Could This Be a Clue About the Origin of Pathogens?

A house finch, which is now susecptible to a new eye infection. (Click for credit)
The origin of pathogens is of particular interest to creationists. When God finished creating the world, he pronounced it “very good.” Now as I have pointed out previously, the term “very good” does not mean perfect. Nevertheless, it is hard to understand how disease-causing pathogens could fit into to a “very good” creation. So where did pathogenic organisms come from? One of the first steps toward an answer to that question came in 2003, when J.W. Francis proposed that microscopic organisms were created to serve as a link between macroscopic organisms and their physical environment. This link helped to channel necessary chemicals from the environment to the macroscopic organisms. However, when the Fall occurred, mutations began happening, and those mutations ended up turning beneficial microorganisms into pathogenic microorganisms.1

This makes sense in light of certain forms of cooperation between organisms. For example, a while ago I wrote about a relationship that exists between a grass that flourishes in hot soils, a fungus, and a virus. Scientists don’t know the details of the relationship, but they know that in order for the plant to grow in hot soils, it must be infected by a specific fungus. However, that fungus will not do the plant any good unless it is infected by a virus. Obviously, the fungus supplies some necessary chemicals to the plant, allowing it to live in hot soil. However, in order for the fungus to be able to do that, the virus must be providing necessary chemicals to the fungus. So in this situation, you have a viral link between the environment and a fungus, and then a higher-level link between the fungus and the plant. Obviously, if one of those links was corrupted, it could turn a beneficial relationship into a deadly one.

Over time, other creationists have suggested ideas for the origin of other pathogens. Dr. Peter Borger, for example, has a very interesting hypothesis on the origin of RNA viruses. He suggests that the genomes of all creatures were originally created so that they could produce fast adaptations to changes in their environment. As a result, all genomes contain variation-inducing genetic elements – sections of DNA that are specifically designed to produce changes that will aid in adaptation. He postulates that RNA viruses have been produced as a result of a corruption in certain variation-inducing genetic elements. This idea is intriguing because it solves the the RNA virus paradox, a recognized problem in the evolutionary literature.2

The real question, however, is what are the specific mechanisms by which this might happen? Exactly how could a beneficial microorganism (or genetic element) become pathogenic? As I was perusing the scientific literature the other day, I ran across an article in PLoS Genetics that might help us begin to answer that question.

The article discusses an analysis of a bacterium, Mycoplasma gallisepticum (MG), that is known to cause respiratory infections in turkeys and chickens. However, it was recently implicated in a brand new disease in house finches. The disease was first discovered in 1994, when thousands of house finches in the Washington, DC area died of a mysterious new eye infection. When the infection was investigated, scientists realized that MG had “jumped” species. It previously infected only poultry. Now it is infecting house finches, causing the new eye disease.

Obviously, the mechanics of how MG could make the switch from poultry to finches is critical to understanding the nature of pathogens, so Nigel F. Delaney and colleagues decided to study the genome of the MG that infects finches and compare it to the genome of the MG that infects poultry. The results were rather surprising. In order for MG to be able to infect finches, it had to lose genes! The researchers found that one of the most significant differences between the poultry-infecting MG and the finch-infecting MG is that the finch-infecting MG had lost about 50 genes.3

Now losing 50 genes is pretty significant, since the original MG had only about 1,000 of them to begin with. What genes were lost? That’s the other surprising part. The genes that were lost were the ones MG uses as a part of its own immune system! You might not be aware of this, but bacteria have viruses that can infect them. The viruses are called bacteriophages, and most bacteria have an immune system that tries to fight them off. Obviously, you would expect such an immune system to be rather important for a bacterium, but in this case at least, it is not. Instead, by losing its immune system, MG developed the ability to infect an entirely new host.

How does losing its immune system help MG infect house finches? There isn’t an answer to that question yet. However, I wonder if this is a clue as to how pathogenic bacteria arose in the first place. In order to provide a link between the physical environment and a macroscopic organism, a bacterium would need a whole host of genes. Some genes would allow it to live inside the macroscopic organism without being destroyed by the organism’s immune system. Other genes would allow it to extract necessary chemicals from the physical environment, while still other genes would allow it to transfer those chemicals to the macroscopic organism. What would happen if it lost some of those genes? It might lose the ability to do anything useful for its host, and it also might gain the ability to jump to a completely different organism. In a completely different organism, the bacterium might produce devastating consequences, since its biochemistry wasn’t designed for that organism.

