Scholars are mainly concern with finding explanations for the things we see around us. Their goal is not only to provide good arguments for why something acts or looks the way it is, but more importantly to use those explanations to create new understandings, based on analogies, natural rules and so on.
Scientific thinking is based on finding hard evidences for well-defined questions. Such evidences can be found through experiments, observations and prior knowledge, all are based on generally accepted mythologies, statistics and logical pattern of drawing conclusions. Many scientists using axioms in their thinking processes, assuming that some facts do not require further investigation.
However, scientific methods suffer from several significant disadvantages. One of the main disadvantages is the dependency of science on the limitations of human perception and intellect, as well as the tools that are used for the scientific research. The result is providing evidences which may be proven in the future, using more sophisticated technology, as false or that can be only partially true. Language also may lead to manipulations, as the usage of a word to define something serves not only as a name but also tells us something about the object itself.
Let us take, for example, my blue t-shirt. I think it is blue and so are 100 of the people I ask. However, the 101st person might be colour-blind. For him, my t-shirt is grey. Another person might say that the shirt is neither blue nor grey; his explanation will be that there is some chemical on the shirt that makes us to believe it is blue, because that is the way our brain analyse the visual information e gets from our eyes.
The metaphysical thinking understands these limitations and suggests that just because we cannot see or understand something does not mean that this thing is not real. Metaphysics goes beyond the physical world to offer the possibility that many things around us cannot be explained by the structured ways of science. Some things do not exist, but were created by imagination, while others are important forces that science tends to ignore because it cannot put them down into logical measurements.
Let us use one more example. Modern science can tell us a lot about the way our body operates. However, reasonable scientific thinking will lead us to conclude that we are nothing more than a combination of atoms and molecules, building together organs. However, this is not necessarily true, as some metaphysical theories (e.g. some religions) will assume that there is also a soul in us, and the being of a person is not his brain, legs and liver but the soul they host. A good metaphysical thinker will consider the possibility that souls exist, and will not neglect it just because no one was able to prove this theory so far.
Metaphysical and scientific thinking are very different but support each other. By considering the limitations of human understanding, metaphysical thinkers raise questions on the issues which are beyond science and develop analysis that can be later transformed into more conventional research methods.
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