The scientific method involves making precise, verified observations about some aspects of the external world, formulating usually mathematically expressed ‘laws’ about the relationships between those aspects of the external world, and then, based on those laws, making precise, verifiable predictions about observations of what will happen in the future in relation to those aspects of the external world. It is essential that the observations can be repeated by comparably situated observers.
The Placebo Effect: However, as the Heisenberg Principle has demonstrated at the quantum level and the placebo effect has demonstrated at the level of medical trials, all observation has an effect on what is observed. In fact, what the scientific method does is try to minimize that effect, so as to be able to obtain results that are approximately verifiable by different observers using similar procedures.
In fact, the problem goes much deeper. The scientific method tries to correct for the impact of the act of observation on what is being observed, but it assumes that the future will be essentially the same as the past, at least as regards the aspects of the external world being observed.
If you are studying magnetism and observing magnets and formulating laws about magnetic polarity and then predicting the behavior of magnets in the future, you are assuming that the universe will stay constant, at least as it relates to magnetism, in the future. If the nature of the universe as it relates to magnetism were to change in the future, your predictions wouldn’t be accurate and, therefore, your laws would be wrong.
The Continuity of Time: The hidden assumption about time probably won’t trip you up in relation to predictions about magnetism, but that hidden assumption about time may be very significant in relation to emergent phenomena. That’s why it’s much harder to predict the economic and political behavior of human beings. The hidden assumption that things will be the same in the future, in relation to what is being studied, as they were in the past may very well be, and often is, wrong in relation to human behavior.
Consciousness: The problem goes deeper still. The scientific method was designed to use precise observations to focus on the external world. But it’s hard to study the nature of consciousness that way. Yet, everything we know about any aspect of the universe comes through our consciousness. Research on how the brain works is exploding and extremely interesting, but all that knowledge comes through the consciousness of the brain researchers and comes to us through our consciousness.
So, we have come full circle to something analogous to the Logical Positivist’s conundrum. Consciousness is required for the scientific method to operate, but the scientific method (with its mechanic deterministic/probabilistic metaphysics) based on objective observation, can’t directly study the consciousness that is central to its operation. Science isn’t going to get us out of this problem. Philosophy is, but a philosophy deepened and strengthened by a truer understanding of consciousness.