Scientific Theories: A Parade of Interesting Scientists’ Stories is NOT a Defense

When defending the causal efficacy of a scientific theory, such as germ theory, it is critically important to ensure that the story telling embeds both the casual arguments and mutually exclusive evidence that proves one explanation is correct and the other is false. Telling compelling stories is nice, but defense requires logical rigor, not just emotions. The SUCCES acronym (Simple, Unexpected, Concrete, Credible, Emotional, Stories) created by the Heath brothers in their book Made To Stick is not enough for defending science. We need storytelling that communicates the logical exclusivity between the central dogma and the important competing theories that are rejected by that rhetorical structure. 

Recently a post claiming that germ theory is false appeared in my Facebook feed. The author claimed that disease is not contagious. I don’t know what claim for the origin of disease was behind the claim, but I am not going to get on their e-mail list to find out. It is probably something along the lines of systemic vulnerability which makes the presence of germs a symptom, a merely correlated factor, not the cause of the disease. 

The author was promoting a “secret protocol” that would cure any disease. He can be confident that some portion of the people who enact his protocol will get better and gratefully attest to the miracle cure that he provided. Those that don’t get better will mostly move on with their lives without a second thought for the failure of his protocol. And those few who don’t get better and decide to call him out will be dismissed as having failed to do it properly. That will happen no matter what ultimately caused the disease, so he and the other quacks have a reliable business model. 

After seeing the post I asked, “Would the defenders of germ theory please articulate the causal argument, explain how the experimental data would look in the case of support for AND against the germ theory explanation, and then point out the experiments that provide causal proof? This would be really helpful to those of us that believe in germ theory but do not have the chops to fully defend it.”

My helpful friend Greg immediately found a couple of videos about germ theory to answer my call:

“It's not hard to find sources. it took me all of sixty seconds to find these.

https://www.youtube.com/watch?v=N9LC-3ZKiok

https://www.pbs.org/video/how-we-discovered-germs-ots3wv/

The problem is that these videos are nice story telling ABOUT the parade of scientists who developed germ theory but they fail to satisfy my request. They are nice historical reviews but they do not articulate the causal argument and neglect to convey how the relevant experiments isolated causal factors in a manner that enables the result to provide mutually exclusive evidence for one explanation over another. 

Here’s a NatGeo video that explains one of Pasteur’s demonstrations of vaccination on sheep, it is closer to what I was requesting:

https://www.youtube.com/watch?v=1lLNZQVPpQA

It does not explain what the competing hypothesis was, so as good as it is, it still does not quite meet my criteria. 

One version of what I want is embedded in Steven Johnson’s great book The Ghost Map. He tells the story of the cholera epidemic that hit London in 1854 by focusing on both Doctor John Snow (as the TED-Ed video does) but also his antagonist-collaborator the Reverend Henry Whitehead who wanted to prove him wrong about the possibility of a particle in the water. Whitehead was instrumental in gathering good data because it was his parish in which the outbreak of cholera happened. He was a trusted figure in the community so he was able to thoroughly document the deaths and contribute substantially to the observational and logical corpus that enabled them to work out what was really going on. 

The key to the causal argument is pitting the expected data pattern from Whitehead’s miasma theory against Snow’s proto-germ theory (germ theory as we know it today  wasn’t fully developed until decades later by Pasteur, Lister, Koch, etc.) For instance, the prevailing winds through that area of London would have carried the “miasma” in a particular direction from the source, a water well, perpendicular to a Regent’s Road that had very few intersections. This particular feature cut the neighborhood of the well pump off from other neighborhoods. This means that if miasma were the true cause of the disease the wind would have carried the disease over the road and into the cut-off neighborhoods. That was not the case. 

Snow’s theory was that a particle in the water was the cause of the outbreak. After the data was collected and mapped the pattern showed that households that had to take fewer steps to get to the Broadstreet water pump tended to have more deaths than those that had to take more. The pattern was strongly correlated with the steps but not the wind. 

But the anomalies in the data were important, too. The nearby brewery had almost no cholera deaths because despite using the same water, the brewery employees drank beer, not straight water. The brewing process must have been eliminating the cholera. 

Another anomaly was a woman in an outlying area who died of the cholera. Upon investigation it turns out that she used to live near the Broadstreet well and had her children bring her that particular well water, which ended up killing her and many of her children, too. There were even more anomalies that consistently reinforced the idea that the cause had to be in the water, not the air.

