Consciousness and how it got to be that way

Monday, April 27, 2020

Is a Virus Alive?

The pandemic has brought this question much more public attention than usual. It seems to be an interesting question - but on scrutiny, the problem evaporates.

Viruses are replicators. The question of whether they (or anything) is alive is not a useful one.

It boils down to this: in most of these discussions, what we're really asking, when we ask if COVID-19 is "alive", is whether it can make us sick. If it can replicate, it can make us sick, and we know that viruses can replicate. Categorizing things as "alive" turns out to be an arbitrary exercise that neither organizes our knowledge nor adds information - it's much like asking if a submarine swims. What this exposes is that we have no definition of "alive" to begin with. "Alive" is just the label in English for an intuitive category in our animal brains having to do with animacy or agency, and at the molecular level or with non-intuitive strange entities like viruses (or slime-molds, or jellyfish) these intuitions fail us.

More explanation:
  1. Specific to COVID-19, most of them time people ask "Is it alive?" when we're talking about the virus "remaining alive" for certain lengths of time on surfaces. Of course what we really care about is whether it can make you sick. Poison oak oil (urushiol) can cause a Type IV allergic reaction after decades. Is it alive?

  2. "Make you sick" corresponds to "reproduction". Fire, stalagmites, and black holes (if you follow Lee Smolin's argument) all grow and/or reproduce. Why aren't those alive?

  3. You might have rolled your eyes when I mentioned fire, and not been wondering whether that is a living thing. We instinctively recognize there's a distinction, but it's worth spending time on. There IS something qualitatively different between a virus, and fire. Viruses are discrete entities that are alike - with elements ordered in a certain way - despite having been made from those elements when they were NOT so ordered. But fire does not carry historical information in this way. That is to say - if two coworkers get infected with COVID-19, despite being genetically different people with different cells, they will produce identical viruses. You can tell the viruses came from other coronaviruses. In contrast, if you light two identical sticks, one by sticking it in a campfire and the other from a cigarette lighter, it doesn't matter - they will burn the same way. You can't tell where that fire is "descended" from.

  4. Being more specific, viruses and people are both replicators. That is a useful category which encodes a qualitative difference. Fire is not a replicator. Viruses are. While fire might not be an interesting boundary case, transposons, prions and computer viruses might be. Viroids shouldn't really be considered a boundary case since they're really just naked viruses that take advantage of intercellular junctions in plants, but somehow people seem to think viroids are less alive than viruses.

  5. Interestingly, we don't have to be explicitly taught what things are alive and what things are not. Speculatively, there may be a central pattern generator that has some combination of animacy, agency, reproduction, and growth. Which does usefully capture all the living things knowable in the macroscale world that our ancestors inhabited for millions of years.

  6. Part of the problem with asking this question is there is no definition of "alive". Molecular biologists got bored with this question very quickly because it didn't advance any hypotheses. (Think of it as the "how many angels can dance on the head of a pin" question for this field; or if you're given to Eastern thought, "since yang is both hard and white, what is the logical relationship between these two things". That is, a problem which only seems to be a problem because of other assumptions which turned out to be wrong or unnecessary, and even if the question was meaningful, answering it turned out to be uninformative and arbitrary.) The most common definition used - again, not necessary for any experiment - is independent metabolism. You might say that an organic virus is not alive because they have no independent metabolism - this is the usual cutoff. What about chlamydia? This is an actual genus of bacteria which is obligately parasitic on host ATP. (A medically relevant genus no less, because it causes diseases humans.) Yes, it uses ATP. So do viruses once they're inside cells. So instead of "alive" why wouldn't we just say "independently ATP generating"?

  7. And yet, it does seem very unsatisfying to learn that "alive" - an apparently important distinction between the types of objects I see when I look out my window - is actually arbitrary. That's because I don't see anything that the term doesn't seem to work for. I see on one hand rocks, clouds, the roof of my porch, and on the other, flowers, birds and grass. Naked-eye observers of the natural world are the Newtonians of biology. Looking out your window, you can't encounter anything where your instinct of "alive" and the better category of "replicator" don't line up...

  8. ...but as soon as you see viruses or viroids or prions, your assumptions are falsified and these traits no longer overlap. Another place where the same debate happened, interestingly also outside the realm of every day experience was in the nineteenth century attack on the idea of vitalism, where a supposed distinction between living and non-living materials was shown empirically not to exist. So to stretch the analogy, Woehler was molecular biology's Planck, and instead of the ultraviolet catastrophe, he demonstrated the urea epiphany.

Saturday, April 18, 2020

Number of COVID-19 Cases Correlates With Population Density

It seems fairly obvious that density should correlate with how fast a virus spreads. Comparing across countries or even states is difficult due to time of introduction as well as many other variables. This should be less of a problem (but certainly not zero problem) for a study of of cases by county within a single state. Therefore I looked at the relationship between density and cases. Keep in mind this is an ongoing pandemic so time of introduction will still make a difference, and for that matter there is no effort to control for other variables (e.g., difference in testing frequency by county.) Both axes are log 10 mostly to group points together. As you can see from the R^2 there's quite a close association.

The next and less obvious question is, if viral load (total number of viruses an infected person was exposed to) correlates with illness severity, you would expect that density would also correlate with deaths. There are even more variables that come into play with deaths - age and health of the population which definitely differs, as well as access to medical care and ICU beds. So I did the same thing for deaths; I'm not showing it since I found an R^2 of only 0.0845. I predict that a month from now that R^2 will be higher.