Down the rabbit hole: More on multispecies organisms

I just tripped and fell down another rabbit hole. I was going to skip this week, but I would love input on this issue, so here it is. Earlier I argued that the organism was a multispecies entity. This makes perfect sense if we consider mitochondria to be symbiotic bacteria in a host cell, and we talk about the microbiome. Now here is the question: If you catch the flu, or get a bacterial infection (to keep it cellular), is that disease part of you as an organism?


Dang another rabbit hole.

There are two important points to remember. First, in the phenotypic view I am advocating considering the phenotype to be a vector through time, with every trait (a measured aspect of the phenotype) having a time element. Thus, it is not my weight, but my weight when I am 19001055824 seconds old (that is approximately how old I am while writing this). This means that even very temporary things such as whether you are inhaling or exhaling is technically a valid trait. Thus, if you have a fever of 104 degrees on a Saturday morning, that is the value of the trait “body temperature”  at that particular moment. The question is, do we make a distinction because that temperature is “caused” by a flu virus? The truth is I am beginning to believe we cannot make that distinction.

Taking a clearer example. Consider a person who chooses to dye their hair purple. This color comes out of a bottle, and it is no sense genetic or otherwise heritable (well, maybe in some odd cultural sense). That said, it is part of the phenotype. If you were to categorize people by the trait “hair color”. this person would go into the “purple”. Thus, it is a valid trait, and a valid part of their phenotype. How do we deal with this? I would argue that the best way would to consider the bottle of hair color to be a non-heritable or environmental influence on the phenotype. By analogy, I think it is perfectly reasonable to suggest your 104-degree fever is also part of your phenotype.

purple hair

This woman has a purple hair. It is certainly part of her phenotype, but probably not heritable.   (from

So, your fever is part of your phenotype, but is the virus part of you as an organism? Certainly, we would not consider the bottle of hair color to be part of an organism. It is an external aspect of the environment that changes your hair color. Cold air temperatures may cause you to put on a coat (the coat wearing trait?), but it is certainly not part of your body. However, the virus differs here. It is IN your body, and in fact it is in your cells.

Consider our microbiome. There certainly are aspects of the microbiome that are acquired from our parents, either at birth, or because we live next to them as infants, and many of these we will pass on to our children.   Thus, they are heritable from the phenotypic perspective. However, others are picked up late in life, perhaps when we temporarily change our diet, and then lost again, perhaps when we revert to our old diet, and are not heritable. I think a strong argument can be made that this microbiome should be considered part of the multispecies organism: Selection acts on the whole organism; outside of perhaps prokaryotes, single species organisms don’t exist; as far as I know, animals cannot survive without their symbionts. From an experimental perspective, it is difficult or impossible to separate symbionts that are heritable from those that are non-heritable, and perhaps more important both can have significant effects on our phenotypes in ways that can affect our fitness. Thus, I think it can be argued that all aspects of the microbiome, whether heritable or not, should be considered part of the organism. Nor does it makes sense to me to argue that there is a minimum residence time before a symbiont or disease should be considered part of the organism. Such a waiting time is necessarily arbitrary, and as a result there will always be situations that are ambiguous.

Now comes the question: Should we make the distinction between the bacteria that we picked up on vacation that makes it easier to digest shrimp from another bacteria that gives us diarrhea? I cannot think of a criterion that does not require special pleading that incorporates the former, but not the latter into the organism.

One final caveat is that it is important to remember that the most appropriate unit to assign fitness depends on the trait being investigated. Thus, the colony might be the appropriate unit if we are examining colony defense, the organism if we are examining foraging behavior, and the cell if we are examining cancer. Perhaps the organism is best thought of as being equally fluid. A flu infection is an assault on our bodies, thus if our trait is immune response, maybe the organism is everything but the flu virus, whereas if we are looking at body temperature the organism is everything including the flu virus. This is a bit of a conundrum for me, and I am happy to get any feedback that anybody else may have.


7 Responses to “Down the rabbit hole: More on multispecies organisms”

  1. Joachim says:

    Your “transmission equations” seem to come close to what I mean, though you do not really have any equation, because they’d be too complex. Anyway, the distinction would translate into something like: if the transmission channels are identical or run in parallel, then it’s one multi-entity organism.

