 by natural selection of chance variation presupposes the intelligent design of those animal species (bats and humans) that serve as hosts for this parasitic virus, which cannot be explained by undirected evolution. It is not even clear that viruses are living beings, because unlike living species, viruses cannot reproduce themselves on their own. They reproduce only by parasitically using the metabolic machinery of the living cells that they invade. And if viruses are not alive, then the evolution of viruses through random mutation and differential reproduction does not show the evolution of life. "The coronavirus's evolution--the pandemic--depends on the living specified complexity of humans and bats. Intelligent design in nature is the prerequisite for all natural selection--nature without teleology would be chaos, and no evolution at all."
Egnor claimed that his point here was recognized by Aristotle. "Aristotle saw this in his definition of chance in nature--chance is the accidental conjunction of purposeful events. Without purpose there can e no chance. His example is instructive: he considered a farmer who ploughs his field and by chance discovers a treasure buried by someone else. The treasure is discovered by chance, but everything else--the farmer's ownership of the field, his decision to plough it, the accumulation and burial of the treasure by the other man--is purposeful, and in fact the only reason the accident of discovery happened is because it is embedded in a world of purpose. Chance can't happen--the word has no meaning--in an entirely accident world. Chance presupposes design."
Notice what Egnor does here: he jumps from claiming "intelligent design in nature" to Aristotle's account of human intelligent design. Here he employs the sophistical technique that runs through the intelligent design rhetoric of the Discovery Institute--the fallacy of equivocation in conflating human intelligent design, which we know by ordinary experience, and divine intelligent design, which we do not know by ordinary experience. I have written about this here and here.
Notice also that in saying that viruses show how "natural selection corrodes and destroys life and plays no role in creating it," Egnor ignores that fact that most viruses support life in mutualistic relationships with plants and animals. So, for example, we know that viruses are part of the human microbiome in the human gut, and that some parts of the human genome originated from viruses.
Egnor also ignores the fact that even if viruses are not living, other infectious pathogens--such as bacteria, fungi, protozoa, and helminths (worms)--clearly are living things; and they evolve by natural selection just as viruses do.
Contrary to Egnor's argument, our explanation of the evolution of SARS-CoV-2 and other parasitic pathogens by natural selection does not depend upon any assumption of divine intelligent design.
THE DARWINIAN ETHICS OF A VIRUS
Any scientific account of the COVID-19 pandemic must explain why the SARS-CoV-2 virus is so good at being a bad virus.
In the scientific writing, it is common to see it said that the SARS-CoV-2 virus is better than the SARS-CoV virus, because SARS-CoV-2 is much more effective than SARS-CoV in successfully infecting host cells (Cyranoski 2020). SARS-CoV-2 is good at forcing entry into human cells because this virus has a receptor-binding domain that has evolved for a particularly snug fit with the membrane of human cells in the upper respiratory tract and the lungs.
But this good functional complexity of SARS-CoV-2 makes it a bad virus for us. What's good for this parasitic virus is bad for its human hosts.
This manifests the general character of Darwinian ethics. There is no cosmic good for all living beings, because what is good is relative to each species, and what is good for one species can be bad for other species.
It is possible, however, for different species to enter relationships of symbiotic accommodation in which one species cooperates with another for mutual benefit. And so, for example, the viruses and bacteria in the human gut benefit themselves even as they benefit their human host. In fact, the number of these viruses and bacteria in the human body exceed the number of human cells. Walt Whitman was right: "I am large, I contain multitudes" (Yong 2016).
To see why SARS-CoV-2 is so good in causing a bad pandemic, one needs to follow the virus through the five steps in his invasion of human cells (Cyranoski 2020).
First, one of the virus's spike proteins has a special receptor binding domain that binds to a receptor enzyme on the surface of human cells, which is called angiotensin converting enzyme (ACE2). This enzyme helps to regulate blood pressure, which is good for us, but it's bad for us when this enzyme is used by the virus as the first step in its invasion of our cells.
Second, furin or another enzyme on the surface of the human cell breaks the spike protein at one of its cleavage sites.
Third, this releases small chains of amino acids that fuse the viral membrane with the membrane of the human cell.
Fourth, the fusion of the membranes allows the virus's RNA to enter the human cell, where it hijacks cellular machinery to produce more viral RNA and proteins that are assembled into new viral particles.
Fifth, the new viral particles break out of the human cell, and these new particles can then either attack other cells or leave the body and infect other people.
While the four coronaviruses that cause common colds are most successful in attacking the upper respiratory tract, and the MERS-CoV and SARS-CoV viruses are most successful in attacking cells in the lungs, the SARS-CoV-2 viruses are good at doing both, which makes them more effectively infectious. This might explain the differences in symptoms. If the virus starts in our nose or throat, and does not go into the lungs, this might produce a cough and fever, but not much more. If the virus gets into our lungs, the attack on our respiratory system might become more severe, and even kill some of us.