So it is possible that many of the pathogenic organisms we see today are really just beneficial organisms that have lost sections of their genome. Obviously, it is too early to tell how likely this explanation is, but I think it is a fruitful area of research for some of the bacteriologists, virologists, and geneticists in the young-earth creationist community.


1. Francis, J. W., “The organosubstrate of life: A creationist perspective of microbes and viruses,” Proceedings of the Fifth International Conference on Creationism, R. L. Ivey, Jr., ed., Creation Science Fellowship 2003, pp. 434–444
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2. Holmes E.C., “Molecular clocks and the puzzle of RNA virus origins,” Journal of Virology, 77:3893–3897, 2003
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3. Nigel F. Delaney, et. al., “Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum,” PloS Genetics, 8(2): e1002511. doi:10.1371/journal.pgen.1002511, 2012
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22 thoughts on “Could This Be a Clue About the Origin of Pathogens?”

  1. Todd Wood discussed this same issue from another angle last week,reviewing a Q&A essay in the journal, BMC Biology. He writes, “What hasn’t been nearly as emphasized in the creationist literature is the idea that the host is at least as much to blame as the “pathogen” for the origin of disease, but surely that seems like an obvious place to look for problems.”

    Wood then goes on to quote from the essay:

    “But surely in the case of immunity the pathogen is still a pathogen, it’s just that immunity prevents you from getting sick, right?
    Not really. The question implies that the ability to cause damage or disease is an inherent microbial property, but in fact these characteristics only exist in the context of a susceptible host. Therefore, when a host is immune, pathogenicity is not expressed. What is important to recognize is that pathogenicity and virulence are microbial properties that can only be expressed in a susceptible host.”

  2. So, Yahwey was too busy deciding the proper rules for slave trading, who should be to death, what parts of the animal to sacrifice and what Balaam’s talking donkey would say to notice that bacterium were losing their genes?

    1. L.W., its “Yahweh,” not “Yahwey,” and of course He knew what was going on. He knows the number of hairs on each of us (Luke 12:7) and when each sparrow falls (Matthew 10:29).

  3. And he knows how to start a good bar-b-que-

    “And thou shall eat it as barley cakes, and thou shall bake it with dung that cometh out of man….Then he said unto me, “See, I will let you have cows dung instead of human dung, on which you may prepare your bread.”-Ezekiel 4:12-15

    “But the flesh of the Bullock, and his dung, shalt thou burn without the camp:it is a sin offering.”-Exodus 29:14

    For your next cookout, Jay, just break open the Old Testament!

    1. Thanks so much for quoting Scripture, L.W.! While you might consider dung-burning to be odd, it has been quite common throughout history. In fact, it is still common in many parts of the world today. As Witt, Weyer, and Manning say in that article, “In fact, dung can be as good or better than wood as cooking fuel.”

  4. Gee, your article didn’t mention burning human feces. Your god seems to rather enjoy it.

    And would you call it a “sweet odor unto the Lord” as your bible does?

    And would you call it an appropriate “sin offering” as your bible does?

    It takes a special god to enjoy the smell of dead animals and their feces burning! Praise the Lord!!!!!

    1. L.W., I thought you had read those passages. I guess I was mistaken. As you can read from both passages, human dung was never used. In Ezekiel 4:12-15, God replaced human dung with cow dung. Why? Because as the passage says, using human dung would make the food unclean. Thus, rather than enjoying human dung burning, God calls it “unclean.” The other passage (Exodus 29:14), of course, never mentions human dung.

      Yes, of course a sacrifice is a sweet odor to the Lord. The offering described in Exodus 29:14 is also an appropriate sin offering. Once again, I think you are a bit confused, and that confusion probably comes from not reading the passages you are quoting. It’s not the smell of the fire that God enjoys. It is the smell of the sacrifice itself. When I make a sacrifice for the Lord, it smells sweet to him, even though I am not burning anything.