Finally, Snow and Whitehead were able to find patient zero of that neighborhood outbreak was an infant whose mother dumped the soiled diapers into a basement cesspool, a common practice of the time. That particular cesspool was less than 3 feet from the Broadstreet well and had a leaky wall that introduced its foul contents into the well. Uncovering this specific information required two excavations because the first was done under the direction of miasmists who were not thorough enough. The second excavation was undertaken with the particle theory in mind so the excavation was done in a manner that could reveal relevant facts. Ultimately, the Broadstreet well was the source of death for the whole neighborhood, including a variety of outliers. 

The point is that compelling story telling is only part of the challenge that I posed. The critically important part is conveying how the evidence supports a mutually exclusive logical interpretation in support of one theory against the competing theory. I agree that the burden of proof is on those who make claims against germ theory, but we need to be proactive about making precise arguments in the context of compelling stories. Sloppy arguments embedded in compelling stories might be fun, but they are not doing the work that needs to be done. 

To restate my request to defenders of germ theory: tell (and share access to) compelling stories that embed the logic of mutually exclusive hypotheses about the causes of disease. A thorough defense should be able to explain what pattern of data the opposition needs to present in order to both undermine germ theory and support their own. If they come up with that pattern, defenders need to admit that a challenge is in play and figure out how each theory can be further tested to settle the challenge. 

It has also turned out in prior scientific controversies that mutual exclusivity itself proves to be the error. When physicists concocted the double slit experiment to settle the debate about whether light is a particle or a wave both sides legitimately claimed the results supported their hypothesis. Eventually, every legitimate physicist had to admit that both sides were right and light can have both sets of properties. 

Maybe germs are only part of the causal story. If the critics have some legitimate data that calls germ theory into question, we should be grateful. If they are making specious arguments then that should be demonstrable with data we already have. We need some storytellers who can be true to the logic of the experiments that can settle causal questions with mutually exclusive interpretations of good data.

I get that we should not address every crank who objects. Don’t feed the trolls, right? However, we also should be careful not to dismiss them entirely because if they build up sufficient political power they can simply deny the relevance of expertise, as the current federal administration here in the USA is doing. There is a political dimension to defending science that we ignore at our peril. We need skillful story tellers who can embed the logic of scientific argument in their stories, not just focus on a parade of interesting people.  

Simulated (A.I.) vs. Human Intelligence

A computer uses equations to seek verification from data; the human brain uses actions to seek falsification from the unexpected.

Computers, in other words, are passive learners. They amass facts and act only when prompted. Humans, meanwhile, learn dynamically. We take the initiative — and base our behavior not just on what we’ve previously memorized but also on the newness of our current environment. In familiar circumstances, we repeat what worked before. In novel circumstances (i.e. when our neurons sense unknown unknowns), we perceive: I don’t know exactly what to do. So, we improvise, experiment, and venture original behaviors.

That’s why human experts are able to act almost as smart as computers in regular environments — and why human experts are able to act much, much smarter than computers in volatile environments where newness (and therefore, not-knowing) is high. 

Excerpt by Angus Fletcher for Big Think 

https://bigthink.com/business/why-warren-buffetts-superpower-is-an-achilles-heel-for-ai/

A Classic Case of Correlation Being Mistaken For Causation: Excerpts from The Ghost Map by Steven Johnson, 2006

[William] Farr had been hired to track the most elemental of demographic trends: the number of births, deaths, and marriages in England and Wales. Over time, though, he had refined the statistics to track more subtle patterns in the population. “Bills of Mortality” dated back to the plague years of the 1600s, when clerks first began recording the names and parishes of the dead. But Farr recognized that these surveys could be far more valuable to science if they included additional variables. He waged a long campaign to persuade physicians and surgeons to report a cause of death wherever possible, drawing upon a list of twenty-seven fatal diseases. By the mid-1840s, his reports tallied deaths not only by disease, but also by parish, age, and occupation. For the first time, doctors and scientists and health authorities had a reliable vantage point from which to survey the broad patterns of disease in British society. [John Snow is investigating the possibility that the cause of a cholera outbreak in London is in the water, not as the most popular theory of the day claims bad air, a.k.a. miasma.] Without Farr's Weekly Returns, Snow would have been stuck in the street-level view of anecdote, hearsay, and direct observation. He might still have been able to build a theory of cholera on his own, but it would have been almost impossible to persuade anyone else of its validity.

