Francis Bacon and the four barriers to truth

Truth might be hard to find, but we can take steps to eliminate common cognitive biases.

Francis Bacon and the four barriers to truth
Credit: Paul van Somer I via Wikipedia / Public Domain
  • The human mind is designed to experience the world a certain way, and so it leads us to biases, prejudices, and heuristics.
  • Francis Bacon, the father of the scientific method, identified four of the most common of these, 400 years before our modern idea of "cognitive biases."
  • If we are serious about finding truth, we ought to minimize these biases and use logic, science, and reason as much as possible.

You are not objective.

We bring all of ourselves to every moment of every day — our experiences, our beliefs, our feelings, our worries. It's impossible to ignore all the baggage we have. Our culture and even our language also provide a lens through which we see the world. As a result, we come draped in a heavy cloak of cognitive biases and prejudices. And yet, that does not mean we shouldn't try to discover things about the world, nor should we give up on truth. It just means we need to work harder.

Philosophy might be able to help. In the very DNA of philosophy, which goes back to the ancient Greeks, there lies a need to probe deeper and question everything. It's no surprise, then, that along the way, philosophy has unearthed and disarmed various biases or snares of the mind.

Four barriers to the truth

Francis Bacon, to whom we owe the idea of the scientific method, simply and clearly identified four barriers to the truth, what he called "idols and false notions." They are:

1. The idol of the tribe. We have a tendency to anthropomorphize and project our human condition onto the world. We see order in randomness, we think dogs feel things the same way as us, we see faces in clouds, we call weather "angry," and we feel that even colors can be happy or sad. We fail to see this "false mirror" for what it is, and seeing things tinged with humanity only "distorts and discolors the nature of things by mingling [our] nature with it."

2. The idol of the cave. Our culture, upbringing, and education define how we experience reality. We are all inclined to see the world through some book we've read, film we've seen, story we've been told, or "authority whom [we] esteem." It could be that we've read and become so engrossed in a thinker, such as Freud or Marx, that we see everything as they would see it. "Our cave" could be why social media keeps feeding us the same kind of (often biased) information over and over again.

Set your brain free.Credit: ERNESTO BENAVIDES via Getty Images

When we see things only from our perspective — e.g., as a middle class member of Western civilization — we often assume our experiences are the default for everyone else. But try going to a foreign country and asking, "What's the greatest country in the world?" Most likely, it won't be the country you're from.

3. The idol of the marketplace. Words matter. They really do. While we "believe that [our] reason governs words," it's equally true that the words we use or hear affect how we understand something. One of the best examples is how the media frames a particular narrative (think "freedom fighter" vs. "terrorist"). Politicians are experts at using rhetoric to persuade or elicit a certain response. We are all susceptible to well framed arguments and cleverly constructed speech. As Bacon notes, "Words plainly force and overrule the understanding."

But, this idol also highlights how inadequate and slippery words can be. We often use words we don't understand, and we each have slightly different understandings of words. The term "genetic modification" means something different to scientists than it does to the average person.

4. The idol of the theatre. Current fads or "systems now in vogue" also influence how we see the world. Even the intelligentsia suffers from fads. Intellectual fads can include religious beliefs, social agendas, political movements, or "the spirit of the times." The analogy of the theatre is in how we assume the particular play we're watching is the template for the universe, yet it's only temporary. Today, everything seems to be connected to climate change or COVID. It's also become a fad to disregard facts in favor of "my lived experience."

It matters less whether these fads are "true." Instead, we should remember that they serve as yet another lens that influences our view of reality.

Smashing the idols

The solution Bacon offers comes, first, in recognizing these idols for what they are. Once we see that we have certain biases, we can take pains to rid ourselves of them. Of course, it's impossible to be entirely free of prejudice. (How can we, for instance, stop being human and understand what it's truly like to be a fruitfly?) But it is possible to minimize biases and try to overcome them in some way.

Second, we ought to be careful to hold only "ideas and axioms by true induction… [and] common logic." We might not be able to adopt an objective "view from nowhere" or eliminate all cognitive biases, but logic and rationality might be the best possible way to achieve it.

In short, to overcome the barriers to truth, look to philosophy, logic, and science to test everything. By casting down the idols of the mind, we can try to see as clearly as possible.