  5. Umm, J-bird, nothing in the text states that is is the “sacrifice itself” that God is enjoying. You are simply reading that into the text to avoid facing the fact that your ancient holy book is saturated with the Stone Age thinking of primitive people who believed that burning the carcass of a dead goat and then sprinkling its blood around their temple was ordained by God himself!

    That’s why your ancient holy book has page after page describing precisely which parts of the intestines should be burned and also demanding that the animals testicles shall not have a blemish!

    No blemishes on the testicles!!! Boy, your God really does sweat the details!!!

    1. L.W., once again, you should actually read the passages you quote. If you did, you would read, “You shall offer up in smoke the whole ram on the altar; it is a burnt offering to the LORD: it is a soothing aroma, an offering by fire to the LORD.” Note what the passage says: it is the offering that holds the soothing aroma.

      The burning of a dead goat and the sprinkling of its blood was, indeed, ordained by God. This is because, as Hebrews 9:22 tells us, “In fact, the law requires that nearly everything be cleansed with blood, and without the shedding of blood there is no forgiveness.”

  6. Umm Jay, how exactly does an “offering” hold an aroma? Can you explain that?

    When you make a financial offering in your church, would your Lord find that a “sweet savor”?
    And when you “offer” up prayer, does your Lord find a “sweet savor” in that, too?

    Read it again, Jay. It states “…it is a BURNT offering to the Lord: is is a soothing aroma, an offering made BY FIRE to the Lord.”

    Did you get that, Jay? A BURNT offering by FIRE. And what’s being burned by the fire? A Goat!!

    And gracekalman, are you truly not aware of the incredibly crude and barbaric details that are common in the bible, particularly the Old Testament?

    Here’s a site where you can learn a lot about the “details” of the bible that your Sunday school teacher probably never mentioned:

    1. Thanks for asking, L.W. I would be happy to explain how an offering holds an aroma to God. When we make a sacrifice, we are giving up something to show how important God is to us. That smells wonderfully sweet to God. You seem to be confused by the language, so let me help clear up that confusion. God doesn’t have a nose. He doesn’t smell things like we smell things. He doesn’t live in the sky. Thus, the smoke from a fire doesn’t rise up to him so that He can smell it. What He smells is the heart of an individual. When an individual makes a sacrifice, Gods smells the individual’s heart, and that’s the wonderful aroma. So of course God finds my financial offering a sweet savor. If I pray something that indicates my willingness to sacrifice for Him or someone else, that also produces a sweet savor. This is why Philippians 4:18 refers to material gifts given to Paul as an offering that produces a fragrant aroma for God:

      But I have received everything in full and have an abundance; I am amply supplied, having received from Epaphroditus what you have sent, a fragrant aroma, an acceptable sacrifice, well-pleasing to God.

      This is why you need to actually read the Scriptures to understand them. Old Testament sacrifices were, indeed, burnt, but the Scriptures don’t indicate that it is the burning that God smells. As I showed you previously, the Scriptures clearly say that the offering is what produces the soothing aroma.

      Not surprisingly, you are quite wrong about Jesus’ sacrifice. As Ephesians 5:1,2 says:

      Therefore be imitators of God, as beloved children; and walk in love, just as Christ also loved you and gave Himself up for us, an offering and a sacrifice to God as a fragrant aroma.

      So yes, Jesus’ sacrifice is described as a fragrant aroma to God. If you really want to understand the Scriptures, L.W., you need to read them. If you do, you will find that most of your preconceived notions about them are wrong. This is why your Skeptics Annotated Bible is not a surprise to me or any other Christian who takes the Scriptures seriously, like Grace does. She knows the Bible well enough to distinguish between misconceptions like those listed there and what the Scriptures actually say. Based on your many errors that I have patiently corrected, it is you who needs help when it comes to learning what the Bible says. Here is a good source to get you started.

  7. Oh, and Jay, I don’t believe that the offering of Jesus’s sacrifice is ever described as a “sweet savor unto the Lord.”

    It’s the burning of animal flesh and intestines and feces that is described as a pleasing odor to your Lord. No matter how desperately you try to show otherwise.

