April 7, 2020 | David F. Coppedge

Viruses in Context

A microbiologist explains the extreme abundances of viruses and the many good things they do for us.

Dr Joe Francis is professor of biology at The Master’s University, and dean of the school of science, mathematics, technology and health. With two colleagues, he presented a paper in the 2018 Proceedings of the International Conference on Creationism, “Bacteriophages as beneficial regulators of the mammalian microbiome.”

Recently Dr Francis shared some facts about viruses to put their role in the biosphere in context. He gave CEH permission to share his comments on how these facts may contribute to discussions about how viruses can be included in theodicy, the study of explanations for evil.

How many viruses do humans encounter in their daily lives? And what about plant and animals—what is their connection with viruses?

Dr Francis: We can easily estimate that 20,000 species of virus [are] associated with the human body.  Most of these are bacteriophages and I predict that they are helping to preserve the human bacterial microbiome.

The dominant non-bacteriophage viruses in the human gut are plant viruses… with probably hundreds of species. In comparison only approximately 200 animal viruses infect the human body and only reside in the body for a short period of time as they are cleared by the immune system.

We hear in the news about viruses jumping from animals to humans. How common is that? Do these ‘zoonotic’ viruses always cause trouble?

Probably less than 10 animal viruses remain in the human body for a lifetime like the herpes virus.

Two long term, life-time associated animal viruses are an engima:  The Torque Teno virus and the JC virus infecting a large percentage of humans who carry a “normal” load.  They are not known as pathogens, but in immunosuppressed individuals Torque teno has been associated with illness.

Since the focus on animal virus infection in humans has been on medically important viruses I would predict there might indeed be more commensal animal viruses in the human body.

How many viruses cause pandemics like the current SARS-CoV-2 virus?

Perhaps less than two dozen viruses have caused pandemics or important revolving epidemics, polio virus, smallpox, SARS, influenza, West Nile virus, rabies, ebola, etc. More than 66% of the 200 or so viruses that infect humans are zoonotic, and I think if you look [only] at those that cause serious life threatening infection, that number can be over 90%.  It may be that the animal source of these zoonotic viruses are playing a beneficial role in their hosts. But who is looking?

Are there any other things that viruses do for us or the biosphere?

Because cyanophages may be the most dominant virus on earth and they contribute to carbon recycling we can say that viruses are probably responsible for recycling of 50% of the world’s carbon.

I think we can say with confidence that most viruses … are beneficial to life on earth!

Dr Francis also shared these facts with CEH in an email:

Published papers predict 10,000 species of microbiome bacteria that live on us. Each bacteria species could have at least two bacteriophages. That’s how I came up with 20,000 as an estimate for human associated bacteriophages.

I forgot to mention that we have more endogenous retroviral sequences in our DNA than our typical functional genes.

In summary, viruses are a big part of our lives, and have been since creation. The Abstract of the paper in ICC says this about their functional purposes:

Much of the research on viruses has concentrated on their disease causing ability. The creation model biomatrix theory predicts that viruses play a beneficial role in cells and organisms. In this report we present a new theory which proposes that mammalian phages (bacteriophages), the most abundant organism associated with mammals, guard and regulate growth of the mammalian microbiome. We base this theory on nearly a century of published evidence that demonstrates that phage can insert into the bacterial genome and cover the surface of bacteria. We propose that this “cloaking” of the bacterial cell surface is an elegant mechanism whereby the normal flora bacteria are protected from immune detection and pathogenic bacteria can be directly lysed by the same phage. Additionally, both phage genome integration and cloaking can be used to prevent normal flora bacteria from conversion to a pathogenic state. Further support for the phage cloaking aspect of our theory has been demonstrated in recent studies which show that phage proteins bind specifically to microbial-associated molecular patterns (MAMPs), which are known to be the major ligands that activate the mammalian immune system. Although these phenomena have been documented separately over decades, we postulate for the first time that these functions work together to promote the integrity of the mammalian microbiome.

These facts can help guide discussions about so-called ‘natural evil.’ In the natural world, Dr Francis has discussed in lectures, one set of entities keeps another set of entities in check. Beneficial bacteria are good for our bodies, but could overrun our systems if not kept in check by bacteriophages. Viruses are kept in check by depending on particular hosts for their replication, and by the host’s immune system. Within their proper hosts, their numbers are kept in balance, and homeostasis is maintained.

Many aspects of the curse on sin in our fallen world could be due to (1) good things turned bad, (2) specific judgments God put on the world such as thorns on plants and hardship on agriculture, (3) Satan’s role in corrupting God’s good creation, or (4) God simply relaxing his controls on some aspects of creation, letting them degenerate over time. This includes the accumulation of mutations that cause aging and decay in the human body, and the gradual degeneration of the human genome (genetic entropy). The amazing thing is not that we get sick, but that many people can enjoy decades of strength and health this long after the fall.

Paul said to the pagans at Lystra, that the Creator God “did not leave himself without witness, for he did good by giving you rains from heaven and fruitful seasons, satisfying your hearts with food and gladness” (Acts 14:17). Paul used the goodness of God in creation to reach out to these pagans: “we bring you good news, that you should turn from these vain things to a living God, who made the heaven and the earth and the sea and all that is in them.”

In this pandemic, would should be our reaction? We should be thankful for what we have, do our part to help the pandemic slow down and stop, and carry on with diligence after it passes. God “knows our frame, that we are dust,” Psalm 103:14 says. David the psalmist continues,

15 As for man, his days are like grass;
    he flourishes like a flower of the field;
16 for the wind passes over it, and it is gone,
    and its place knows it no more.
17 But the steadfast love of the Lord is from everlasting to everlasting on those who fear him,
    and his righteousness to children’s children,
18 to those who keep his covenant
    and remember to do his commandments.
19 The Lord has established his throne in the heavens,
    and his kingdom rules over all.

In this week of remembering the passion of Christ, we can meditate on the fact that he came to give people eternal life. This required payment to remove our sins. He took our death for us, and now offers salvation freely. He told Martha, “I am the resurrection and the life. Whoever believes in me, though he die, yet shall he live, and everyone who lives and believes in me shall never die” (John 11:25). That’s the answer to evil: live and believe in Jesus. Because he paid our debt, his life is available to those who trust him and follow him. When he comes again, he will put away sin forever. Until then, our bodies are subject to degeneration and physical death—but our souls can be secure in him by faith. The faith he requires is not blind faith, but faith in the evidence he displayed by rising from the dead (I Corinthians 15). The evidence can give us courage through our trials. He told his disciples the night before his crucifixion, “In the world you will have tribulation. But take heart; I have overcome the world” (John 16:33).


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