Farr was a man of science, and shared Snow's belief in the power of statistics to shed light on medical riddles. But he also shared many assumptions with the miasma camp, and he used the number-crunching of the Weekly Returns to reinforce those beliefs, Farr thought that the single most reliable predictor of environmental contamination was elevation: the population living in the putrid fog that hung along the riverbanks were more likely to be seized by the cholera than those living in the rarefied air of, say, Hampstead. And so, after the 1849 outbreak, Farr began tabulating cholera deaths by elevation, and indeed the numbers seemed to show that higher ground was safer ground. This would prove to be a classic case of correlation being mistaken for causation: the communities at the higher elevations tended to be less densely settled than the crowded streets around the Thames, and their distance from the river made them less likely to drink its contaminated water. Higher elevations were safer, but not because they were free of miasma. They were safer because they tended to have cleaner water.

Farr was not entirely opposed to Snow's theory. He seems to have entertained the idea that the cholera was somehow originating in the murky waters of the Thames, and then rising into the smoggy air above the river as some kind of poisonous vapor. He had clearly followed Snow's publications and presentations closely over the years, and engaged the theory on occasion in the editorials that would sometimes accompany the Weekly Returns. But he remained unconvinced by the purely waterborne theory. He also suspected that Snow would have a difficult time proving his theory. "To measure the effects of good or bad water supply," Farr editorialized in November of 1853, “it is requisite to find two classes of inhabitants living at the same level, moving in equal space, enjoying an equal share of the means of subsistence, engaged in the same pursuits, but differing in this respect,—that one drinks water from Battersea, the other from Kew.... But of such experimenta crucis the circumstances of London do not admit.”

Snow must have taken that last line as a slap in the face, having heard the exact same Latinate phrase used against him after the publication of his original cholera monograph four years before. Yet despite his skepticism, Farr had been intrigued enough by Snow's waterborne theory to add a new category to his Weekly Returns. In addition to tracking the age and sex and elevation of the cholera victims, Farr would now track one additional variable: where they got their water. [pp. 101-102]

Miasma’s hegemony had one other biological basis [the first was the olfactory alarm system of disgust that is triggered by our detection of certain molecules, like hydrogen sulfide or cadaverine]. Our noses are far more adept than our eyes at perceiving the very small. It takes only a few molecules of cadaverine attaching to the olfactory receptors in your upper nasal passages for you to become aware of the smell of decay. But your eyes are useless at the scale of molecules. In many respects, human visual perception is unrivaled among earth's life-forms—the legacy of a nocturnal mammal who needed to forage and hunt in the dark. But molecules remain several orders of magnitude below the threshold of human visual perception.

We can't see most ordinary cells that those molecules build, even whole populations of cells. A hundred million v. cholerae floating in a glass of water would be invisible to the naked eye. Microscopes had been in use for more than two centuries, and while a few isolated researchers had caught a glimpse of microbes in their labs, the existence of a bacterial microcosmos was still the stuff of fantasy and conjecture for the mid-Victorian mind. But the stench of decomposition was all too real. Smelling was believing.

The miasma theory drew on other sources for its power as well. It was as much a crisis of imagination as it was pure optics. To build a case for waterborne cholera, the mind had to travel across scales of human experience, from the impossibly small the invisible kingdom of microbes—to the anatomy of the digestive tract, to the routine daily patterns of drinking wells or paying the water-company bills, all the way up to the grand cycles of life and death recorded in the Weekly Returns. If you looked at cholera on any one of those levels, it retreated back into the haze of mystery, where it could be readily rolled back to the miasma theory, given the pedigree and influence of miasma's supporters. Miasma was so much less complicated. You didn't need to build a consilient chain of argument to make the case for miasma. You just needed to point to the air and say: Do you smell that?

And of course there were more than a few instances where the statistical evidence did in fact seem to stack the odds in miasma's favor: Neighborhoods with unsanitary water supplies generally suffered from poor air quality as well; many of them lay at the lower elevations that Farr relentlessly documented in his Weekly Returns. For every sewer-hunter [a poor person who roved about in the sewers for any items or substances of value that could be sold] living happily into his sixties, there were a hundred false positives dying in the low elevations of Bermondsey.