    You don’t have a leg to stand on with your “interpretation” of what ‘sweet savor to the Lord’ refers to in the Old Testament.

  8. Preconceived notions: The arch-enemy of science, indeed. Unfortunately, most uninformed people, and sadly some well-informed ones seem to have them.

  9. In Philippians, Paul is calling the gift from Epaphroditus a fragrant aroma to himself, not to God. He states that it is pleasing to God, but does not say that it was a sweet fragrance to God, not do we know what gift that Paul is actually talking about.

    And while you did seem able to find a single verse in the bible that does refer to Jesus’ sacrifice as a fragrant aroma, what that does is show me that your inane religion is even more grotesque, vile and sickening than I realized.

    The very idea of a savage human sacrifice being offered up to an invisible fairy is, by itself, the single most vile, wicked, immoral and disgusting belief about the worship of god in the history of human kind’s existence on this earth. It is absolutely Neanderthal-level thinking.

    But to then suggest that this sadistic, barbaric, cave man lunacy is actually a pleasurable odor to the sky-deity raises the wickedness to a new level.

    And of course you offer no evidence to support your silliness about God smelling the heart of a person. That kind of nonsense is ridiculous even coming from you. And I notice that you quote no bible verses to support you.

    But the Old Testament verses clearly refer to the “burning” of the animal as a sweet odor to the Lord, regardless of what you try to say.

    Gen. 8:20- “Then Noah built an altar to the Lord, and took of every clean animal and of every clean bird, and OFFERED BURNT OFFERINGS on the altar. And when the Lord SMELLED THE PLEASING ODOR…

    Exodus 29:18- “It is a BURNT OFFERING to the Lord, a PLEASING AROMA, an offering made to the Lord by FIRE.”

    Exodus 29:25- “Then take them from their hands and BURN THEM on the altar along with the BURNT OFFERING for a PLEASING AROMA TO THE LORD.”

    Lev. 1:13 “It is a BURNT OFFERING, an offering MADE BY FIRE, an AROMA PLEASING TO THE LORD.”

    Lev. 4:31- “and the Priest shall BURN IT ON THE ALTAR AS AN AROMA PLEASING TO THE LORD.”


    Lev. 17:6- “the Priest shall sprinkle the blood on the altar…and BURN THE FAT FOR A PLEASANT AROMA TO THE LORD.”

    Numbers 15:3- “and you present to the Lord offerings MADE BY FIRE AS A PLEASING AROMA TO THE LORD.”

    You see, Jay, there is simply no getting around the fact that is was the BURNING of an animal sacrifice that was a pleasing odor to the Lord. Not the offering itself. The text is clear, Jay. Please stop acting like a dolt about this.

    1. L.W., you need to actually read the Scriptures that you are trying to understand. I realize this might be difficult, because actually reading the Scriptures will show you all the misconceptions you have about them. However, I will try to educate you as best I can. As Philippians 4:18 says:

      But I have received everything in full and have an abundance; I am amply supplied, having received from Epaphroditus what you have sent, a fragrant aroma, an acceptable sacrifice, well-pleasing to God.

      Note that Paul talks about himself in the first part (I am amply supplied) but about God in the last part. Where is the fragrant aroma? In the last part. Obviously a financial gift has no aroma, so there is no way Paul could have smelled anything. However, since God smells what is in the heart, the aroma is to God, not Paul.

      You say that I quote no Bible verse to support my view, but I do. In fact, both Philippians 4:18 and Ephesians 5:1,2 support my view. They show that it isn’t the physical smell that produces the aroma. It is the sacrifice itself, which is an indication of a person’s heart. I also note that once again, when faced with facts that contradict your errant views, you quickly try to change the subject. Let me remind you what you said:

      Oh, and Jay, I don’t believe that the offering of Jesus’s sacrifice is ever described as a “sweet savor unto the Lord.”

      Of course, like most of what you have written in your various comments, that was wrong. Ephesians 5:1,2 does, indeed, describe the sacrifice of Jesus in just that way. To detract from this error, you immediately changed the subject, saying that this somehow shows that God is barbaric. Of course, that’s not true, either. After all, what you fail to realize is that Jesus offered Himself up as the sacrifice, because of love. As He said, “Greater love has no one than this, that one lay down his life for his friends.” (John 15:13) Rather than being barbaric, then, Jesus’s sacrifice was the ultimate expression of love. Once again, that’s what made it a sweet aroma to God.