    Jonny Thomson teaches philosophy in Oxford. He runs a popular Instagram account called Mini Philosophy (@philosophyminis). His first book is Mini Philosophy: A Small Book of Big Ideas.

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    "I was intrigued," says Ron Fouchier, in his rich, Dutch-accented English, "in how little things could kill large animals and humans."

    It's late evening in Rotterdam as darkness slowly drapes our Skype conversation.

    This fascination led the silver-haired virologist to venture into controversial gain-of-function mutation research — work by scientists that adds abilities to pathogens, including experiments that focus on SARS and MERS, the coronavirus cousins of the COVID-19 agent.

    If we are to avoid another influenza pandemic, we will need to understand the kinds of flu viruses that could cause it. Gain-of-function mutation research can help us with that, says Fouchier, by telling us what kind of mutations might allow a virus to jump across species or evolve into more virulent strains. It could help us prepare and, in doing so, save lives.

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    The Dutch virologist, based at Erasmus Medical Center in Rotterdam, caused a firestorm of controversy about a decade ago, when he and Yoshihiro Kawaoka at the University of Wisconsin-Madison announced that they had successfully mutated H5N1, a strain of bird flu, to pass through the air between ferrets, in two separate experiments. Ferrets are considered the best flu models because their respiratory systems react to the flu much like humans.

    The mutations that gave the virus its ability to be airborne transmissible are gain-of-function (GOF) mutations. GOF research is when scientists purposefully cause mutations that give viruses new abilities in an attempt to better understand the pathogen. In Fouchier's experiments, they wanted to see if it could be made airborne transmissible so that they could catch potentially dangerous strains early and develop new treatments and vaccines ahead of time.

    The problem is: their mutated H5N1 could also cause a pandemic if it ever left the lab. In Science magazine, Fouchier himself called it "probably one of the most dangerous viruses you can make."

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    Recreated 1918 influenza virionsCredit: Cynthia Goldsmith / CDC / Dr. Terrence Tumpey / Public domain via Wikipedia

    For H5N1, Fouchier identified five mutations that could cause three special traits needed to trigger an avian flu to become airborne in mammals. Those traits are (1) the ability to attach to cells of the throat and nose, (2) the ability to survive the colder temperatures found in those places, and (3) the ability to survive in adverse environments.

    A minimum of three mutations may be all that's needed for a virus in the wild to make the leap through the air in mammals. If it does, it could spread. Fast.

    Fouchier calculates the odds of this happening to be fairly low, for any given virus. Each mutation has the potential to cripple the virus on its own. They need to be perfectly aligned for the flu to jump. But these mutations can — and do — happen.

    "In 2013, a new virus popped up in China," says Fouchier. "H7N9."

    H7N9 is another kind of avian flu, like H5N1. The CDC considers it the most likely flu strain to cause a pandemic. In the human outbreaks that occurred between 2013 and 2015, it killed a staggering 39% of known cases; if H7N9 were to have all five of the gain-of-function mutations Fouchier had identified in his work with H5N1, it could make COVID-19 look like a kitten in comparison.

    H7N9 had three of those mutations in 2013.

    Gain-of-function mutation: creating our fears to (possibly) prevent them

    Flu viruses are basically eight pieces of RNA wrapped up in a ball. To create the gain-of-function mutations, the research used a DNA template for each piece, called a plasmid. Making a single mutation in the plasmid is easy, Fouchier says, and it's commonly done in genetics labs.

    If you insert all eight plasmids into a mammalian cell, they hijack the cell's machinery to create flu virus RNA.

    "Now you can start to assemble a new virus particle in that cell," Fouchier says.

    One infected cell is enough to grow many new virus particles — from one to a thousand to a million; viruses are replication machines. And because they mutate so readily during their replication, the new viruses have to be checked to make sure it only has the mutations the lab caused.

    The virus then goes into the ferrets, passing through them to generate new viruses until, on the 10th generation, it infected ferrets through the air. By analyzing the virus's genes in each generation, they can figure out what exact five mutations lead to H5N1 bird flu being airborne between ferrets.

    And, potentially, people.

    "This work should never have been done"

    The potential for the modified H5N1 strain to cause a human pandemic if it ever slipped out of containment has sparked sharp criticism and no shortage of controversy. Rutgers molecular biologist Richard Ebright summed up the far end of the opposition when he told Science that the research "should never have been done."

