Another Example of Three-Way Mutualism

Mealybugs feeding on a hibiscus plant (Click for credit)

As anyone who has been reading this blog for a while knows, I am fascinated by the phenomenon of symbiosis: two or more species living together in a relationship. In my opinion, the most interesting form of symbiosis is mutualism: two or more species living together in such a way that each species benefits. I have written several different articles about it over the years (see here, here, here, here, and here, for example), and I personally think it is a picture of what creation was like before the Fall.

As scientists have studied mutualism over the years, they have found some really complex examples. In the past, I wrote about a three-way mutualistic relationship that exists between a grass, a fungus, and a virus. Later on, I wrote about a three-way mutualistic relationship that exists between seagrasses, clams, and bacteria. Well, I just learned about another example of a three-way mutualistic relationship. Scientists have known about it for more than 10 years, but it was the subject of a recent study that comes to some rather startling conclusions.

The biggest member of this relationship is the mealybug, which is shown above. It feeds on the sap of plants, but that presents a bit of a problem. In order to make all the proteins it needs to survive, the mealybug must have certain amino acids at its disposal. It can get some of them from its diet, but plants don’t make all the amino acids that the mealybug needs. As a result, it must manufacture some of them. By itself, however, it can’t get the job done. It can make some of the chemicals that are necessary to produce the amino acids, but it can’t make them all. If left on its own, then, the mealybug could not survive.

In 2001, Carol von Dohlen and her colleagues demonstrated that the mealybug has help in making those amino acids. A bacterium, Tremblaya princeps, lives in the mealybug, and it helps the mealybug make the amino acids it can’t get from its diet. However, the bacterium can’t do that job on its own. As a result, a smaller bacterium, Moranella endobia, lives inside it. Together, these two bacteria make the chemicals that the mealybug needs but cannot make itself. All three species are needed in order for the mealybug to survive.1

So here’s the arrangement: a bacterium inside a bacterium inside a bug. It reminds me of an exchange from one of my favorite Dr. Who episodes:

Lily:Where are we?

The Doctor:In a forest, in a box, in a sitting room. Pay attention!”

Now here’s why I learned about this amazing relationship. I ran across a study published this year in the journal Cell2. It analyzed the genetics behind this relationship, and they are truly astounding. First, the article informs the reader that despite its size, the larger bacterium in the relationship (Tremblaya princeps) has the smallest genome of all known bacteria. It has only 120 genes in a genome that consists of only 139,000 base pairs. The smaller bacterium in the relationship (Moranella endobia) has a larger genome – 406 genes in a genome that consists of 538,000 base pairs. By way of comparison, one of the most common bacteria studied, Escherichia Coli, has 4,200 genes in a genome that consists of 4,600,000 base pairs.3

Why do these two bacteria have such small genomes? Because they don’t have to perform all the functions of life. They live inside the mealybug, receiving both food and housing. As a result, they don’t need to do all the things that free-living bacteria (like Escherichia Coli) do. They just need to help the mealybug make its amino acids and eat the food that the mealybug provides for them.

Since the authors believe in evolution, they think that these bacteria were probably once free-living but were incorporated into the mealybug millions of years ago. At that time, of course, their genomes were a lot larger. However, as the relationship between the three species evolved, the two bacteria began losing a lot of the genes they didn’t need. That’s why their genomes are so small today – evolution removed most of the unnecessary genes. Here’s the problem, though: evolution also removed some of the necessary ones! The genomes of these two bacteria don’t make everything they need, even after considering what the mealybug does for them.

So how do the two bacteria survive? The mealybug has the extra genes they need. The authors first thought that perhaps in the course of evolution, the bacteria transferred those genes to the mealybug. However, their analysis doesn’t support that idea. They found 22 genes (actually, they say there may be more) in the mealybug that resemble bacterial genes, and the majority of them are necessary for the survival of the two bacteria that live inside it. However, none of those genes have the sequences you would expect if they came from those two bacteria! Instead, they have sequences that are similar to other species of bacteria.

So how do the authors explain this? They think that as the relationship between these three species was was evolving, the two bacteria lost the genes they didn’t need, but they hung on to the genes that they did need. At one time, then, the two bacteria had the 22 bacterial genes that are now in the mealybug’s genome. However, over the course of time, the mealybug was infected by other bacteria, and during those infections, these other bacteria transferred the 22 genes to the mealybug. Once the mealybug had those genes, the two bacteria living inside the mealybug were free to lose them.

In my mind, there is a more reasonable explanation. The mealybug has always been designed to live with these bacteria. As a result, its genome was created with some genes that the bacteria need, and the bacteria were created with some genes that it needs. In my mind, this gets rid of the need to believe in unlikely events. After all, how likely is it that an infecting bacterium would just happen to transfer a gene to the mealybug that its mutualistic bacteria need? Furthermore, how likely is it for that to happen at least 22 times?

As I have stated before, I think the best explanation for bacteria and viruses is that they were created to live in relationships with other organisms, allowing those organisms to have access to the rich chemistry that is available from the surroundings. The mutualism we see today is a reflection of that. Once the Fall happened, however, some of the mutualistic bacteria and viruses were subject to mutations, and they eventually mutated to the point where they lost their ability to help other organisms. As a result, they became pathogenic.

I think the more we investigate mututalism, the more clear this will become.

REFERENCES

1. CD von Dohlen, S Kohler, ST Alsop, anhd WR McManus, “Mealybug beta-proteobacterial endosymbionts contain gamma-proteobacterial symbionts,” Nature 412:433-6, 2001
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2. Filip Husnik, Naruo Nikoh, Ryuichi Koga, Laura Ross, Rebecca P. Duncan, Manabu Fujie, Makiko Tanaka, Nori Satoh, Doris Bachtrog, Alex C.C. Wilson, Carol D. von Dohlen, Takema Fukatsu, and John P. McCutcheon, “Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis,” Cell 153:1567–1578, 2013
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3. Leon E. Rosenberg and Diane Drobnis Rosenberg, Human Genes and Genomes: Science, Health, Society, Academic Press 2012, p. 95
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14 Comments

  1. Evan Arcadi says:

    Intriguing! One would think that the large amount of coincidences required in order for evolution to be plausible would cause at least some evolutionists to re-examine their views. As a side note, you may wish to warn viewers of the obscene language on PZ Meyers blog. As always an interesting read!

