It is widely claimed that we have many chakras(7 major chakras) situated at different locations along the spinal cord. Each of the chakras is said to be associated with certain energy channels, the activation of which leads to heightened control over certain aspects of one's being and life. Has there been enough scientific inquiry in this topic? What could be the reasons for this claim?
If we define science as the investigation of nature from a naturalistic perspective (as opposed to a supernatural perspective), then the chakra are a part of an ancient scientific theory. In this sense, scientific medicine in India and China probably predate scientific medicine in Europe (Greece), although the earliest known naturalistic medical theories are from Mesopotamia and Egypt.
In ancient Mesopotamia, they divided medicine up into what we might call surgery and sorcery. The surgeons dealt with injuries and got their training on the battlefield, so they had genuine experience to guide their practices, and they had some good techniques. The sorcerers, of course, dealt with demons and gods, which probably had a placebo effect but was otherwise useless. However, they did have useful examination practices and were reasonably competent at prognosis if not treatment.
The earliest known document of naturalistic medicine is the Kahun Gynaecological Papyrus. It seems a bit comical to read it now (everything is caused by secretions of the womb) but it is notable for being naturalistic; that is, the causes and treatments were natural; they mostly didn't refer to supernatural beings. Curiously, Egyptian medicine seems to have been more oriented toward the supernatural in later times than it was when this papyrus was written.
The problem with ancient medical science such as chakra or the Greek four humors (India also had four humors, though it's not as well known) is that although the doctors were seeking natural solutions, they simply did not have the tools to test their theories outside of the field of surgery. They did not have the instruments of today, nor the notion of statistical studies. Consequently, all of the medical (as opposed to surgical) theories of that time are wrong and mostly useless for the treatment of disease. In some cases such as the Hippocratic practices of bleeding and of using blistering agents to worsen infections, the practices were actually harmful.
So, in short: yes, the chakra are part of a scientific theory, given a generous-enough concept of science, but they are an outdate theory that ought to be discarded now that we have better theories tested by much better experimental evidence.
To the best of my knowledge there is no known biological mechanism that relates to the chakras. That’s not to say that it’s pseudoscience necessarily, unless the proponents claim that there’s a scientific basis when there isn’t one. It may or may not be that there’s a biological basis for these regions that we are yet to understand.
To assert that there are such things as Ajna or Agya that are claimed to be the subtle center of energy, where the tantra guru touches the seeker during the initiation ritual is at best metaphorical, therefore it is a pseudoscience. Science does not metaphorically state that a neuron releases X and Y chemicals, it is empirically proven.
There is some correspondence with the endocrine system, e.g. Hormonal Health - Revealing the Secrets of the Endocrine System.
Hermeticists and other esoteric philosophers noticed that every chakra is linked to an endocrine gland: the crown chakra with the pineal, the brow centre with the pituitary and hypothalamus, the throat centre with the thyroid gland, the heart centre with the thymus gland, solar plexus with pancreas, sacral chakra with the reproductive organs and the base chakra with adrenals.
The clearest and best articulation of the science/pseudo-science border was made by Karl Popper. Popper was trying to characterize what was wrong with his psychology professor's claims that
- symptom X confirmed the diagnosis of (a Freudian neurosis)
- The lack of symptom X would also confirm that same diagnosis
- The Freudian method was scientific
Popper's solution was to clarify that science requires not just observations and detailed theory, and "confirmations" but also refutations. And any claim to be "scientific" which allows one to explain any possible outcome is not actually science, but is pseudoscience.
Popper's criteria captures an essential feature of science. Subsequent thinkers have noted that Popper treated refutations as more fatal than science actually does. For example, the Big Bang Theory has been widely accepted, despite at any given time it its history there being up to a half dozen refuting observations. Subsequent work either adapted the theory, or found the observations to be in error. Imre Lakatos proposed a slightly less stringent version of Popper's boundary, where science engages in Research Programmes, which are productive families of a theory, and at any given time a Programme may be working to address challenging observations -- that is ongoing work in the programme. But for it to be a science Programme, its pursuers have to accept the possibility and sometimes actuality of contradictory observations, and the need to correct/modify the theory to adapt to those observations.
