Posts in: science

House of quicksand and fog

Yesterday, I quoted John Ioannidis’s description of how the pandemic was changing the norms of science:

There was absolutely no conspiracy or preplanning behind this hypercharged evolution. Simply, in times of crisis, the powerful thrive and the weak become more disadvantaged. Amid pandemic confusion, the powerful and the conflicted became more powerful and more conflicted, while millions of disadvantaged people have died and billions suffered.

First, note that no one person or thing (or a few countable ones) was responsible for the transformation, but rather that it was a natural property of the system. Then note that the pandemic sped up (or “hypercharged”) the system’s transition to its (breaking) endpoint. The American clinical trial ecosystem is even closer to its breaking point than science overall, and for the same reasons: its postulates make it untenable, and the influx of ZIRP-conjured pandemic-stamped money hypercharged the transition to this.

People go looking for ways to speed up clinical trials like they would for speeding up house construction. They ask: what is one key piece of legislation — the parking and zoning requirements of clinical research — that could either be tweaked or removed to break open the damn, so that trials would be as fast as they were in the 1960s? And why won’t the clinical trial hobbits tell us what those obstacles are, so that we can crush them?

But there is no one, or two, or two dozen such obstacles, the serial removal of which could speed up trial design, approvals, execution and readouts. The clinical trial path does not have boulder problem. Boulders would in fact be great: at least you can, while climbing over or making a 3-day detour around, fantasize about crushing them.

No, the problem with the path is that it runs through quicksand while being covered by a dense fog. Move too fast or stand in place and you die; move too slowly and you don’t get anywhere. Not that you know where to go: with all-encompassing fog you can only see five inches ahead anyway. There is not much time to think about anything else when you are in that kind of a quagmire, and how exactly would you imagine dealing with the fog? Drive it away with a big fan?

By “quicksand” I mean the moral, ethical and physical safety risks inherent to any clinical trail This is why every introductory course on the topic must start with the ignominious history of experimenting on humans… and the systems we developed to deal …immediately followed by a description of Institutional Review Boards and other regulatory matters. with them.

By “fog” I mean that much of the deliberation is not a matter of legislation but of opinion, values, principles and — the most loaded of words — comfort of people sitting on these IRBs and in the regulatory agencies. Depending on comfort level of individual members a question on whether a trial can proceed may take much deliberation or none at all. We can hardly know our own minds, and good luck about reading other people’s.

This is why I am skeptical that uncovering the FDA’s records would be of help to anyone but historians: the people who wrote them and interpreted them are no longer in play; different brains run the show, and the archives won’t reveal their thought process. Sure, sometimes there is one person sitting there that makes things worse than they should be, by being too slow, or thoughtless, or obstinate. But is “find better people” a tenable solution, when those people could be doing anything else, and with more reward of all kinds?

The pandemic hypercharge made everything worse. In addition to wading through quicksand while blinded by fog you now have to deal with many, many invisible neighbors elbowing you in the chest and kicking you in the groin, some intentionally, some out of carelessness, confusion, or not knowing any better. IRBs are overloaded and so are the regulators. What difference would any legislative change make?

Except, of course, it is to abolish one or both. It would lift the fog, sure, but would need a new kind of system to avoid making everyone sink to the bottom of the ethico-moral pit. Tearing down institutions is easy, building them is hard, as we see one but not the other being played out under our inattentive eyes.


Sunday links, short but with a punch

  • Rachel Kwon: Slowing Down. It is about living life in the slow lane after 40. As a recent entrant into the fifth decade I observed the same. For me, this only applies to the physical world — I still tend to be impatient with bits and bytes.
  • Raghuveer Parthasarathy: Some data on homework and its correlations. This is about assigned work at university level courses, and in my mind “homework” should be kept in grade school. I remain a big proponent of oral exams, though we don’t use them in the one course I teach.
  • Katarina Zimmer for the journal Nature: ‘Lipstick on a pig’: how to fight back against a peer-review bully. Quoth reviewer two: “The first author is a woman. She should be in the kitchen, not writing papers.” Should we trust science more or less when we have this kind of information? (ᔥDerek Lowe)
  • Nori Parellius: What the left hemisphere might tell us about large language models. Very much a plug for Ian McGilchrist’s The Master and His Emissary which I have yet to read. I, too, would much prefer we use “confabulation” instead of “hallucination”, though it also has some troubling assumptions of its own.

To increase trust in science, button it up

1

Two academics discuss science communication over BBQ and reach the wholly unoriginal conclusion that for increased trust in science, the American research community needs to:

  • acknowledge uncertainty
  • create meaningful participation
  • increase transparency
  • recognize broader concerns

These seemed redundant, as we have been marching towards more openness in science of every kind since at least the early 2000s. Would any scients be able to say, with a straight face, that their average peer projects more certainty, advocates for more gatekeeping, promotes reduced transparency and does not acknowledge controversy as much now compared to the 1950s?