    1. jlwile says:

      Thanks for the suggestion, Evan. When I originally posted his site, he wasn’t quite as open with his foul language. He has gotten worse over the years. I will add a warning.

  2. Alex Coeles says:

    How likely is it an infecting bacterium would just happen to transfer a gene to the mealybug that its mutualistic bacteria need?

    I read the original paper. The mutualistic bacteria never needed the gene. But as the mealybug possessed bacterial genes that would allow the mutualistic bacteria to survive with, its existing genes became redundant and no longer were needed. Horizontal Gene Transfer is common in unicellular organisms, but it is not clear how prevalent these cases are in multicellular organisms, so saying such a thing is unlikely has no foundation in reality. Further, it is not that they transferred genes independently 22 times, because the entire three way symbiosis is dependent on genes from only around six distinct organisms. But you do not mention this in your post.
    Traditional Creationism does no better to offer a comprehensive answer. The assertion is that animals were meant to be mutualistic from the beginning and they were merely supernaturally created to be so, but this pales in comparison to the assumptions that go into the idea that pathogens developed only after the Fall. Not only do these ideas remain unsupported by scientific and biblical data but are both merely a construct meant to support the Young Earth Creationist interpretation.

    1. jlwile says:

      Thanks for your comment, Alex. I think you missed where I discussed the author’s explanation. As I say in the post:

      So how do the authors explain this? They think that as the relationship between these three species was was evolving, the two bacteria lost the genes they didn’t need, but they hung on to the genes that they did need. At one time, then, the two bacteria had the 22 bacterial genes that are now in the mealybug’s genome. However, over the course of time, the mealybug was infected by other bacteria, and during those infections, these other bacteria transferred the 22 genes to the mealybug. Once the mealybug had those genes, the two bacteria living inside the mealybug were free to lose them.

      So yes, I do discuss the author’s contention that the mutualistic bacteria had the genes and then lost them. However, as I state in the post, this requires that 22 separate genes that just happened to be genes the mutualistic bacteria needed got transferred to the mealybug’s genome before the mutualistic bacteria lost them. That seems rather unlikely. And yes, there is a basis in reality for saying it is unlikely. The simple fact is that while many cases of horizontal gene transfer among bacteria have been documented, very few have been documented between bacteria and animals. As a recent paper in the Proceedings of the National Academy of Sciences of the United States of America tells us:

      Horizontal gene transfer (HGT) involves the nonsexual transmission of genetic material across species boundaries. Although often detected in prokaryotes, examples of HGT involving animals are relatively rare, and any evolutionary advantage conferred to the recipient is typically obscure. (emphasis mine)

      And yes, they did transfer genes independently at least 22 times. True, the authors think the genes might have come from around six distinct organisms, but each gene had to be transferred. Thus, 22 transferred genes means that gene transfer happened 22 times.

      Of course, traditional creationism does a much better job in providing a comprehensive answer to the issue of mutualism. It gives a much more realistic explanation for why mutualism is widespread throughout creation, and it also explains why mutualism works so well. Also, it provides a significantly better explanation for how pathogens have developed over time. Loss of genetic information in mutualistic organisms as a result of the Fall is a mechanism that can produce pathogens in a way that is most consistent with what we know about genetics.

  3. Alex Coeles says:

    Thank you for taking the time to respond.
    The bacteria never “needed” these genes in the first place. Existing genes in the bacteria became redundant because the mealybug had acquired similar genes elsewhere. The bacteria lost them as a result. This scenario is far from improbable. There are other cases where an insect acquires most of a bacterial genome through gene transfer (1).
    Besides this, the paper you reference states that the symbiotic bacterium Tremblaya’s genes may have become redundant from genes expressed by Moranella – the bacterium with the bacterium. It is plausible many of Tremblaya’s missing genes may have been substituted for by Moranella’s genes, further complicating the situation (2).
    Scientists are just now beginning to uncover the extent of horizontal gene transfer between bacteria and eukaryotes. Making hasty or unsupported judgements on how such relationships work won’t get anyone anywhere meaningful, especially when not much is known about these relationships as a whole.
    Any idea can seem brilliant at first, but if the underlying philosophy is unreliable, then it is faulty at its roots. There is no reason, scientific or biblical, to believe pathogens came about directly or indirectly from the Fall of man. This tenet of traditional creationism is merely one of the many that rely on massive assumptions to support itself. There is not one part of Scripture proclaiming that the nature of all life forms was ever altered after the Fall. It is only the nature of man that was changed. Nothing exists to suggest that evolution cannot account for a large number of transferred genes in an insect. It has been believed it’s an incredibly rare event, but even this is being reconsidered. The reason for this is not because scientists are being forced into a corner, but because more similar relationships are being uncovered. In the future, research will ascertain the frequency of horizontal gene transfer in higher organisms.

    References:
    http://www.scienceagogo.com/news/
    http://download.cell.com/pdf/PIIS0092867413006466.pdf?intermediate=true

    1. jlwile says:

      Thanks for your reply, Alex. Of course the bacteria needed them, or they wouldn’t have been in the bacterial genome to begin with! The point is that an infecting bacterium has all sorts of genes that it could transfer to its host. However, in this case, you have to believe that a completely different species just happened to transfer a gene to the mealybug that just happened to be a gene that the mutualistic bacterium also had (and therefore needed). Not only that, you have to believe this happened 22 times! Once again, that seems rather unlikely.

      Your reference to the entire bacterial genome being transferred to an insect doesn’t work. I assume you are referring to this story. First, this doesn’t mean such transfer is common. As the article states, Wolbachia is a very common parasite (found in 70% of invertebrates). Yet, this is the first such study to demonstrate a transfer. In other words, it’s relatively rare for this to occur, as the study I quoted previously indicates. Second, Wolbachia‘s lifecycle includes making its way to the egg or sperm of the host. This, of course, makes such transfer more likely. So if you want to use this study to indicate that the authors’ explanation for the mealybug system is correct, you now have to add yet another unlikely event – that infecting bacteria from other species had a lifecycle that included making their way to the sperm or egg of the host. Obviously, then, the authors’ explanation is very unlikely.

