Science starts with observations and studying the empirical results. Observation of the whole thing or any peculiar phenomenon is the initial stimulus for pursuing the particular subject. But the real science typically involves dissecting the problem and examining the parts to have the idea of nature and working of the things of interest. This is the standard approach of science and biology. Although this seems to be very successful, at least on the surface and for the lay people, it has its own limitations. If your experimental design, even in theory, cannot explain the nature of the phenomenon that you are studying then how you can expect that approach of studying will give you the answer. If a particular theory cannot logically proceed towards understanding of the nature of things then what is the point of exploring that field of study based on science which in turn based on logic. Some scientists, seeing the experimental results getting illogical and often self-contradictory, are trying to patch the problems by introducing additional dogmatic assumptions like "Something coming out of nothing principle", "Time contraction or dilatation", "Extra Dimensions", "Dark matter and Dark energy", "Every Biological Phenotype have Genetic or Epigenetic origin", "Only brain has the capacity to think and store memories" and so on. When nothing seems to work, then the resort to probability theory, uncertainty principle and the system of fuzzy logic. And with all those, they claims to know everything, at least in principle. All that remains is to do more experimentation. At the end they gives us some answers based on their theory and experiential results. Finally they think they have solved the problem but there is only one problem. The answers that science so far has provided, have not satisfied our thirst for understanding. It is like drinking a salt rich soda that people think will quench their thirst but after drinking the soda they are even more thirsty than before! Thirst needs pure water, not junk like salt-rich soda. Similarly we are now more perplexed than ever before science took the project of understanding. Our mind and true-self, at the core, yearns for understanding, not just a probabilistic interpretation of relativistic many world multiverse string theory. What we want is Certainty, which is analogous to pure water to quench the thirst of our mind. This is irony of "contemporary" science. It looks like that science itself is a potential trap against the tangled journey for the understanding the nature and its relation with ourselves. This does not mean that science has no value in this journey. In fact, science is the starting point but definitely science is and will not be enough to go to the next level of understanding, i.e. Wisdom.

Let us examine how contemporary science works in practice. Science divides the problems in parts and then they examine and manipulate the parts to see what the parts are doing. Then they induce or deduce the interpretation about the whole, which in turn heavily dependent on logic. So if your experimental results becomes illogical and you use logic to justify your results, then it becomes literally an oxymoronic endeavor. Examining the parts to understand the whole is a tricky business. You might miss the beauty of a flower and its role in nature while you are dissecting the petals and examining the parts! Even those dissections and examinations are fraught with fallacies. First of all, you have to know all the constituents [which you do not know] to understand the function of the whole. Then you have to know the sequence of those known and unknown interactions among the constituents, because uniting Hydrogen and Oxygen before (which makes water, H2O) the third item such as Carbon, it will become unmixable but uniting Hydrogen, Oxygen  and Carbon together in right order creates carbohydrate, which is entirely a different thing! Even in those individual steps of the long long series of events, you do not know what co-factors, facilitators or modifying factors are involved. To make the situation even worse, some of the events are unique and happens only rarely when everything (you do not know what those everything were!) is in right time and proportion. If you dig deeper into the subatomic and quantum realm, you will be utterly lost. Additionally, some of the emerging phenomenon is only clearly measurable at respective level of complexity but not in more basic or lower levels. Even at more macroscopic level such as those are routinely used in neuroscience to study the function of the different parts of the brain, the problem remains. For example, resecting a part of the brain and trying to see what deficit it produced does not give you the real function of that part in situ. There are some studies that have demonstrated that removing some part of brain can impair some forms of memory, recollection, calculation ability, music sense, social appropriateness, and so on. But none of them can tell us why we enjoy the music, why we feel nostalgic about our childhood memories and so on. Examination of the parts can help you understand the whole, only with the aid of reason. That means you are taking absolute reliance of your reason to connect gaps of the understanding the parts with the whole. How do you know that your reason is valid across different levels of complexity? Have you done any experiments to prove that? If yes, then what is the rationale of that new experiments. Have you proved the rationale of the rationale? It is an infinite regress where you have to rely on your reasoning power without any further experimentation or proof, because your reason precedes any experiments that you can devise. So if you just analyze the constituents, do not assume that you know what is happening above the level and below the level. If you do or pretend to understand, then you are fooling yourself (acceptable) and fooling others (not acceptable).

If you believe in the theory of relativity, aren't you saying everything is relative? Then why you are not treating one levels understanding as a relative and hence limited degree of understanding of the next levels? Why are you treating your understanding at one level as infallible evidence for the next level? This is an absolutism of reason, which is itself a paradox. What gives your reliance of reason the absolute validity over the principle of relativism? Why understanding at one level can explain the other levels below or above? Do you really know? In contrast, if you examine the whole then you have a better chance to understand the whole and if you are lucky, may be part of the constituents too, by extension. This is the real reason behind the power of phenomenology and behaviorism. But phenomenology and behaviorism is just the beginning and it is really powerful only for the same level of analysis. It will help you understand what the entire individual organism is doing, but it still fails and will fail to give you the "why". The ability to see why is contingent upon your degree of need and how much you really want. This is the only secret formula of knowing the "why" part. This can be illustrated by the following analogy. For a general audience all the crying of the babies sounds the same and all of you can recognize what is a baby's cry, but only the person who really needs to know and wants to know will know the "why" behind the cry. Hence the mother of the baby can see why the baby is crying. She knows and can distinguish what cry is for hunger, what cry is for diaper change, what cry is for emotional attention and what cry is a danger sign of something else. She not only knows the "what" but also the "why". On the surface it looks like a miracle, or instinct of blind gut feelings from the mother but if you observe carefully you will see the mechanism. The secret is that the mother needs to know and she wants to know. She is not going to compromise on that. When you really want something that genuinely, your ears, eyes, sense organs of perceptions work more sharply than the ordinary situations and you begin to see the subtle differences in the cry, the facial expressions, the tone of the cry, the context, the environment etc., which are otherwise unnoticeable. This the way and there is no other way. You have to have the wanting for knowing the "why" that solemnly even at great cost. Intense wanting, devotion and attention will show you the "why". This is the real meaning and goal of traditional Bhakti Yoga, Buddhist Dhyāna [Zen], Prayer/Ṣalāt in Monotheistic traditions and Meditation in general. It will take you to the next level of understanding, your eyes will be opened and you will begin to see the world better than earlier. Reason and experimentation are good for same level analysis but to understand why at the level above and below, reason and experimentation is powerless because they will take you towards infinite regress which is a no no for science, mathematics and logic (reason). You need something beyond all those "Sciences", such as desire, devotion and attention. This will open the opportunity to understand what is below and what is above which in turn started from the examination of the parts. If you can discover this secrete by yourself then you will not only see what "is" but also the "why" in the below as well as above. Only that perspective gives you the validity of cross-/trans-levels of "Why".