    "When I first heard about the experiments that make highly pathogenic avian influenza transmissible," says Philip Dormitzer, vice president and chief scientific officer of viral vaccines at Pfizer, "I was interested in the science but concerned about the risks of both the viruses themselves and of the consequences of the reaction to the experiments."

    In 2014, in response to researchers' fears and some lab incidents, the federal government imposed a moratorium on all GOF research, freezing the work.

    Some scientists believe gain-of-function mutation experiments could be extremely valuable in understanding the potential risks we face from wild influenza strains, but only if they are done right. Dormitzer says that a careful and thoughtful examination of the issue could lead to processes that make gain-of-function mutation research with viruses safer.

    But in the meantime, the moratorium stifled some research into influenzas — and coronaviruses.

    The National Academy of Science whipped up some new guidelines, and in December of 2017, the call went out: GOF studies could apply to be funded again. A panel formed by Health and Human Services (HHS) would review applications and make the decision of which studies to fund.

    As of right now, only Kawaoka and Fouchier's studies have been approved, getting the green light last winter. They are resuming where they left off.

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    Here's the thing: the work is indeed potentially dangerous. But there are layers upon layers of safety measures at both Fouchier's and Kawaoka's labs.

    "You really need to think about it like an onion," says Rebecca Moritz of the University of Wisconsin-Madison. Moritz is the select agent responsible for Kawaoka's lab. Her job is to ensure that all safety standards are met and that protocols are created and drilled; basically, she's there to prevent viruses from escaping. And this virus has some extra-special considerations.

    The specific H5N1 strain Kawaoka's lab uses is on a list called the Federal Select Agent Program. Pathogens on this list need to meet special safety considerations. The GOF experiments have even more stringent guidelines because the research is deemed "dual-use research of concern."

    There was debate over whether Fouchier and Kawaoka's work should even be published.

    "Dual-use research of concern is legitimate research that could potentially be used for nefarious purposes," Moritz says. At one time, there was debate over whether Fouchier and Kawaoka's work should even be published.

    While the insights they found would help scientists, they could also be used to create bioweapons. The papers had to pass through a review by the U.S. National Science Board for Biosecurity, but they were eventually published.

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    They are essentially an airtight cement bunker, negatively pressurized so that air will only flow into the lab in case of any breach — keeping the viruses pushed in. And all air in and out of the lap passes through multiple HEPA filters.

    Inside the lab, researchers wear special protective equipment, including respirators. Anyone coming or going into the lab must go through an intricate dance involving stripping and putting on various articles of clothing and passing through showers and decontamination.

    And the most dangerous parts of the experiment are performed inside primary containment. For example, a biocontainment cabinet, which acts like an extra high-security box, inside the already highly-secure lab (kind of like the radiation glove box Homer Simpson is working in during the opening credits).

    "Many people behind the institution are working to make sure this research can be done safely and securely." — REBECCA MORITZ

    The Federal Select Agent program can come and inspect you at any time with no warning, Moritz says. At the bare minimum, the whole thing gets shaken down every three years.

    There are numerous potential dangers — a vial of virus gets dropped; a needle prick; a ferret bite — but Moritz is confident that the safety measures and guidelines will prevent any catastrophe.

    "The institution and many people behind the institution are working to make sure this research can be done safely and securely," Moritz says.

    No human harm has come of the work yet, but the potential for it is real.

    "Nature will continue to do this"

    They were dead on the beaches.

    In the spring of 2014, another type of bird flu, H10N7, swept through the harbor seal population of northern Europe. Starting in Sweden, the virus moved south and west, across Denmark, Germany, and the Netherlands. It is estimated that 10% of the entire seal population was killed.

    The virus's evolution could be tracked through time and space, Fouchier says, as it progressed down the coast. Natural selection pushed through gain-of-function mutations in the seals, similarly to how H5N1 evolved to better jump between ferrets in his lab — his lab which, at the time, was shuttered.

    "We did our work in the lab," Fouchier says, with a high level of safety and security. "But the same thing was happening on the beach here in the Netherlands. And so you can tell me to stop doing this research, but nature will continue to do this day in, day out."

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    "If these three traits could be caused by hundreds of combinations of five mutations, then that increases the risk of these things happening in nature immensely," Fouchier says.

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