      I agree that the situation might be even more complex, which once again, makes the author’s explanation even more unlikely. I also agree that making hasty or unsupported judgements (like your judgement that the authors’ explanation is correct) won’t get us anywhere meaningful. However, my conclusion is neither hasty nor unsupported. Based on what we know now, horizontal gene transfer between bacteria is relatively rare. Thus, the idea that it happened 22 times from several different bacteria and ended up putting the genes that the mutualistic bacterium needed into the mealybug is rather unlikely.

      There are very good reasons, both scientific and Biblical, to believe that pathogens are a result of mutualistic organisms losing genetic information because of mutations that began with the Fall. As I have already tried to explain to you, the idea that pathogens were mutualistic and then became pathogenic relies only on the loss of genetic information. This is entirely consistent with what we know about genetics. To believe that pathogens first evolved to be free-living and then started infecting people requires an increase in genetic information (the information needed to avoid the host’s immune system). Adding genetic information is hard to understand based on what we know about genetics. It is also hard to understand what selection pressure would cause a free-living organism to develop new genetic information that would allow it to infect a host. Thus, the traditional explanation suffers from scientific problems. The young-earth creationist explanation does not.

      In addition, the Bible clearly states that all life forms were affected by the Fall. Romans 8:19-23 tells us:

      For the anxious longing of the creation waits eagerly for the revealing of the sons of God. For the creation was subjected to futility, not willingly, but because of Him who subjected it, in hope that the creation itself also will be set free from its slavery to corruption into the freedom of the glory of the children of God. For we know that the whole creation groans and suffers the pains of childbirth together until now. And not only this, but also we ourselves, having the first fruits of the Spirit, even we ourselves groan within ourselves, waiting eagerly for our adoption as sons, the redemption of our body.

      Note that it’s the whole creation that is groaning. In addition, Genesis 3:17 tells us that God cursed the ground because of Adam’s sin. Thus, not only were all living organisms affected by the Fall, even the ground was affected by it!

      So as you can see, from both a scientific and a Scriptural standpoint, the young-earth creationist view is the most reasonable explanation for this situation.

  4. Alex Coeles says:

    Many times, expansion of genetic information comes about through duplication and mutation. Mutations can add and subtract genetic information under selection pressure. This is a basic tenet of biology. It’s not hard to understand at all – it’s very simple.

    Mealybugs:
    Nothing exists to suggest the same exact genes were substituted – they were merely similar enough to render existing bacterial genes redundant. The bacteria lost its own genes because it had no further need of them. On the other hand, if these organisms had been created and ordained to be in such a relationship, there would have been no need to manufacture the bacteria with genes it would no longer need. The mealybug’s prior horizontally transferred genes did not pre-prepare the symbiotic relationship with the bacteria, it merely rendered the bacteria’s existing genes useless. Studies show rapid gene loss occurs in bacteria transitioning to symbiotic lifestyles.
    The study I first brought up does not indicate horizontal gene transfer in animals is commonplace. I will agree on that, but that was not my point. The study does show gene transfer in prokaryote/insect relationships is more of a widespread occurrance than previously anticipated. Besides this obvious truth, all of the horizontally transferred genes procured came from bacteria that exist as known symbionts of insects. Most Rickettsiales can only survive as endosymbionts of other cells. Cardinium is involved in varied reproduction alterations of arthropod hosts. Sodalis is an insect endosymbiont that is maternally transmitted to progeny. Serratia is a well known aphid symbiont. Pantoea is found in the gut of locusts. Pseudomonas acts as a symbiont by producing the toxin pederin, which insect hosts can utilise in defense. All of the contributors to the transferred genes in the mealybug are known symbionts. These symbiotic bacterium must have been utilised in the past for different purposes and ultimately lost, leaving only remnants in the mealybug genome. Given the mealybugs’ long, parasitic history, this scenario is certain.

    “So as you can see, from both a scientific and a Scriptural standpoint, the young-earth creationist view is the most reasonable explanation for this situation.”
    In no way does any Scriptural passage ever imply all life forms were direcly affected by the Fall. In Romans 8:19, “Creation” means “the world” or more specifically, “mankind”. Quite frankly, anything apart from this interpretation makes little sense. It was commanded to preach the gospel to every “creature”, but nobody preached to sea anemones and turtles. Man is responsible and suffering for his sin, the plants and animals are not. Even so, there would be no reason to believe “creation” referred to life forms only. Everything to do with geology, chemistry, physics, and astronomy would have also been affected.
    The ground was indeed cursed. Scripture says Adam would have to toil in labor to survive. Man came from the ground, would make his living off the ground, and eventually return to the ground. However, there is no indication that the very composition of the ground changed at all. The flimsy and untenable assumption that man’s fall somehow directly affected the natural realm, organic and inorganic, is hopelessly unscientific and unbiblical.

    1. jlwile says:

      Of course duplication and mutation cannot expand the information in the genome! It is a major tenet of evolution, but genetics tells us it doesn’t work. This isn’t hard to understand at all. It’s very simple. When a duplicate gene mutates away from functionality, its expression is reduced to the point that even if it found a new, useful sequence, the new protein would not be expressed. In addition, we know that the useful gene sequences are so rare that the probability of random mutations producing a new, useful sequence is on the order of 1 in 10^77. There are several other genetic facts that tell us duplication plus mutation cannot produce new information (see here and here, for example). Once again, then, the creationist view of pathogen development is the most scientifically viable view.

      You want to believe that the genes received by the mealybugs from the other infecting bacteria are not exactly the same as those once held by the mutualistic bacteria, but that requires you to ignore selection. After all, the existing gene in the mutualistic bacterium would have been tuned to its needs. If a different gene were added to the mealybug, the protein it produced would not be as efficient for the mutualistic bacterium as its own gene. Thus, the mutualistic bacterium’s gene would not be redundant. Until the gene inserted into the mealybug was identical to the one in the mutualistic bacterium, the mutualistic bacterium would not lose the gene that produces the better protein!