      I might interject one more thing at this point. You seem to be very angry at God. I would suggest that you deal with that anger. Perhaps you should read this web article. If you really think that the God of the Bible doesn’t exist, I am not sure why you are so angry at Him!

      I do appreciate you quoting all those Scriptures, as they prove my point quite well. In the Old Testament, offerings were made by fire. Thus, they were called burnt offerings, and they made a pleasing aroma to the Lord. But was it the burning or the offering? As you can see from Philippians 4:18 and Ephesians 5:1,2 it is the offering, not the burning. The Philippians burnt nothing for Paul, and Jesus was not burnt. Nevertheless, both sacrifices are described as a pleasing aroma to God. Thus, as is often the case, the New Testament helps us understand the Old Testament. Since the offerings discussed in the Old Testament were burnt, it is impossible to separate the burning from the offering. Thus, someone who doesn’t know much Scripture might think that it was the burning that produced the pleasing aroma to God. However, someone who knows Scripture understands that the New Testament shows that the aroma is in the offering, not the burning.

      In your final comment, you seem confused about what Leviticus 16:29-34 says. First, let’s quote it from a reliable translation (the New American Standard):

      “This shall be a permanent statute for you: in the seventh month, on the tenth day of the month, you shall humble your souls and not do any work, whether the native, or the alien who sojourns among you; for it is on this day that atonement shall be made for you to cleanse you; you will be clean from all your sins before the LORD. It is to be a sabbath of solemn rest for you, that you may humble your souls; it is a permanent statute. So the priest who is anointed and ordained to serve as priest in his father’s place shall make atonement: he shall thus put on the linen garments, the holy garments, and make atonement for the holy sanctuary, and he shall make atonement for the tent of meeting and for the altar. He shall also make atonement for the priests and for all the people of the assembly. Now you shall have this as a permanent statute, to make atonement for the sons of Israel for all their sins once every year.” And just as the LORD had commanded Moses, so he did. ”

      Now your claim is that a “permanent statute” needs to go on forever. However, that’s not true. Remember, a statute is a part of a large body of Law. A “permanent statute” simply means that it is a constant part of that body of Law. However, if there is no need for the Law anymore, the permanent statute is no longer relevant. This is, of course, what happened when Christ offered His sacrifice, which provided a pleasing aroma to God. As Hebrews 10:10-14 tells us:

      By this will we have been sanctified through the offering of the body of Jesus Christ once for all. Every priest stands daily ministering and offering time after time the same sacrifices, which can never take away sins; but He, having offered one sacrifice for sins for all time, SAT DOWN AT THE RIGHT HAND OF GOD, waiting from that time onward UNTIL HIS ENEMIES BE MADE A FOOTSTOOL FOR HIS FEET. For by one offering He has perfected for all time those who are sanctified.

      So in the end, there is no need for atonement over and over again. Jesus was the perfect sacrifice, and as a result, we are atoned once and for all. Thus, there is no longer a need for the permanent statute that is mentioned in Leviticus 16:29-34. Once again, you don’t really know much about the Scriptures. As I said before, you should try to learn more about them so as to avoid making all these errors. As I said before, this would be a great place to start your education.

  10. Oh, and according to Leviticus 16:29-34, animal sacrifices are commanded by YAHWEH to be offered forever:

    “This shall be an everlasting statue for you, to make atonement for the people of Israel.”

    Jay, better get to atoning!!

  11. This actually makes clearer L.W’s confusion as to how science is actually done. He states several passages where the data would seem to indicate that he is correct. However, if there is one instance where data doesn’t fit with his hypothesis (i.e.. the passage Jay posted about the evidence for figurativeness in this case,) then it doesn’t matter how many pieces of evidence don’t point that out, the matter simply isn’t a closed case, and must be looked into further, (because in this case the others aren’t specifically pointing out the antithesis of what Jay is saying.) It’s fascinating how this illogical behavior quickly spreads to all areas of thought.