One could in fact, if they were less charitable, blame this newly found openness for the collapse in trust. On one hand you see scientists fighting for clout on social networks, calling each other names, and blowing up small arguments — on the level of angels dancing on the head of a pin — into debates of the century. On the other, everyone and anyone, homeschooled child geniuses and crackpots alike, now has open access to much of specialized scientific literature, and to preprint servers for some samizdat science.

So maybe it is time to own it: yes, openning the kimono has lead to decreased trust in the estabilshment. But was that not the widely understood part of the bargain? I imagine Paul Feyerabend would have been proud of these recent developments.

2

How did the fellows above come up with the idea that more of the same would help shore up trust? Being academics, they have a reference — to the work of Sheila Jasanoff whose work on “civic epistemiology” is described thusly:

Jasanoff’s research identifies distinctive features of how Americans evaluate scientific claims:

Public Challenge: Americans tend to trust knowledge that has withstood open debate and questioning. This reflects legal traditions where competing arguments help reveal the truth.

Community Voice: There’s a strong expectation that affected groups should participate in discussions about scientific evidence that impacts them, particularly in policy contexts.

Open Access: Citizens expect transparency in how conclusions are reached, including access to underlying data and reasoning processes.

Multiple Perspectives: Rather than relying on single authoritative sources, Americans prefer hearing from various independent institutions and experts.

But of course this is hopelessly outdated, if it were ever true to begin with. Jasanoff herself cautions in the chapter of her book “Designs on Nature” where she describs the concept, that the framework offers conceptual clarity at enormous risk of reductionism, as it does not account for differences across social strata, through time, etc. The book is from 2005 and the research it is based on is even older. The “Americans” described above no longer exist.

Jasanoff’s civic epistemilogies were tied to countries. In the last twenty years these countries have lost ground as unifying social forces to a variety of cultures and subcultures. Her descripton of 2005 America may today better apply to the upper-middle-class across a subset of countries more so than a single nation. In each country, the different epistemiologies are becoming more and more opposed. How could we possibly trust each other?

3

There may be no way to return the trust in scence to the 20th century levels. But if we were to try, the most obvious method would be a return to gatekeeping. Leave the science to the scientists and let the outcomes speak for themselves. Keep all discord inside conference halls and university cafeterias. Show more decorum and respect, if grudging, to every scientist colleague while being more discriminatory of who is “a scientist”: PhDs from recognized universities only, please.

This would, of course, be a step back and I in no way, shape or form condone a turn of events quite like this — least of all because it would exclude me from the conversation.

4

Is there a way to stick to the “open science” principles while keeping some modicum of community trust? Being a fan of Costco, their sort of low but effective barrier to entry is appealing. For the uninitiated: Costco charges a modest annual membership ($65, or $130 for their “executive tier”) for the privilege of shopping for premium and premium-mediocre products at incredibly discounted prices. Their only profit is from the membership, as there is little to no margin. But then they also don’t need to spend money on things like advertising, keeping the shelves pretty, or monitoring for shoplifters.

The space between payinh $65 per year and earning a PhD is vast. Whatever the new gate is, it should probably not be degree-based. Maybe have it be a professional society that also takes up interested laypeople using its own criteria. Or a verified subscription to Experimental History. Whatever it is, make it official, make it publich, and make it stick. Then, keep most of the conversation inside the circle. Keep all ambiguity inside the tower, please, just make the tower entrance bigger and charge for entry.

5

Is this the way? I am not sure. Maybe science doesn’t deserve the public’s trust and attempts to increase it are like plugging tiny holds on a massive damn about to burst. But to those who care, let this be some food for thought.


Labor day links, and there are many of them

Happy grilling!


If you constantly cry corruption, could it be because you yourself are corrupt?

There are few pieces of advice as misguided as the one to “follow the science”. The most recent example for why that is comes from Tim Nguyen who describes While giving a shout-out to the podcasting grifter Lex Friedman, but I won’t hold that against him.a remarkable set of physics grifters:

We thus have a disturbing truth. Eric Weinstein, the man who waxes poetic about a Distributed Idea Suppression Complex, is a hypocrite willing to use his own influence to squash criticism. Weinstein’s grievances and tale of persecution are frequently invoked to serve his narrative, yet when he receives opposition, he is willing to use his own power to suppress others.

In that way Weinstein seems remarkably similar to a certain other grifter who — setting everything he can control in his own favor — sees everything not in his favor as rigged. This very phenomenon was discussed recently on the Dithering podcast, but was recognized a long long time ago.