      Once again, the creationist view makes much more sense scientifically. There is no reason to think the organisms had been “ordained” to live in such a relationship. However, if mutualism among bacteria and insects was the starting point, it is much easier to understand how such a relationship would develop over time.

      I am glad that you are willing to admit that such horizontal gene transfer is not commonplace, however, you don’t seem to grasp the implications of this simple fact. If such transfer is not commonplace, then the chance of it happening 22 different times in such a way that it just happens to help the current mutualistic bacteria is ridiculously unlikely! Look at the scenario you have to create to believe this happened! You have to make up stories of past symbionts that once existed in the mealybug and just happened to give it the genes that its future mutualistic bacteria had so that its future mutualistic bacteria could then lose its own genes. If you have that kind of faith, that’s great. However, such absurdly unlikely events are beyond the faith that I have!

      You claim that the word “creation” in Romans 8:19-23 means specifically “mankind,” however, we know that is wrong. Note what verses 22 and 23 say:

      For we know that the whole creation groans and suffers the pains of childbirth together until now. And not only this, but also we ourselves, having the first fruits of the Spirit, even we ourselves groan within ourselves, waiting eagerly for our adoption as sons, the redemption of our body.

      So the passage makes the distinction between “creation” and “ourselves.” Thus, the word “creation” is clearly not talking only about people. If so, there would be no need for the bold words above.

      You are correct that Mark 16:15 says:

      And He said to them, “Go into all the world and preach the gospel to all creation.”

      This passage uses the same Greek word as Romans 8, but it is clearly referring to just the world of man. However, the same word is used in several other passages where it clearly means the entire creation, not just man:

      For those days will be a time of tribulation such as has not occurred since the beginning of the creation which God created until now, and never will. (Mark 13:19)

      For since the creation of the world His invisible attributes, His eternal power and divine nature, have been clearly seen, being understood through what has been made, so that they are without excuse. (Romans 1:20)

      and saying, “Where is the promise of His coming? For ever since the fathers fell asleep, all continues just as it was from the beginning of creation.” (2 Peter 3:4)

      Since the word can mean many things (as is common in Greek), it is important that you read the context to find out what the word means in each case. Since Romans 8 clearly distinguishes the world of man (ourselves) from the rest of the world (creation), it is clear that in this passage, the word “creation” is referring to all of creation.

      You claim that man is responsible for his own sin. I agree. However, you go on to claim that plants and animals would not suffer as a result of his sin. However, you then contradict that idea by agreeing that the ground was cursed. You can’t have it both ways, Alex. Either man’s sin affected only the world of man, or it also affected the other parts of the creation. Since you agree that it affected the ground, then you must agree that man’s sin affected parts of creation other than just the world of man.

      The flimsy and untenable assumption that man’s Fall did not affect all of creation is hopelessly unscientific and unBiblical.

  5. Alex Coeles says:

    Dr. Wile, you might find this article interesting: http://pandasthumb.org/archives/2007/01/92-second-st-fa.html

    Now then:
    Your argument is that the substituted gene, however different, would not be as efficient as the bacteria’s own gene. This is untrue not only because we cannot know for sure whether the substituted genes do in fact accomplish the job better than the bacteria did with its own genes, but also because if the substituted gene managed to produce the protein just as well, it would not matter that they were somewhat different. Substituting the bacteria’s gene for a different one would not hamper its productivity if it completed the same function.
    It is important to recognize the distinction between these transfers being commonplace (that is, all over the place) as opposed to being widespread (they happen several times in different organisms). I have demonstrated that they are indeed widespread. Nobody is making up any stories. The footprints of mealybugs’ symbiotic past is clearly apparent in their genome, and the fact that these transferred genes all came from known insect symbionts makes this scenario all the more likely. I fail to see where any of this provides support to the anti-evolution movement. You call it absurd, but there really is no reason to.
    In Romans 8:22-23 , the word “creation” clearly is only talking about people, “ourselves” being the believers. The distinction is not to illustrate anything between humans and the universe around us. It makes no sense! I agree that many times in different passages “creation” is probably meant to refer to the created universe, but context is key. Context, context, context. Here the context simply lends it no credibility. There is no reason to believe it.
    “Since you agree that it affected the ground, then you must agree that man’s sin affected parts of creation other than just the world of man.”
    Here you are wrong. In my comment I very clearly explained the ground was cursed because Adam would be forced to make his life on it. But there is nothing to suggest the ground itself changed or was altered in any way. Even if I am to be considered wrong, then it was only the ground that was affected. It would not lend much support to your idea either way. But if there is any reason to believe the Fall directly affected the natural world (besides through man’s blatant destruction of it) please show me where. Beyond the tangled mass of assumptions and unsupported postulates, on what biblical basis do you justify the notion that God did not create bacteria, fungi, and viruses to be pathogenic?

    1. jlwile says:

      Thanks for the link, Alex. Unfortunately, like most of the material at The Panda’s Thumb, the article is severely flawed. This article does a nice job of correcting Hunt’s misunderstandings. Note that the article also points out several other studies that come to the same conclusion.

      You claim that substituting the mutualistic bacteria’s gene for a different one would not hamper its productivity if it completed the same function. However, we know that’s not true. Proteins are finely tuned for each organism so as to be most efficient in that organism’s biochemistry. Even a tiny change in the chemical surroundings has a huge effect on the efficiency of a protein. A gene from another organism will not produce a protein that is as finely tuned to the mutualistic bacterium’s biochemistry. As a result, the mutualistic bacterium would continue to use its own protein, as that will produce the most survivability. You can’t have it both ways, Alex. If you think selection drives evolution, you can’t suddenly ignore it when it become inconvenient!

      You have not demonstrated that horizontal gene transfer is widespread between bacteria and mealybugs. I agree that you desperately want it to be widespread so that the authors’ explanation is not absurdly unlikely. However, you have not shown this. Instead, you have only been able to show what the article I previously quoted from makes clear – such transfer is relatively rare. Once again, if it is relatively rare, then the chance of it happening 22 times with just the right genes is absurdly low.

