Consciousness and how it got to be that way

Sunday, June 7, 2020

Parasite Burdens and the Flynn Effect

The Flynn Effect is the real, not-test-based increase in IQ seen in first-world countries, about 3 IQ points a decade. In the last couple decades the effect has leveled off in much of developed world. There's a lot of discussion over why this should be.

One obvious candidate is parasite burden. As countries develop, public sanitation gets better, and public health improves. If it's public health (pathogens plus nutrition) and offering standardized schooling to all, you would expect to see an eventual plateau in developed countries, and the developing countries begin to follow their trend.

Any parasite which directly damages the brain is an obvious candidate as one causative agent. This is especially interesting when you read that up to one-third of people in, e.g. Peru, have radiographic evidence of neurocysticerosis - tapeworm damage in the brain. This study shows that of people with evidence of the disease, 18.2% of them in childhood have IQ < 70. Starting to connect dots, we can start making an estimate of IQ improvement from eradication of neurocysticercosis alone.

  • Let's assume that (as the Peruvian study showed) 33% of people have neurocysticerosis.

  • Let's assume that of the people with neurocysticercosis, 18.2% (4% of the total population) have IQ < 70, the mean IQ is 69. This is obviously simple and actually quite conservative, but the higher we make the mean number for this subgroup, the more modest the effect of eradicating neuroscysticercosis.

  • Let's also assume that the 70 and above IQ folks are evenly distributed between 70 and 100. Also simplifying, but I doubt neurocysticercosis makes many people smarter.

  • With those assumptions, then a 3-point IQ increase in the general pouplation could be brought about by a one-third decrease in NC cases.

  • Of course the 3-point IQ trend goes on for more than 3 decades (when all three-thirds of would-be neurocysticercosis patients were prevented from getting it) so it can't just be that.

To test the hypothesis, we could look at average IQ increases going forward in developing countries currently getting de-wormed. You could also look at existing Flynn Effect curves for the developed world and compare it against the % population getting on clean public water supplies. Of course it's hardly controversial that lower parasite burden would correlate with better outcomes, and indeed the de-worming projects have already shown an improvement in school attendance in participating areas. And while parasite diseases cause massive human suffering, this is still interesting even just by purely pragmatic reasons: a country's economic well-being is linked to the average IQ.

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.

Friday, March 27, 2020

Why We Failed to React to the Pandemic

Given how the pandemic dominates all other news, an appropriate warning about it should have done the same. Yet in the West there was no such thing that I was aware of, including in the rationalist community.

  1. We can't call it a failure to predict. I think few people in the rationalist community would have argued that a pandemic could NOT happen, before NYE 2019. It's a failure to react, even once we saw THIS non-hypothetical pandemic coming. Am I missing people who were sounding the alarm? If not, it seems rationalists are no better at spotting information important to survival than anyone else.

    (Side lesson: most cognitive skills are not as generalizeable as we would like to think. Because you are good at thinking critically about software does not necessarily mean you're good at thinking critically about epidemiology. I suspect this is because understanding the relevant variables is mostly about memorized instinctive system 1 associations and weightings that come from experience.)

  2. Very few people saw this coming - "this" meaning "a possibility of a pandemic we must plan for". Including rationalists. Including superforecasters. People in epidemiology knew it was possible but it's hard to evaluate their claims of danger over any other profession that predicts low-probability high-consequence events in a way connected to professional success (they're always thinking about pandemics, appropriately); Bill Gates and a few other smart people outside the epidemiology world tried to raise consciousness about the possibility prior to this particular event. Was there a way to pull the signal out from them above all the other constantly-broadcasted jeremiads at the time? And it wasn't like an earthquake where one second it was there, the next it wasn't, and so far as we know there's no way to spot it early; it has been there since December and the large majority of us in the US, including rationalists, did not care much until early March. This was in no way a black swan. We knew it could happen, it had happened several times before, and we had weeks of growing warnings. It was a white swan, walking slowly toward us from the horizon, just like the last few white swans did.

    [Added later: Nassim Nicholas Taleb uses exactly the same language in this Bloomberg interview. And read more here about why it was so hard to raise the alarm.
  3. Most depressingly, all this occurred after we (in the rationalist community, in parts of the psychology and media and data world) had for years pointed out the failures of predictors repeatedly and tried explicitly to improve. It's depressing because this raises the question of what else we're missing, and indeed if we ever can NOT miss things like this. Again: not even a failure to predict. A failure to react. Why? Denial, fear of social censure by others not on board? Bounded rationality, ie most of us are too stupid to extract important signals and extrapolate?

  4. As a result, I am now particularly concerned about the likelihood of Carrington events and nuclear war - see here and here for near-misses (never mind their intentional use, which is also possible - indeed, that's why they were built and why they continue to be maintained.) The 1983 event is particularly chilling and came down to the career-risking, intuitive, principled judgment of ONE MAN. Petrov should be a name repeated with reverence around the world, since arguably it's because of him that there still IS a world. Our overconfidence that it can't happen occurs on a similar time scale with the Asian flu of 1957-58 which resulted in school closures and an economic downturn, though not on the scale we're seeing with COVID-19.

  5. We have never seen runaway AI. We have seen nuclear weapons used in war. I wouldn't argue against the possibility of a hard AI takeoff, but you canNOT argue against the possibility of nuclear weapons used in war, because it has already happened once. Interestingly, of all the stupid denialisms out there, I have never run into Hiroshima-Nagasaki denialists.

    Another white swan on the horizon that rationalists should spend more time stopping.

Added later:

Here's Scott Alexander's review of the book written by Toby Ord, which besides AI lists pandemics and nuclear war. Before you're too thrilled that he gives lower numbers for nuclear war than AI, those numbers are for TOTAL EXTINCTION OF THE HUMAN RACE, not the chance of it happening. There's a lot of space between "extinct" and "a lot of the people you love will die and all of you will suffer horribly" just like there's space between "okay" and "needs intubation" with COVID-19, so don't think mild to moderate means okay.] Yet another time we survived by dumb luck:
...even when people seem to care about distant risks, it can feel like a half-hearted effort. During a Berkeley meeting of the Manhattan Project, Edward Teller brought up the basic idea behind the hydrogen bomb. You would use a nuclear bomb to ignite a self-sustaining fusion reaction in some other substance, which would produce a bigger explosion than the nuke itself. The scientists got to work figuring out what substances could support such reactions, and found that they couldn’t rule out nitrogen-14. The air is 79% nitrogen-14. If a nuclear bomb produced nitrogen-14 fusion, it would ignite the atmosphere and turn the Earth into a miniature sun, killing everyone. They hurriedly convened a task force to work on the problem, and it reported back that neither nitrogen-14 nor a second candidate isotope, lithium-7, could support a self-sustaining fusion reaction.

They seem to have been moderately confident in these calculations. But there was enough uncertainty that, when the Trinity test produced a brighter fireball than expected, Manhattan Project administrator James Conant was “overcome with dread”, believing that atmospheric ignition had happened after all and the Earth had only seconds left. And later, the US detonated a bomb whose fuel was contaminated with lithium-7, the explosion was much bigger than expected, and some bystanders were killed. It turned out atomic bombs could initiate lithium-7 fusion after all! [my emphasis] As Ord puts it, “of the two major thermonuclear calculations made that summer at Berkeley, they got one right and one wrong”. This doesn’t really seem like the kind of crazy anecdote you could tell in a civilization that was taking existential risk seriously enough.

Added still later: depressing results that cognitive biases are extremely difficult to avoid even with explicit high stakes incentives.]