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Francis Bacon and the Scientific Method

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In 1627, a year after the death of the philosopher and statesman Francis Bacon, a short, evocative tale of his was published. The New Atlantis describes how a ship blown off course arrives at an unknown island called Bensalem. At its heart stands Salomon’s House, an institution devoted to “the knowledge of causes, and secret motions of things” and to “the effecting of all things possible.” The novel captured Bacon’s vision of a science built on skepticism and empiricism and his belief that understanding and creating were one and the same pursuit.

No mere scholar’s study filled with curiosities, Salomon’s House had deep-sunk caves for refrigeration, towering structures for astronomy, sound-houses for acoustics, engine-houses, and optical perspective-houses. Its inhabitants bore titles that still sound futuristic: Merchants of Light, Pioneers, Compilers, and Interpreters of Nature.

Engraved title page of \u201cThe Advancement and Proficience of Learning\u201d with ship and globes Francis Bacon wrote The Advancement and Proficience of Learning.Public Domain

Bacon didn’t conjure his story from nothing. Engineers he likely had met or observed firsthand gave him reason to believe such an institution could actually exist. Two in particular stand out: the Dutch engineer Cornelis Drebbel and the French engineer Salomon de Caus. Their bold creations suggested that disciplined making and testing could transform what we know.

Engineers show the way

Drebbel came to England around 1604 at the invitation of King James I. His audacious inventions quickly drew notice. By the early 1620s, he unveiled a contraption that bordered on fantasy: a boat that could dive beneath the Thames and resurface hours later, ferrying passengers from Westminster to Greenwich. Contemporary descriptions mention tubes reaching the surface to supply air, while later accounts claim Drebbel had found chemical means to replenish it. He refined the underwater craft through iterative builds, each informed by test dives and adjustments. His other creations included a perpetual-motion device driven by heat and air-pressure changes, a mercury regulator for egg incubation, and advanced microscopes.

De Caus, who arrived in England around 1611, created ingenious fountains that transformed royal gardens into animated spectacles. Visitors marveled as statues moved and birds sang in water-driven automatons, while hidden pipes and pumps powered elaborate fountains and mythic scenes. In 1615, de Caus published The Reasons for Moving Forces, an illustrated manual on water- and air-driven devices like spouts, hydraulic organs, and mechanical figures. What set him apart was scale and spectacle: He pressed ancient physical principles into the service of courtly theater.

Drebbel’s airtight submersibles and methodical trials echo in the motion studies and environmental chambers of Salomon’s House. De Caus’s melodic fountains and hidden mechanisms parallel its acoustic trials and optical illusions. From such hands-on workshops, Bacon drew the lesson that trustworthy knowledge comes from working within material constraints, through gritty making and testing. On the island of Bensalem, he imagines an entire society organized around it.

Beyond inspiring Bacon’s fiction, figures like Drebbel and de Caus honed his emerging philosophy. In 1620, Bacon published Novum Organum, which critiqued traditional philosophical methods and advocated a fresh way to investigate nature. He pointed to printing, gunpowder, and the compass as practical inventions that had transformed the world far more than abstract debates ever could. Nature reveals its secrets, Bacon argued, when probed through ingenious tools and stringent tests. Novum Organum laid out the rationale, while New Atlantis gave it a vivid setting.

A final legacy to science

Engraved title page of Bacon\u2019s *Novum Organum* with ships between two pillars Francis Bacon also wrote Novum Organum.Public Domain

That devotion to inquiry followed Bacon to the roadside one day in March 1626. In a biting late-winter chill, he halted his carriage for an impromptu trial. He bought a hen and helped pack its gutted body with fresh snow to test whether freezing alone could prevent decay. Unfortunately, the cold seeped through Bacon’s own body, and within weeks pneumonia claimed him. Bacon’s life ended with an experiment—and set in motion a larger one. In 1660, a group of London thinkers hailed Bacon as their inspiration in founding the Royal Society. Their motto, Nullius in verba (“take no one’s word for it”), committed them to evidence over authority, and their ambition was nothing less than to create a Salomon’s House for England.