      In Romans 8:19-23, the word “creation” is clearly referring to the entire creation. This is why the passage distinguishes between “creation” and “ourselves.” You want to believe that “ourselves” refers to believers and “creation” refers to the rest of mankind. However, we know that’s not correct. As you say, the issue is context, context, context. However, you seem to be ignoring the context. If “creation” refers to the world of man, then the believers are a part of the creation, as they are a part of the world of man. Thus, there would be no way to distinguish between “creation” and believers – believers are a part of the world of man. If the passage were trying to distinguish between believers and unbelievers, it would have used the Greek word kosmos, which is used in other parts of the Old Testament to refer to unbelievers (John 15:19; 1 Corinthians 4:13; 1 John 2:15,16; 1 John 3:1,13; and 1 John 4:3,4). However, the passage does not use the word kosmos. It uses the word ktisis, which in this context clearly means all of creation.

      You agreed that the ground is cursed, but you are trying to avoid the clear implication of this fact. It doesn’t matter whether or not the ground was changed or altered in any way. You agree it was cursed. That means something outside the world of man was cursed by the Fall. You can’t get out of this by then claiming it was “only the ground” that was cursed. Remember, you are trying to claim that Romans 8:19-23 refers only to the world of man. However, the ground is not a part of the world of man. Thus, if the ground was cursed in any way as a result of the Fall, that tells us what good exegesis of Romans 8:19-23 already tells us – “creation” does not refer just to the world of man. Thus, “all creation” means (not surprisingly) all creation.

      There are several Biblical reasons to believe that bacteria, fungi, and viruses were not made to be pathogenic. First, we are told six times that creation was “good” and at the end, we learn it was “very good” (Genesis 1:4–31). I am not sure how pathogens fit into a “very good” creation. Second, the Old Testament patriarchs lived a long, long time. It would be hard to do that fighting diseases created by God. If diseases took a long time to develop, it would be easier to explain the long lives of the patriarchs and the dwindling lifespan throughout most of human history. Third, Isaiah 65:17–25 talks about the new heavens and new earth, and they are free from disease. Revelation 21:1–5 tells us the same thing. This seems to be a picture of creation restored, indicating that disease was not a part of the original creation.

      Beyond the tangled mass of assumptions and unsupported postulates, on what Biblical basis do you justify the notion that God created bacteria, fungi, and viruses to be pathogenic?

  6. Alex Coeles says:

    Thank you for your kind response.
    These links, in turn, clarify some misconceptions about the study. I recognize PZ Myers isn’t the most gracious person alive, but after all, he is a biochemist.
    http://freethoughtblogs.com/pharyngula/2011/10/20/how-not-to-examine-the-evolution-of-proteins/

    Let’s begin:
    So in summary, the evidence you use to believe pathogens did not exist before the Fall is the fact that the new heavens and earth will be free of disease (even though the new universe will have radically different physical properties than our current one and cannot be considered a restoration of the pre-Fall world), pathogens cannot be part of a ‘good’ creation (even though they are natural functions and therefore cannot be more evil than an asteriod or black hole), the unlikeliness that the patriarchs could have lived so long if they were fighting pathogens created by God (even though their long lifespans should not be attributed to a simple lack of disease, and I do not believe pathogens were hand-crafted by God to wreak as much destruction as possible on humans), the impossibility of making a distinction between “believers” and “mankind” in Romans 8 (A, Romans 8 illustrates those who have the firstfruits of the spirit and those who do not, and B, it is equally unlikely that you can make a distinction between “mankind” and “the creation”), and that Romans is referring to creation because something besides humanity was cursed and therefore I cannot exclude it (even though the ground’s condition was never altered and was never subjected to spiritual frustration as humans were, but you still assert there is reason to believe something besides the nature of humans was somehow altered, that is, pathogens). There is still no reason for you to believe pathogens only came after the Fall. Whatever reasons you have for believing it still, it certainly comes not from Scripture or theology. Clearly, it does not work.

    You claim that “A gene from another organism will not produce a protein that is as finely tuned to the mutualistic bacterium’s biochemistry”. Whether you believe the substituted genes are the result of a natural process or purposefully and intelligently placed there, the genes coded for proteins still came from another organism. What you seem to overlook is that many bacteria share the same exact proteins. Gene substition is still plausible, because these same proteins would cause the same function in the symbiotic bacteria as they did before, even if they did not cause the same function in the original bacteria they might have come from.
    According to your viewpoint, you must believe the Creator personally took a mealybug and purposefully planted genes from different bacteria into its own genome just to substitute for a future symbiotic bacteria’s genes, even though the bacteria in question already had the genes and it would not need to lose them in the first place. This is entirely unnecessary, and is far more reasonable to believe it developed on its own.
    I never intended to demonstrate horizontal gene transfer is widespread among bacteria and mealybugs, although 22 transferred genes from six species ought to prove that it somewhat is. What I was arguing for was that the article shows that scientists are reconsidering horizontal gene transfer might be more common among insects as a whole. This is crucial to understand. As the link supported demonstrates, flies have been known to absorb entire bacterial genomes, which arises from symbiosis. As I will say yet again, all the transferred genes recovered from the mealybug (yes, they were transferred, even though for some reason you do not believe they were) have been shown to have once belonged to symbiotic bacteria. What I find amusing is that you pick and choose data from the scientific community in your favor to say that gene transfer is all too rare between bacteria and insects, while ignoring the simple fact that the extent of gene transfer in this scenario is being investigated and reconsidered by biologists because of the evidence that it is more widespread than previously anticipated. I will continue to repeat this again and again until you take notice of this simple fact. I am quite sure you have legitimate scientific reasons for believing symbiosis could have only been ordained by the Creator, but this simply is not one of them.

    1. jlwile says:

      Thanks for the link, Alex, but you really need to get better resources when it comes to science. Like the previous article you linked, the Myers article is full of mistakes. Here is a good article that clears them up for you. Also, you might be interested to know that Dr. Myers is not a biochemist. His undergraduate degree is in zoology, and his PhD thesis was in developmental biology. He doesn’t seem to do any original research today (unlike Drs. Axe and Gauger), so I am not sure if he is still honing that speciality. Also, as my front page indicates, I read Dr. Myers’s blog regularly. Thus, I read the article shortly after he wrote it. Even without Dr. Gauger’s excellent article (linked above), I could see how he did not understand the study.

