I reject the notion that hypotheticals are actually a powerful tool, let alone a useful one. Or, at least, hypotheticals of the 'very simplified thought experiment' sort you seem to be talking about. Take the Trolley Problem, for example. The moral intuition we're supposed to be examining is when and if it is right to sacrifice the wellbeing of smaller groups for larger groups. The scenario is set up in such a way that you cannot "dodge" the question here, and you have to choose whether you'd rather be * A tyrant who appoints himself arbitrator over who lives and who dies, but in doing is empowered to save more people than could be saved through inaction alone, or * A passive non-entity who would rather let people die than make a morally difficult choice and thus defaults to inaction whenever matters become too difficult.
But someone might answer: "In the hypothetical, yes, you should obviously pull the lever because that leads to less deaths. But the problem assumes many premises which would not be true in real life, and changing those counterfactual premises to match reality would change my answer. In particular, humans in real life cannot be trusted to make life or death choices like this one fairly and accurately without their natural biases rendering their judgement unsound. It follows that a moral person should take precautions to prevent such temptations from arising and that, in practice, such precautions might take the form of seemingly dentological injunctions against hurting one person to help another, even when it appears to the actor that the greater good would be served."
Or they might answer: "In the hypothetical, no, you should obviously not pull the lever, because killing is wrong. But the problem assumes many premises which would not be true in real life, and changing those counterfactual premises to match reality would change my answer. In particular, it seems implausible that there is no other possible action which could save anyone on the tracks. Although it may seem callous to do nothing when helping others is within your power, the principle of 'do no harm' must come first. It follows, then, that a wise and moral person would prepare themselves in advance to take effective and decisive action even in cases where they are morally constrained from taking the most expedient option."
Both of these are contrary to the spirit of the hypothetical, but they also constitute more nuanced and useful moral stances than "yes, always save the largest number of people possible" or "no, never take an action which would hurt others"
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The Second Law of Thermodynamics causes the Kolmogorov complexity of the universe to increase over time. What you've actually constructed is an argument against being able to simulate the universe in full fidelity.
This is not and can not be true. I mean, for one the universe doesn't have a Kolmogorov complexity*. But more importantly, a hypothesis is not penalized for having entropy increase over time as long as the increases in entropy arise from deterministic, entropy-increasing interactions specified in advance. Just as atomic theory isn't penalized for having lots of distinct objects, thermodynamics is not penalized for having seemingly random outputs which are secretly guided by underlying physical laws.
*If you do not see why this is true, consider that there can be multiple hypothesis which would output the same state in their resulting universes. An obvious example would be one which specifies our laws of physics and another which specifies the position of every atom without compression in the form of physical law.