    For example, if part of our mirobiome is exclusively transmitted from parents to offspring, then that part of the microbiome would be part of the complex organism. As the transmission channel of mitochondria runs not only in parallel to that of its hosts but is the same (their eggs), they are part of the complex organism for sure.

    P.S.: While “complex organism” seems apt, it’s a historically loaded term, because John Phillips used it to mean a Clementsian superorganism (e.g., vegetation as an organism).

  2. Joachim;

    I think you raise some very good points. As soon as you start trying to define phenotypes and individuals you quickly discover that it is not easy. I do not pretend to have the final answer, and I would love to see more thoughtful discussion on the topic.

  3. Joachim says:

    P.S.: Note that nothing I’ve said requires the concept replicators or other Dawkinisms you hate. You can draw the distinction of entities having the same channel into the next generation or different ones without recourse even to genes, if you must.

  4. Joachim says:

    Maybe it helps to put the virus example to its extreme in order to see whether that leads ad absurdum. Suppose the virus is lethal and kills the body. I, then, do not see a big difference between this and a parasitoid that eats up its host from the inside. In both cases, one organism is growing and/or reproducing at the expense of another. And from that perspective the difference with a predator simply catching and eating a pray also vanishes.

    I know, you don’t Dawkins, but he did propose a useful distinction in The Extended Phenotype suggesting that those entities that use the same lineage into the next generation form one extended phenotype, whereas entities that can ‘exit’ the lineage at some point are parasites or something. The difference is that in the first case the fate of entities is bound together, whereas in the second case entities like mere commensals can leave a sinking ship. In the case of pathogens a parasites, they even do the damage before leaving the sinking ship.

    From this perspective, the flu virus is not part of the organism, even though it does not kill the host, because it leaves the lineage of the host and reproduces otherwise.

  5. radish says:

    Very thought provoking. I’ve seen plenty of similar “part of the phenotype” arguments for things like symbiosis, agriculture, husbandry, and prosthetic technology, but I am now seeing those arguments in a whole new light.

    So I guess I can’t help with the conundrum except to suggest that this might be one of those seemingly reasonable empirical questions — like “how long is the coast of Britain?” — which does not have a neutral answer.

    In the coastline case you need a unit of length in order to measure the coastline, and the unit you choose determines — literally — the length of the coastline. Without choosing the “correct” unit you cannot get the “correct” answer. But units are inherently arbitrary. If we want an answer at all, we must make do with one which, in a very real sense, we ourselves chose. It’s not merely that “length” requires an observer — it’s that this seemingly simple and independent measurement is inextricably coupled to the observer’s internal model of the world.

    The notion of “phenotype” seems similar. If you want to use it, whether for modeling purposes, as an observed variable, or whatever, you have no choice but to first make some decisions about what goes into it. Which in practice means that at least one solution is the conventional one of observing average values, and not looking too closely at the details.

  6. Clem says:

    Agreed, it is quite interesting. My first reaction as I saw the image of the purple hair is that it is NOT an aspect of the phenotype. Cut her hair off and it will not grow back purple. But on reflection I suppose one might consider her choice to color her hair a sort of niche construction… rabbit holes indeed.

    I know someone in a college town in the Midwest who battled with squirrels in his garden. He would trap them and take them out of town and turn them loose. Curious if he was taking them farm enough afield so they were not returning to his garden he would spray paint them while in the cage trap. I once asked how many squirrels he thought he’d treated in this manner. “At least a dozen, and the first summer alone, probably six or seven”. [BTW, I also wondered if he’d ever seen or recaptured a painted squirrel… he hadn’t]

    So if someone studying the feral squirrel population in the region of this particular town were to come across one or more of these squirrels, what should be done? To record an orange haired squirrel phenotype would surely be an artifact. If two orange squirrels of opposite sex should mate their offspring won’t be orange.

    So while I agree phenotypes do change over the course of an organism’s ontogeny, my instinct would be keep phenotype somehow connected to genotype. Bjorn is right – Nature doesn’t care what we call things. But the moment we try to communicate with one another we ourselves have to be concerned with what we call things.

  7. This is very interesting, and I think I lean towards agreeing with you that it makes the most sense to think of the phenotype as a very fluid entity. Perhaps this is one of the times when it is useful to keep in mind that nature doesn’t care what we call things.

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