      You claim that the new heavens and earth cannot be considered a restoration of the pre-Fall world. However, you give no reason why this is the case. Yes, the new heavens and earth will have radically different properties than our current one, because the effects of the Fall will be gone. That will make it like the pre-Fall world. In addition, in all these pictures of the new heavens and new earth, all the familiar organisms are present. In Isaiah 65:17–25, for example, we learn that people will plant vineyards. In Isaiah 11:6-9 we read:

      And the wolf will dwell with the lamb, And the leopard will lie down with the young goat, And the calf and the young lion and the fatling together; And a little boy will lead them. Also the cow and the bear will graze, Their young will lie down together, And the lion will eat straw like the ox. The nursing child will play by the hole of the cobra, And the weaned child will put his hand on the viper’s den.

      If this is some radically new system that has nothing to do with the pre-Fall world, why are all the animals and plants mentioned recognizable?

      You claim that pathogens can’t be considered evil because they are part of the natural world. Once again, how do you know they are part of the natural world? All you know is that they are part of the sin-infested world we live in now, just as is pedophilia, murder, rape, etc. How do you know they were a part of the original creation? You say that pathogens are like black holes and asteroids, but not surprisingly, that’s not true. Does a black hole need to cause pain to stay alive? No. Does an asteroid need to make people miserable in order to survive? No. Pathogens are nothing like black holes and asteroids. They are dependent on causing pain and suffering. How does a “very good” creation include organisms whose sole means of survival is causing misery for others?

      Once again you claim the ground’s composition was never altered, but you have no evidence for this. You simply don’t want its composition to be altered, so you are reading that into the passage. Certainly it was never spiritually frustrated, as it has no spirit. Nevertheless, you have to admit that it was cursed, as the Scriptures clearly say this. Thus, something other than man was cursed as a result of the Fall. Once again, then, this tells us what a good exegesis of Romans 8:19-23 already tells us – “creation” does not refer just to the world of man. Thus, “all creation” means (not surprisingly) all creation.

      You say Romans 8 distinguishes between those who have the first fruits of the Spirit and those who do not. However, once again, we know that’s not true. When the New Testament refers to the world of unbelievers, it uses the Greek word kosmos. However, Romans 8 does not use that word. It uses the word ktisis, which in this context clearly means all of creation. Once again, then, regardless how how you want to force your own views on Scripture, Romans 8 and Genesis 3 tell us quite clearly that the entire creation was affected by the Fall.

      You say that that many bacteria share the exact same proteins. You need to go back and learn a bit of biochemistry, because that is not true. They produce many proteins that perform the same function, but they are usually different from one another. Once again, that’s because each organism has proteins that have been finely tuned to its individual chemistry.

      You really should read what I write rather than make up things that I supposedly believe. Nowhere in any of my writings did I even remotely imply that “the Creator personally took a mealybug and purposefully planted genes from different bacteria into its own genome just to substitute for a future symbiotic bacteria’s genes.” All I said was that the idea that unrelated infecting bacteria could randomly insert the 22 genes needed by the current mutualistic bacterium is absurdly unlikely, which is what the current research in the field tells us. I also said that if you start with the idea that the mealybug was designed to live with mutualistic bacteria, you get rid of absurdly unlikely events. The genes didn’t come from different bacteria. You might find them in different bacteria (because they do an equivalent job), but that doesn’t mean they came from the bacteria. They were a part of the initial creation of this kind of insect so that it could live with mutualistic bacteria.

      Why would it be unnecessary for the mutualistic bacteria to lose the genes once it found a host? Any good Designer would put all sorts of failsafe devices in His design. Most likely, these bacteria were designed to serve lots of purposes, so they probably have a lot of different environments for which they were designed. As a result, they were given a full complement of genes. However, those who ended up becoming part of another creature that was designed for them didn’t need all their genes, so they lost them over time. Once again, gene loss is very easy to understand in terms of what we know about genetics. As the evidence I have already linked to you clearly shows, there isn’t a viable mechanism to produce new, innovative genes. As a result, the young-earth creationist view is consistent with the science we currently know. The evolutionary view is not.

      You claim that the “transferred” genes (which were probably not transferred) have been shown to have once belonged to symbiotic bacteria. That is simply not true. They have been interpreted to have once belonged to symbiotic bacteria. There is a big difference! You also claim that you didn’t want to show horizontal gene transfer among insects is widespread, but nevertheless, it is. However, once again, the evidence doesn’t support that. Based on what we know now, as the study I linked to you a few days back clearly shows, such transfer is “relatively rare.” Thus, in order to believe the wild evolutionary scenario, you have to believe a relatively rare event happened 22 times with just the right genes. You might have that kind of faith in random chance. I do not. I am quite sure you have your reasons for believing that mutualism like this can occur as a result of random chance guided by selection (when you want selection to work – when it is inconvenient, you ignore it). However, this study is certainly not one of them. This study shows how absurdly unlikely it is.

      I notice that you completely ignored a question I asked you. You asked me:

      Beyond the tangled mass of assumptions and unsupported postulates, on what biblical basis do you justify the notion that God did not create bacteria, fungi, and viruses to be pathogenic?

      I gave you my reasons (which you unsuccessfully tried to argue against), and I then asked a similar question of you, but you didn’t reply. I will as again:

      Beyond the tangled mass of assumptions and unsupported postulates, on what biblical basis do you justify the notion that God did create bacteria, fungi, and viruses to be pathogenic?

      Kindly reply to the question, since I have patiently answered all of yours.

  7. Alex Coeles says:

    Thank you for patiently waiting for my response. I have been somewhat busy, so I did not respond immediately.

    You somehow claim I’m reading into Genesis and just making things up in a sense, because I just don’t want the ground’s composition to be altered. I’m not reading anything into anywhere. The fact is that you are reading things into the passage. I see no reason to believe the ground’s composition was ever changed, yet somehow you insist that it was, without providing any reason to.