    1. That’s generally the way it happens, W. Brown. When you start letting your emotions and desires govern the way you think about one area (science, for example), they eventually take over other areas, like theology. This is why it is important to look at all sides of an issue. You are less likely to get emotionally attached to a position if you are reading reasonable people on all sides.

  12. From his view, L.W. is seeing a vast amount of suffering in the world that shouldn’t be there. I assume it is rather shocking to be told that there is an omnipotent God that is doing nothing to relieve the suffering. Having been raised “in the truth”, I can’t exactly tell you how I was convinced, but I have never doubted that God loves me, loves all humanity in fact. I’ll try to explain my view for L.W.
    When I look at the Bible, I see the greatest love story on earth. God had angels and cheribims and seraphims. So why did He create earth? The Bible tells us it was for His glory. Considering how little glory God is recieving from His creation currently, you should be thankful the universe still exists. But I have no doubt that it will continue to exist for at least 1007 more years. But I’m off on a rabbit trail.
    Take the fall of man. Please don’t turn off your brain now. God created man with a free will. Dr. Wile has pointed that out several times, but I will try to give you the implications of this fact. Free will is a two-sided gift. On the one hand, it makes love and acceptance possible. It also enables us to hate and reject. God wanted us to love Him, and He was willing to risk us hating Him to let that happen. And so Adam was confronted with a choice under the Tree of the Knowledge of Good and Evil. He knew that his wife would die. He could continue to live in perfect communion with God, or he could join his wife in her seperation. He chose his wife. (This is my interpretation, but remember that no scripture has any private interpretation.) God is holy. He had said, “in the day that thou eatest thereof, thou shalt surely die”. The wages of sin is death. Here is were your animal sacrifices come in. Without the shedding of blood there is no remission of sin. So God killed animals to atone for their sin, allowing them to live longer although they would still die. My father likened it to sweeping dirt under a rug. Only Jesus’ perfect sacrifice could remove that sin for good. Ever heard of Abraham’s bosom? Adam and Eve and other “old-testament saints” resided there, seperate from their holy God until Jesus’ ultimate sacrifice erased their sins for good.
    So you see a cruel God who allows wickedness and suffering in this world.
    I see a holy and loving God who loved me so much He was willing to die to save me. “God is not willing that any should perish…” I think it’s the free will thing that has you confused.
    You and I are sinners. I don’t think you will deny that. What will you do when you stand before your Creator and try to defend yourself? You don’t think you ever will, you certainly hope you won’t, and you are desparate to prove you won’t. That’s why you are so angry when anyone threatens your beliefs.
    I think the love of our God is well expressed in this poem by Martha Snell Nicholson: My Advocate

    I sinned. And straightway, posthaste, Satan flew
    before the presence of the Most High God,
    and made a railing accusation there.
    He said, “This soul, this thing of clay and sod,
    has sinned. ‘Tis true that he has named Thy name,
    but I demand his death, for Thou hast said,
    “The soul that sinneth, it shall die.”
    Shall not Thy sentence be fulfilled? Is justice dead?
    Send now this wretched sinner to his doom.
    What other thing can Righteous Ruler do?”
    And thus he did accuse me day and night,
    and every word he spoke, O God, was true!

    Then quickly One rose up from God’s right hand,
    before whose glory angels veiled their eyes,
    He spoke, “Each jot and tittle of the Law
    must be fulfilled; the guilty sinner dies!
    But wait–suppose his guilt were all transferred
    to Me, and that I paid his penalty!
    Behold My hands, My side, My feet! One day
    I was made sin for him, and died that he
    might be presented faultless at Thy throne!”
    And Satan fled away. Full well he knew
    that he could not prevail against such love,
    for every word my dear Lord spoke was true!

    That is what I see. Amazing love, O what sacrifice, the Son of God, given for me. My debt He paid, and my death He died, that I might live.
    However much you hate God, He loves you. He has done everything possible to save you. I have done what I could. When you stand before the throne, will you have an Advocate? To trod underfoot the Son of God is a fearful thing. You will have no excuse.
    Congratulations, you inspired the longest comment I’ve ever posted.

    1. Thanks so much for caring enough to write that, Grace. I pray that it reaches L.W. in a way that I have not been able to.

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