So, for these and other reasons, SARS-CoV-2 is good at being a bad virus.
THE BIBLICAL UNDERSTANDING OF A VIRUS
Some of the scientists who are studying SARS-CoV-2 and looking for a way to fight it are Christians, who are also trying to understand how the Bible might explain the spiritual meaning of this virus and the pandemic that it has caused. Perhaps the most prominent of these Christian scientists is Francis Collins. As the Director of the U.S. National Institutes of Health, Collins is supervising most of the research studying the COVID-19 pandemic and looking for a vaccine. He is famous as the former leader of the Human Genome Project. He is also famous for arguing that natural science and religious faith are not in conflict, because science and faith can actually reinforce one another. A critical part of his argument is that religious believers who reject Darwinian evolution as atheistic are mistaken, because Christians can accept the scientific truth of evolution while seeing natural evolution as God's way of carrying out His creative plan. To promote this kind of thinking, he founded BioLogos as an organization defending the idea of "evolutionary creation." Last week, Collins was honored as the 2020 Templeton Prize Laureate for promoting progress in religious thought through science. (The Templeton Prize website has a lot of material on this.)
I have written a series of posts on Collins as a theistic evolutionist here, here, here, here, here, here, here, and here.
At BioLogos, there is a podcast with Collins on "Where Is God in a Pandemic?" He says that he has been troubled by the old question as to why God permits evil and suffering--such as a pandemic. He says he finds consolation in two Biblical verses. Psalm 46:1-2 promises "God is our refuge and strength, a very present help in trouble. Therefore will not we fear." Joshua 1:9 commands: "Be strong and of good courage; be not afraid, neither be thou dismayed; for the Lord thy God is with thee."
Collins does not hold God responsible for the pandemic. He does not suggest that God is using the pandemic to punish us. Collins probably agrees with Jim Stump, Vice President at Biologos, on this point. As I have indicated in a previous post, Stump argues that God does not intentionally design natural evils like viral pandemics, which actually arise as unavoidable side effects of the naturally good world that God has created. Human life as we know it would be impossible without viruses. Most viruses on Earth are infecting bacteria and thus slowing down their reproduction, so that rapidly reproducing bacteria do not overwhelm us. But for viruses to do that, they must mutate rapidly, and that rapid mutation can sometimes create viruses--like SARS-CoV-2--that are dangerous to human beings. Evolution creates trade-offs in which we have to take the bad with the good.
Collins and Stump reject the traditional way in which some Christians have solved the problem of natural evil by saying that it's a consequence of the Fall. Adam and Eve were created by God to live in a naturally good world, free from death and suffering, but when they yielded to the temptation of the serpent in the Garden of Eden, they sinned, and God's curse on them for their sin included a curse on nature, so that human beings would henceforth suffer and die from natural threats to life, including deadly viruses. In this way, the COVID-19 pandemic is God's punishment for our Original Sin inherited from Adam and Eve.
In this podcast, Gary Bates of Creation Ministries International asserts the literal truth of the Fall in Genesis 2 as the explanation of the COVID-19 pandemic. Most viruses are beneficial for human beings, but some become bad, and this arises as a consequence of God's curse on Adam and Eve.
Although a scientific creationist like Bates (or Ken Ham) would disagree with theistic evolutionists like Collins and Stump on this point, they all agree that as Christians they can take consolation in their faith that they will be redeemed for eternal life after death, and therefore they need not be thrown into despair by the pandemic's reminder of human mortality.
They also agree that in responding to the pandemic, Christians should follow the guidance of the natural scientists--the virologists and epidemiologists--studying the pandemic.
They also agree that since Christians believe that all human beings are "created in the image of God," this gives ultimate value to every human life, and therefore the governmental orders for lockdowns for minimizing COVID-19 deaths must be obeyed, regardless of the catastrophic economic costs. To engage in a cost-benefit moral analysis to see if the economic costs of the shutdown outweigh the health benefits would violate Christian morality.
But is that really true? Shouldn't Christians be morally concerned about the devastating human costs of lockdowns--including the human lives that will be lost or ruined as a consequence of the global Great Depression caused by the lockdowns?
Andersen, Kristian, et al. 2020. "The Proximal Origin of SARS-CoV-2." Nature Medicine 26:450-52.
Cyranoski, David. 2020. "Profile of a Killer Virus: The Complex Biology Powering the Coronavirus Pandemic." Nature 581:22-26.
Gorbalenya, Alexander, et al. 2020. "The Species Severe acute respiratory syndrom-related coronavirus: Classifying 2019-nCoV and Naming It SARS-CoV-2." Nature Microbiology 5:536-544.
Yong, Ed. 2016. I Contain Multitudes: The Microbes Within Us and a Grander View of Life. New York: HarperCollins Publishers.