    What you are saying about the use of the word “ktisis” is simply wrong, at least according to Strong’s Concordance. “Ktisis” actually is used many times to refer to the human creation.
    http://www.teknia.com/greek-dictionary/ktisis
    So I am still curious as to why you would assert this so confidently.
    Besides, in looking at the overall context, why would Paul bring in a reference to the creation in a chapter that, as a whole, is devoted to a discussion of the Spirit in the lives of believers vs unbelievers. It makes absolutely no sense that Paul would be talking about the nonrational creation. What is the point of the whole universe waiting eagerly to be set free if it will, in the end, be destroyed? The Bible does not say the universe will be set free from its current state, it will instead be destroyed, which is also a reason not to believe the idea that the new universe will be a restoration of the old one. Promoting the use of “ktisis” as strictly referring to the entire created universe would, in this context, be unwise.

    It is true that the organisms said to exist in the new universe are recognizable, but there is absolutely no evidence to suggest that this is some restoration of anything. I simply cannot see how the mention of some animals gives you justification in saying that the new universe will just be a restoration of the old one. The whole point of the new universe is to illustrate a new birth, not going back to the first one. There is no reason to believe the very physics of the preFall universe were any different from those today. You are just assuming that because the new universe does not have the effects of the Fall, that somehow means the preFall universe was exactly like it. Besides this, everything indicates that the new universe will be VERY different in its physical composition. I do not know how far you are willing to go to say the extent of the fall radically changed E-MC2 (once you change entropy, you change many things) but there is also no reason to believe anything did change physically.

    The idea that the universe reflects the spiritual condition still makes no sense. After all, it was a spiritual Fall, and not a physical one. The latter is largely inferred just to provide support for the young earth model, which seemingly cannot stand without it. Once you remove the evidence that the new universe will be a restoration of the current one, the young earth creationist finds himself in a difficult position because he can no longer use it to provide support for the absurd notion that carnivory and disease did not exist in the natural world (not the human world) prior to the Fall. When you remove that, you remove a large chunk of support for the young earth model as a whole.

    You say a creation cannot be “very good” if it includes animal and plant suffering. You are simply mistaken. Pain and suffering in the plant, bacteria and animal kingdoms is not evil. Suffering in mankind is different. Asteroids have existed for a very long time, as pathogens have. They have the potential to cause suffering to people, but it is the Fall that triggered our susceptibility to such things. Death existed before the Fall in the plant kingdom, at least. It is no more evil for a plant to die than for an animal. However, when it comes to spiritual creatures as humans, that is quite different. Christ did not defeat animal and plant death, He defeated human death in a very different sense. This argument comes from many young-earth circles but is faulty theologically and doctrinally. Extremely so.

    I find it very likely that these genes came from other bacteria specifically because they are known symbionts, and bacterial symbionts are known to transfer genes. You also claim hese genes were just “similar”, but they definitely came from several lineages and were identical to those identified in the paper. They have several tables to demonstrate this. It is not such a matter of interpretation as you might believe. It is a statement of fact. The horizontally transferred genes were found and verified. Just read the paper.
    http://topicpages.ploscompbiol.org/wiki/Detection_of_horizontal_gene_transfer

    I do not believe God hand-crafted bacteria to be pathogenic (as I have already mentioned) because I believe bacteria, fungi, and viruses developed as part of a natural function known as evolution. I am an evolutionist, scientifically. But the redundant nature of your question I took to be a quote of mine that you had left by mistake.

    Dr. Wile I must ask out of mere curiosity – how did you become a young earth creationist?

    1. jlwile says:

      Thanks for your reply, Alex. Not only are you reading into Genesis, you are reading into my words. Nowhere do I claim that the composition of the ground was altered as a result of the curse. I simply state what the Bible clearly states: that the earth was cursed as a result of the Fall. This tells us, then, that something outside the world of man was cursed as a result of the Fall. This tells us what a good exegesis of Romans 8:19-23 already tells us – “creation” does not refer just to the world of man. Thus, “all creation” means (not surprisingly) all creation.

      Once again, please actually read what I write. I never claimed that the word ktisis can’t refer to all humanity. In fact, I made the very clear statement that in some passages it does. However, I also showed you that in some passages, it refers to all of creation. As a result, you have to use context to determine what it means. The context of Romans 8:19-23 makes it very clear that it refers to all of creation, since the passage makes the distinction between creation and men. You claim that it is trying to make the distinction between believers and unbelievers, but as I have already explained, the original Greek makes it quite clear that’s not true. When the New Testament Scriptures discuss the world of unbelievers, they generally use the Greek word kosmos. Thus, if the passage was trying to do what you claim, it would not have used ktisis. It would have used kosmos instead. Once again, however, that’s not the only piece of information that tells us Romans 8:19-23 is referring to all creation. Genesis 3:17 makes it even more explicit.

      Speaking of Genesis 3, please explain how Genesis 3:14 fits into your theology:

      The Lord God said to the serpent, “Because you have done this, Cursed are you more than all cattle, And more than every beast of the field; On your belly you will go, And dust you will eat All the days of your life;

      If the rest of creation wasn’t cursed as a result of the Fall, why does the Bible say that the serpent cursed? Also, why does the Bible say the serpent cursed more than the cattle and every beast of the field?

      You ask why Paul would bring in a reference to all of creation in a passage that deals mostly with people. The answer is rather obvious. This passage of Scripture wants to make it clear that for now, suffering is the norm. So the passage tells us that all creation suffers until the new heaven and earth. In other words, the passage is telling us that we are not alone. Everything is suffering, but that suffering will be worth it in the end.

      You ask, “What is the point of the whole universe waiting eagerly to be set free if it will, in the end, be destroyed?” I think you need to read the Bible a bit more, because the rest of creation will not be “destroyed” when the new heaven and earth appear. Indeed, as I have already shown you, Isaiah 65:17–25 and Isaiah 11:6-9 make it clear that the new heaven and new earth will have plants and animals that are a part of the creation we are experiencing right now. Thus, the creation we are experiencing right now will not be destroyed. It will be remade, because the effects of the Fall will be removed.

