I do have experience in academic research. I'm not sure I agree with the assessment that pharmaceutical companies play a limited role in clinical research.

> 3. The role of pharmaceutical companies is fairly limited to clinical research, getting over regulatory hurdles and marketing. In a given year approx 100k potentially useful compounds will be discovered, but only a couple are approved by the FDA.

This glosses over almost the entire drug discovery process, which is a crucially important and nuanced process that yields new fundamental science. The positive scientific externalities of clinical trials are unambiguously a good thing.

You are correct that much compound discovery happens in academic settings (though it does happen commercially as well.)

Discovering the basic compound chemistry is just the first step. It must pass through a series of critical scientific assessments to see if the compound yields statistically significant desired biological effects.

https://en.wikipedia.org/wiki/Phases_of_clinical_research

This process is the experimental phase of drug discovery. It involves hundreds to thousands of different researchers, participants, institutions, and explicit organizational dynamics. The cost must be borne and there must be incentive to bear the cost. My entire argument is that the patent system enables this incentive structure.

> Wrt general scientific research, science has always been fine without patents: Einstein, Feynman and Co don't need financial incentive to do their best work, it's just what they do.

This point speaks to a more abstract point that is useful to consider, not only in the pharmaceutical context, but in the context of what makes science: science.

You are correct that fundamental theoretical science has always been fine without patents. The men and women who output some of our species' most beautiful interpretations of nature are rarely motivated by money. (I feel like that aspect of your argument was a bit of a non sequitur, I think all scientists are motivated by intrinsic knowledge, not money. I'm uncomfortable with my perception that you were implying that pharmaceutical scientists are somehow distinct from the examples you provided. Apologies if I misunderstood.)

The distinction between the pharmaceutical industry and the fundamental work of Enstein, Feynman et al. is that the drug discovery process involves two major expressions of scientific thought: theoretical and experimental. In this case, the basic compound discovery would be an expression of theoretical science (and experimental work), which must in turn be validated by more experimental science: the clinical trial phases.

In your example, it is true that Einstein, Feynman et al. did not need financial incentive to make immeasurable contributions to collective Good. They were doing priceless theoretical work, for what they are primarily known for. But (un)/fortunately, we need to do experimental science as well. Sadly, this cannot be done for free.

To continue with the physics analogy, The Higgs boson was theorized "without financial incentive" prior to its experimental validation. Of course, the experimental validation cost billions of dollars and the output of one of the greatest feats of human engineering: the Large Hadron Collider.

In this case, it was incredibly "expensive" (arguably, cost should be no object) to do this experimental validation. The cost was borne by government funding, ostensibly to increase the sum total of Knowledge.

Of course, resources are limited. The government cannot fund all basic research. We have aligned market machinery to incentivize pharmaceutical companies to fund the incredibly "expensive" cost of drug discovery experimental validation. For better or worse.

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The premises to my argument:

- experimental validation (the lion's share of the drug discovery process) is necessary

- this process is expensive in terms of financial burden and opportunity cost

- despite our intrinsic desire to do all research, we must allocate our resources accordingly

- market actors in a (mostly) free market seek to maximize their utility

- a market actor (in a market with no property rights) presented with the choice of:

(a) spend X-Large sum -> manufacture + sell drug

or

(b) wait until other market actor spends X-Large sum -> manufacture + sell drug (at essentially zero input cost)

... can rationally wait to choose (b).

My argument:

- The pharmaceutical patent system provides the economic machinery necessary to incentivize private corporations to fund drug discovery experimental validation.

The point of mutual confusion or "the basics" as you put it:

The drug discovery process doesn't yield any meaningful scientific output, and is essentially an exercise in regulatory avoidance and marketing.

I disagree with "the basics" that you laid out.

I do want to say something explicitly: you've been very respectful and considerate and I really appreciate that. That's an increasingly rare thing on Hacker News.