The Royal Society and its successors realized fragments of Bacon’s dream, institutionalizing experimental inquiry. Over the following centuries, though, a distorting story took root: Scientists discover nature’s truths, and the rest is just engineering. Nineteenth-century “men of science” pressed for greater recognition and invented the title of “scientist,” creating a new professional hierarchy. Across the Atlantic, U.S. engineers adopted the rigorous science-based curricula of French and German technical schools and recast engineering as “applied science” to gain institutional legitimacy.

We still call engineering “applied science,” a label that retrofits and reverses history. Alongside it stands “technology,” a catchall word that obscures as much as it describes. And we speak of “development” as if ideas cascade neatly from theory to practice. But creation and comprehension have been partners from the start. Yes, theory does equip engineers with tools to push for further insights. But knowing often follows making, arising from things that someone made work.

Bacon’s imaginary academy offered only fleeting glimpses of its inventions and methods. Yet he had seen the real thing: engineers like Drebbel and de Caus who tested, erred, iterated, and pushed their contraptions past the edge of known theory. From his observations of those muddy, noisy endeavors, Bacon forged his blueprint for organized inquiry. Later generations of scientists would reduce Bacon’s ideas to the clean, orderly “scientific method.” But in the process, they lost sight of its inventive roots.

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Anthropic says its biology lab has already found something big

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Last week, Anthropic confirmed that it was operating a wet biology lab in the Bay Area where it uses its AI models to run physical experiments. This week, the AI giant announced that this lab has already made what it believes is a big discovery: a new enzyme “system” that has certain “properties reminiscent of CRISPR,” as Anthropic describes it.

CRISPR is a natural immune system used by bacteria to fight off viruses that has become a gene-editing technology widely used by researchers.

Essentially, what Anthropic says it found is a previously unknown enzyme system hidden in the DNA of bacteriophages, which are viruses that infect and replicate within bacteria. Anthropic’s researchers say this system behaves similarly to CRISPR in that it can “perform operations like cutting, copying, and pasting DNA.”

It will be up to the broader research community to validate how big, or new, this discovery actually is. Anthropic CEO Dario Amodei acknowledges that the discovery was based on the previous work of others and that a team from Stanford previously discovered a system “that is in some ways similar to the one Claude found,” he wrote on X.

But Amodei and Anthropic are not just emphasizing the discovery. They are touting it was found “mostly, though not entirely, by Claude,” the CEO wrote.

On the one hand, that is astounding. This lab was only established this spring, (though Anthropic declined to be more specific about how many months it has been open). A discovery in just a few short months would be speedy enough work, but the team said it actually only took Claude 21 hours of concerted effort. Claude searched through data using about 950 agents that burned through 210 million tokens.

Still, the revelation that Anthropic has been conducting biology experiments comes right after AI CEOs, including Amodei, publicly admitted that models have become so capable, and so potentially dangerous, that the industry must slow down and develop safety-testing procedures. This after a couple of his employees publicly said earlier this month that there’s a risk AI could kill us all.

Amodei himself has said one of the things he fears most its that AI could be used for bioterrorism. But he also believes AI will “cure most diseases in 5-10 years,” he wrote. So Anthropic has clearly decided the rewards are worth the risks.

Given that, perhaps the biggest reveal in this news isn’t the discovery itself, but that the biology lab hasn’t let Claude loose. The physical experiments were done by humans.

“Our lab, located in the Bay Area, looks like a typical molecular biology lab. We do research that involves only the lower-levels of the biosafety risk level (BSL-1 and BSL-2) and we do not handle pathogens that can infect humans. All of the lab work is performed by human scientists.”

It’s also true that AI-powered biological research is hardly unique to Anthropic. Researchers from Stanford just published a paper on the work they are doing with LLMs and CRISPR. Researchers at UC San Francisco used AI to design enzymes from scratch. Google launched its first AI-powered biology research tool, AlphaFold, back in 2020. So AI has clearly arrived in biological research beyond the AI labs pursuing it themselves.

Yet, Amodei hasn’t ruled out a fully automated biology lab in the future. “Eventually it may even be possible for Claude itself to safely perform the experiments by autonomously controlling lab equipment, with appropriate safeguards in place, but we aren’t doing that today,” he said.

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