Francis Bacon had a major influence on the development of science, largely because he emphasized that most discoveries emerged from empirical observation rather than from strict deductive reasoning.
Later, the French philosopher René Descartes made people aware that relying solely on reason can lead us into an endless web of fallacies.
One thinker went further, pointing out that logic itself was originally developed to regulate debates in ancient Greek schools, assemblies, and law courts. Its purpose was to help determine which side won an argument. Given this context, it shouldn't be surprising that logic is often ill-suited for science, a field for which it was never designed. In fact, many logicians have made it clear that logic—concerned primarily with correctness and validity—has little to do with the kind of productive, creative thinking that drives scientific breakthroughs.
Logicians typically distinguish between two types of reasoning: inductive and deductive. Inductive reasoning moves from specific instances to broader generalizations—from observed facts to the formation of theories. It seeks to explain relationships between the things we observe. Deductive reasoning, by contrast, moves from general principles to specific cases, applying established theories to particular situations. In deduction, the conclusion is already contained within the initial premise and is valid only if that premise is true.
Because deduction simply applies existing principles, it cannot generate new generalizations or lead to major scientific breakthroughs. Induction, while less certain, is far more productive—it allows for the creation of new theories. However, this productivity comes at a cost: starting from a set of facts, we can often arrive at multiple plausible theories, many of which may conflict with one another or even be entirely incorrect.
In biology, the complexity of phenomena and the limited understanding of many variables make reliable reasoning difficult. Premises are rarely clear-cut, and nature often proves too subtle for tidy logical analysis. In contrast, fields like mathematics, physics, and chemistry operate with more firmly established premises and better-defined conditions. As a result, reasoning plays a more dominant and reliable role in advancing knowledge in those disciplines.
Safeguards
The first safeguard is to carefully examine the foundation from which reasoning begins. This means clarifying the terms we use and scrutinizing our premises. Some premises may be well-established facts or scientific laws, while others may be mere assumptions. Often, researchers must work with provisional assumptions that haven’t yet been verified—and it’s crucial not to forget that these are only temporary stand-ins for established knowledge.
Michael Faraday warned against the mind’s tendency to "rest on an assumption"—once it seems to fit with existing knowledge, we can easily overlook the fact that it hasn’t been proven. This is why most scientists agree that unverified assumptions should be minimized, and that the hypothesis requiring the fewest assumptions is preferable. This idea is known as the maxim of parsimony, or Occam’s Razor.
Unverified assumptions can slip into our thinking without us noticing. They often come disguised by phrases like “obviously,” “of course,” or “surely.” For example, it might seem safe to assume that well-fed animals live longer than underfed ones—but in a surprising experiment, mice whose diets were restricted to the point of stunted growth actually lived significantly longer than those allowed to eat freely.
Another key safeguard is to distinguish facts from their interpretations—to separate raw data from the generalizations we draw from it. Facts are specific observations about the past or present. Moving from “this happened” to “this is how things work” marks a shift from fact to induction—a necessary step, but one that must be taken with awareness and care.
Some of the greatest scientific discoveries have come from experiments that challenged, or outright ignored, widely accepted beliefs. In everyday life, people often rely on fixed ideas and assumptions to make decisions more efficiently. But in scientific research, the mind must remain flexible. Scientists must resist clinging to preconceived notions and remain open to new ideas—especially those proposed by others. We should judge suggestions on their own merits, seeking arguments both for and against them. It's easy to become critical by default, but we must beware of rejecting ideas simply because they conflict with our own.
In fact, one of the most valuable habits a scientist can develop is a healthy skepticism toward ideas that rely on reason alone.
A practical aid in clarifying a research problem is to write a report summarizing all available information. This can be helpful at the start of an investigation, when encountering a challenge, or when wrapping up the work. At the beginning, it also helps to clearly formulate the questions you’re trying to answer. Precisely stating the problem can often lead halfway to the solution. Organizing the data systematically can also reveal flaws in reasoning or suggest overlooked paths of inquiry.
Ultimately, our reasoning happens through language, and writing is the clearest expression of our thoughts. Discipline and training in writing is arguably the best training available in logical, rigorous thinking.
The Role of Reason
Although scientific discoveries often arise from unexpected experimental results, observations, or moments of intuition rather than from deliberate logical thought, reason remains the primary tool in nearly every other aspect of the research process. It guides how we shape hypotheses, evaluate ideas sparked by imagination or intuition, design experiments, choose what data to collect, assess evidence, interpret findings, make generalizations, and explore new applications of our discoveries.
The roles of discovery and proof in science are as distinct as the roles of a detective and a judge. In the process of discovery, the researcher acts like a detective—following clues and pursuing leads. But once a discovery is made, the researcher becomes the judge—evaluating the case through carefully structured evidence and reasoning. Both roles are essential, yet fundamentally different.
In biological research, where complexity and unpredictability are the norms, observation and chance often play a central role. However, even in such cases, the facts gathered through empirical work usually gain meaning only when reason organizes them into a coherent framework of knowledge.
Conclusion
While intuition, observation, and chance may spark the initial flame of discovery, it is reason that sustains the scientific process—shaping raw insights into structured understanding. Reason sharpens our questions, refines our methods, and helps us distinguish between what is merely plausible and what is truly meaningful. Yet, it is a tool that must be used with humility and care, always tempered by awareness of its limits and guided by disciplined habits of thought.
Scientific progress depends not only on imagination and insight but also on the thoughtful application of reason—checked by safeguards, enriched by writing, and open to the unexpected. In the end, the successful researcher is one who balances creativity with critical thinking, skepticism with openness, and logic with curiosity.
Reference
- The Art of Scientific Investigation by W. I. B. Beveridge

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