Raw social prejudice also played a role. Like the other great scientific embarrassment of the period—phrenology—the miasma theory was regularly invoked to justify all sorts of groundless class and ethnic biases. The air was poisoned, to be sure, but the matter of who fell ill, and what disease they suffered from, was determined by the constitution of each individual breathing in the air. So went Thomas Sydenham's internal-constitution theory of the epidemic, an eccentric hybrid of weather forecasting and medieval humorology. Certain atmospheric conditions were likely to spawn epidemic disease, but the nature of the diseases that emerged depended partly on a kind of preexisting condition, a constitutional susceptibility to smallpox, or influenza, or cholera. The distinction was often defined as one between exciting and predisposing causes. The exciting cause was the atmospheric condition that encouraged a certain kind of disease: a specific weather pattern that might lead to yellow fever, or cholera. The predisposing cause lay in the bodies of the sufferers themselves. That constitutional failing was invariably linked to moral or social failing: poverty, alcohol abuse, unsanitary living. One alleged expert argued in 1850: “The probability of an outburst or increase during [calm, mild] weather, I believed to be heightened on holidays, Saturdays, Sundays, and any other occasions where opportunities were afforded the lower classes for dissipation and debauchery.”

The idea of one's internal constitution shaping the manifestation of disease was not just useful for affirming social prejudices about the moral depravity of the lower classes. It also helped paper over a massive hole in the theory itself. If the miasma seemed unusually capricious in its choice of victims for poison allegedly circulating in the atmosphere—if it killed off two housemates but left the remaining two unscathed despite the fact that they were all breathing the same air— the miasmatists could simply point to the differences in constitution between the victims and the survivors to explain the disparity. Although the poisonous vapors were distributed equally through the environment, each inner constitution possessed its own distinct vulnerability.

Like much of the reasoning that lay behind the miasma theory, the idea of an inner constitution was not entirely wrong; immune systems do vary from person to person, and some people may indeed be resistant to epidemic diseases like cholera or smallpox or plague. The scaffolding that kept miasma propped up for so long was largely made up of comparable half-truths, correlations mistaken for causes. Methane and hydrogen sulfide were in fact poisons, after all; they just weren't concentrated enough in the city air to cause real damage. People were more likely to die of cholera at lower elevations, but not for the reasons Farr imagined. And the poor did have higher rates of contagion than the well-to-do, but not because they were morally debauched.

Yet miasma had just as much to offer the liberals as it did the conservatives. Chadwick and Nightingale and Dickens were hardly bigots where the working classes were concerned. Miasma, for them, was not a public sign of the underclasses’ moral failing; it was a sign of the deplorable conditions in which the underclasses had been forced to live. It seemed only logical that subjecting such an immense number of people to such deplorable living environments would have a detrimental effect on their health, and of course, the liberal miasmatists were entirely right in those basic assumptions. Where they went wrong was in assuming that the primary culprit lay in the air. …

Miasma turns out to be a classic case of what Freud, in another context, called “overdetermination.” It was theory that drew its persuasive power not from any single fact but rather from its location at the intersection of so many separate but compatible elements, like a network of isolated streams that suddenly converges to form a river. The weight of tradition, the evolutionary history of disgust, technological limitations in microscopy, social prejudice—all these factors colluded to make it almost impossible for the Victorians to see miasma for the red herring that it was, however much they prided themselves on their Gradgrindian rationality. [Thomas Gradgrind is the notorious school board Superintendent in Dickens's 1854 novel Hard Times who is dedicated to the pursuit of profitable enterprise. His name is used generically to refer to someone who is hard and only concerned with cold facts and numbers. Wikipedia] Every research paradigm, valuable or not, in the history of ideas has been buttressed by a comparable mix of forces, and in this sense the deconstructionists and the cultural relativists-so often the subject of mockery lately—have it right to a certain extent, though they tend to place undue stress on purely ideological forces. (Miasma was as much a creature of biology as of politics.) The river of intellectual progress is not defined purely by the steady flow of good ideas begetting better ones; it follows the topography that has been carved out for it by external factors. Sometimes that topography throws up so many barricades that the river backs up for a while. Such was the case with miasma in the mid-nineteenth century.

But most of these dams eventually burst. Yes, the path of science works within regimes of agreement and convention, and history is littered with past regimes that were overthrown. But some regimes are better than others, and the general tendency in science is for explanatory models to be overthrown in the name of better models. Oftentimes because their success sows the seeds of their destruction. Miasma became so powerful that it inspired a massive, state-sponsored intervention in the daily lives of millions of people, clearing the air by draining the cesspools. That intervention, miscalculated as it was, had the paradoxical effect of making the patterns of the epidemic more visible, at least to eyes that were capable of seeing them. And seeing the patterns more clearly means progress, in the long run at least. [pp. 131-135]