Andrew Gelman writes:

One reason why these celebrity scientists have such great stories to tell is that they’re not bound by the rules of evidence. Unlike you or me, they’re willing to make strong scientific claims that aren’t backed up by data.

So it’s not just that Sapolsky and Langer are compelling figures with great stories who just happen to be sloppy with the evidence. It’s more that they are compelling figures with great stories in large part because they are willing to be sloppy with the evidence.

An under-appreciated fact which reminded me of this old post of mine.


Out today in Annals of Clinical and Translational Neurology: Durability of Response to B-Cell Maturation Antigen-Directed mRNA Cell Therapy in Myasthenia Gravis. It only took 18 months to get here from the pre-print but hey, we were able to get longer follow-up!


A wonderful example of why you should always check the primary sources from Andrew Gelman: When fiction is presented as real: The case of the burly boatmen. Caveat lector. Yes this applies to peer-reviewed literature as well. (ᔥAndrew Gelman, who self-cited)


For your weekend reading pleasure

Happy Friday, etc.


A brief note on AI peer review, education and bullshit

When I wrote about formalizing AI “peer” review I meant it as a tongue-in-cheek comment on the shoddy human peer review we are getting anyway. “Wittgenstein’s ruler: Unless you have confidence in the ruler’s reliability, if you use a ruler to measure a table you may also be using the table to measure the ruler. The less you trust a ruler’s reliability (in probability called the prior), the more information you are getting about the ruler and the less about the table.”, Nassim Taleb in Fooled by Randomness. Peer reviewers are the ruler, the articles are the table, and there is zero trust in the ruler’s reliability. It was also (1) a bet that the median AI review would soon be better than the median human review (and remember, the median journal article is not submitted to Nature or Cell but to a journal that’s teetering on being predatory), and (2) a prediction that the median journal is already getting “peer” reviews mostly or totally “written” by LLMs.

Things have progressed since January on both of these fronts. In a textbook example of the left hand not knowing what the right hand is doing, some journals are (unintentionally?) steering their reviewers towards using AI while at the same time prohibiting AI from being used. And some unscrupulous authors are using hidden prompts to steer LLM review their way (↬Andrew Gelman). On the other hand, I have just spent around 4 hours reviewing a paper without using any AI help whatsoever, and it was fun. More generally, despite occasionally writing about how useful LLMs can be, my use of ChatGPT has significantly decreased since I fawned over deep research.

Maybe I should be using it more. Doc Searls just wrote about LLM-driven “Education 3.0”, with some help from a sycophantic ChatGPT which framed eduction 1.0 as “deeply human, slow, and intimate” (think ancient Greeks, the Socratic method and the medieval Universities), 2.0 as “mechanized, fast, and impersonal” (from the industrial revolution until now), and 3.0 as “fast and personal”. Should I then just let my kids use LLMs whenever, unsupervised, like Neal Stephenson’s Primer (“an interactive book that will adapt as the user grows and learns”)? But then would I want my kids hanging out with a professional bullshitter? Helen Beetham has a completely contrarian stance — that AI is the opposite of education — and her argument is more salient, at least if we take AI to mean only LLMs. Hope lies eternal that somebody somewhere is developing actual artificial intelligence which could one day lead to such wonderful things as the “Young Lady’s Illustrated Primer”.

Note the emphasis on speed in the framing of Education 3.0. I am less concerned about LLM bullshit outside of education, in a professional setting, since part of becoming a professional is learning how to identify bullshitters in your area of expertise. But bullshit is an obstacle to learning: this is why during medical school in Serbia I opted for reading textbooks in English rather than inept translations to Serbian made by professors with an aptitude for bulshitting around ambiguity. This is, I suppose, the key reason why we need LLMs there in the first place for there is nothing stopping a motivated learner from browsing wikipedia, reading any number of freely available masterworks online, watching university lectures on YouTube, and interacting with professionals and fellow learners via email, social networks, Reddit and what not. But you need to be motivated either way: to be able to wait and learn without immediate feedback in a world without LLMs, or to be able to wade through hallucinations and bullshit that LLMs can generate immediately. Education faces a bootstrapping problem here, for how can you recognize LLM hallucinations in a field you yourself are just learning?

The through-line for all this is motivation. If you review papers in order to check a career development box, to get O1 visa/EB1 green card status, and/or get brownie points from a journal I suspect you would see it as a waste of time and take any possible shortcut. But if you review papers because of a sense of duty, for fun, or to satisfy a sadistic streak — perhaps all three! — why would you want to deprive yourself of the work? Education is the same: if you are learning for the sake of learning, why would you want to speed it up? Do you also listen to podcasts and watch YouTube lectures at 2x? Of course, many people are not into scientia gratia scientiae and are doing it to get somewhere or become something, in which case Education 2.0 should be right up their alley, along with the playback speed throttle.