      I am not sure why you don’t want to see this obvious conclusion. You claim that the recognizable animals that will be a part of the new creation don’t provide evidence that the new creation is a restoration of the old creation. You claim that there is no evidence that the new creation is a restoration of the old one. However, that is simply not true. Acts 3:19-21 tells us:

      Therefore repent and return, so that your sins may be wiped away, in order that times of refreshing may come from the presence of the Lord; and that He may send Jesus, the Christ appointed for you, whom heaven must receive until the period of restoration of all things about which God spoke by the mouth of His holy prophets from ancient time.

      As you can see, then, the new heaven and earth are not the result of the current creation being destroyed. They are a result of the current creation being restored.

      You claim, “…everything indicates that the new universe will be VERY different in its physical composition.” Can you please tell me exactly where the Bible says the new universe will be very different in its physical composition? As the Scriptures I have given you clearly indicate, it seems that it will be very similar in its physical composition. For example, there will still be the processes of photosynthesis, germination, and reproduction (for the maintenance of vineyards, for example). There will also still be mammals, and children will still nurse. Where, exactly, is the VERY different physical composition of which you speak?

      I am not sure why you refer to entropy, but I assume it is because you are reading into what I write. Nowhere do I even remotely imply that entropy didn’t exist before the Fall or that it won’t exist in the new creation. Entropy isn’t a bad thing. It is a good thing, as it keeps water from freezing at temperatures above zero degrees, for example.

      I am also not sure why you think I am claiming “that the universe reflects the spiritual condition.” I am not. I am just saying what the Bible clearly says – that the entire creation was cursed by the Fall. Also, I am not sure why you think I am claiming that carnivory did not exist before the Fall. I have always made it very clear that the Bible is silent on that point. Indeed, I get a lot of flack from my fellow young-earth creationists for making this clear. No, the absence of disease before the Fall is not some device to “provide support for the young earth model.” It is simply the result of good exegesis.

      Once again, please actually read what I write rather than reading into my views what you want to read into them. I never said that plant and animal suffering and disease cannot be part of a “very good” creation. I simply said, “I am not sure how pathogens fit into a ‘very good’ creation.”

      You say, “Pain and suffering in the plant, bacteria and animal kingdoms is not evil.” Could you please elaborate on that? Does that mean it’s okay for me to start torturing animals, since their pain and suffering is not evil? I think what you want to say here is that pain and suffering in the animal kingdom are natural. I am sure you wholeheartedly believe that, but so far, you haven’t given me any reason to believe that. Instead, you have had to radically alter the meaning of several passages of Scripture in order to get away from the rather obvious conclusion that pain and suffering, even among animals, is bad.

      You claim, “It is no more evil for a plant to die than for an animal.” I am not sure that’s the case. As far as we know, plants can’t suffer pain. We know, however, that animals can. Thus, I would say that plant and animal death cannot be on the same level, since the animal death we see now involves pain and suffering.

      I agree that Christ did not defeat plant or animal death. He defeated human death. However, that tells us nothing about whether or not the entire creation was cursed by the Fall. We know plant death happened before the Fall. The Bible is silent about whether or not animal death occurred before the Fall. It tells us clearly that human death did not occur before the Fall. We also know that Christ died for people, not for animals. Once again, however, this tells us nothing about whether or not all of creation was affected by the Fall. Genesis 3 and Romans 8 tells us quite clearly that it was. This effect may or may not have involved the death of animals. We don’t know. We just know that all of creation was cursed by the Fall.

      When it comes to the source of the 22 genes that are conveniently in the mealybug but needed by the mutualistic bacterium, you claim, “…they definitely came from several lineages and were identical to those identified in the paper. They have several tables to demonstrate this. It is not such a matter of interpretation as you might believe. It is a statement of fact.” I am wondering why the authors weren’t nearly that emphatic. Here is what they say:

      Phylogenetic Analyses Suggest the Source of Most ExHTGs Are Facultative Symbionts

      The inferred phylogenetic positions of these ExHTGs suggest that facultative symbionts—i.e., bacteria that are not required for host survival—have been involved in HGT to the insect genome…

      In case you aren’t aware, “phylogenetic analysis” is an incredibly speculative analysis that involves a lot of assumptions. Indeed, it often produces laughable conclusions. I suspect that’s why the authors are very tentative in their discussion of the source of the these genes. I wonder why you are so emphatic. Do you have access to data that the authors don’t have?

      You also claim, “I find it very likely that these genes came from other bacteria specifically because they are known symbionts.” Once again, however, the authors do not agree. They state:

      We note that none of the putative source facultative symbionts are known to reside in the mealybug population used for RNA-seq (C.D.v.D., unpublished data) and thus seem to be signatures of historical, transient infections.

      It is clear that my description of this being an interpretation is the correct one, unless you are working with data that were unknown to the authors at the time of the study.

      Thanks for answering my question. When you use unnecessarily insulting language, I like to parrot it right back to you, to make it clear that both sides of an argument can be insulting, but it generally doesn’t produce any serious enlightenment. So you think that pathogens just happened to develop as a result of the evolutionary process. However, it seems that you think humans weren’t at risk of infection until after the Fall. Is that correct? If so, I am wondering exactly when this happened in the supposed evolution of man. Was the supposed human/chimp common ancestor also free from the effect of pathogens? Was it just the first human population that was free of pathogens? If so, what were the evolutionary conditions that allowed evolved humans to escape the pathogens while the rest of the evolving world had to deal with them?

      You ask how I became a young-earth creationist. It was a long journey. When I was an atheist, I wasn’t crazy about evolution. Even back then, it was clear that evolution was a hypothesis that was more at odds with the data than it was consistent with the data. However, the more I learned about science, the more it became clear that what we see in science is the result of design. That led me to belief in God. I read several different holy books and commentaries, hoping to find out more about this God. The Bible and the evidence that supports it led me to believe that He is the God of the Bible. At that point, I became a Christian. However, I was happy with the idea that the earth is billions of years old until I started seriously working on my PhD in nuclear chemistry. At that point, several lines of scientific evidence pointed to the fact that the idea of an ancient earth is more speculation than science. As a result, I began to believe there was something wrong with the current dogma related to the age of the earth. Over time, the more I looked at the evidence, the more it became clear that the earth is thousands of years old.