Science is a narrower category than naturalism. Methodological naturalism is the use of observations, theory, testing, and modification of theory to understand a subject. Science is a stricter formalization of this process. One uses informal methodological naturalism to learn how to hit a ping pong ball, to develop skill in welding, or in earlier eras, to fletch an arrow. Ayurvedic medicine includes Chakra theory, and was developed through informal methodical naturalism. Traditional Chinese Medicine, which includes Chi theory and acupuncture, was also developed through informal methodological naturalism. Neither tradition is "pseudoscience", they instead are pre-science naturalist/empirical traditions, whose current theory was developed over eons of informal empirical modifications.
Note my usage of natural/supernatural allows for the spiritual aspects of both theories to be "natural", so long as they follow an empirical/correction process. This is how "natural" is used in science. Both ayurvedic and traditional Chinese medicine have been the working assumptions behind multiple contemporary controlled scientific medical experiments. They both can be and have been treated as scientific Research Programmes, so both can be science.
Your question equivocates the scientific use of natural/supernatural with its usage in metaphysics theory. A medical theory can be "natural" per science and not have a "biological basis". In contrast, in metaphysics, Physicalists in particular like to describe anything spiritual as "supernatural". This definition is fine -- there are many definitions for basically every word. But this is a metaphysical/ontology usage, not a scientific one. Spiritual theory is not necessarily immune to testing and error correction, and physical theory can easily end up being structured so it IS immune to it, as Popper's psychology professor illustrated.
Chakra theory CAN be "pseudo-science" depending on the attitude of the user of it (dogmatically claiming everything one sees confirms it) and the strength of the claims made by its advocate (to be pseudoscience, per Popper, one must falsely claim to be scientific), but it is not intrinsically pseudoscientific. It is instead a pre-scientific informal empirical theory, that postulates specific features of a spiritual world, and that includes matter/spirit interaction. And it has been used as the working assumption behind medical Research Programmes, which are explicitly scientific, per Popper and Lakatos.
Most educated people think the flat earth theory is a joke. But actually it is scientific. At first glance, the earth looks flat. And this is a useful approximation in many Newtonian problems. Of course, the earth is not flat, it is spherical. Nevertheless, this is a theory that arose later. And it's important to recall here that scientific theories on the same subject are successive approximations, sometimes involving a paradigm shift. Thus the flat earth theory occupies a very special place in the history of astronomy as one of the very earliest of theories.
However, if someone presented the flat earth theory as an upto date scientific theory, he would be simply wrong. It isn't. Is it pseudoscience? Well, it's not a pseudoscience in the way astrology is. This suggests that one ought to have a typology of pseudosciences and the like.
Now, according to Wikipedia, "chakras are various of focal points used in a variety of ancient meditation practises, collectively denominated as tantra". This makes it more complex to evaluate as it combines both physiology, psychology and religion. They also note the following verse from the yoginihrdaya:
Shining she holds
The noose made of the energy of will
The hook which is the energy of knowledge
The bows and arrows made of the energy of action
Split into support and supported
Divided into eight, bearer of weapons
Arising from the chakra with eight points
She has the ninefold chakra as a throne
They also say:
The chakras relate to subtle body [spirit], wherein it has a position but no definite nervous node or precise physical connection. The tantric systems envision it as continually present, highly relevant and a means to psychic or emotional energy ... it is useful in a type of yogic rituals and meditative discovery of radiant inner energy and mind-body connections.
Hence we can provisionally say it belongs to the kind of science that say psychoanalysis belongs to - in the Indian tradition of medicine. But given that modern science has completely supressed the notion of spirit, it is not an exact correspondance.