mm well that's true...
Though still how do you justify Chakra in a scientific format??
That which we call "Magic" can be integrated into Science. But first, we must understand the Four Magical Bases (Basis-plural):
1) Mediums in which to channel certain forces or desires.
2) Forces or (Vital) Energies which, when channeled through specific mediums, create certain effects.
3) Structures or Engravings like Ley Lines which direct Vital Energy flows and connect various points of interest.
4) Inscriptions like Runes which can be used as command prompts to create given effects by using certain forces/energies, often applied to mediums.
In RuneScape, these are used perfectly. There are various altars throughout that world (Gielinor) which are most likely connected by Ley Lines. Each altar has its own unique element. Rune Essence is not a metal but CAN be "mined" in certain hard to find areas. This Rune Essence can be "embedded" with an element (also gaining an inscription attributed to that element) at an altar. This elemental rune can then be used to channel vital energy (energies) which then create destructive physical effects such as a Fireball or Tsunami out of nowhere.
In this way, Magic has been fully explained by using the Four Magical Bases. You should be able to find these in whatever media happens to use magic.
Chakra does the same thing, though it does not need all four. It is a vital energy which the Arkana (as the medium) can channel to do various things: protect herself, deal more damage, unleash the elements, heal others, etc.
The Whipper's Flame Whip is a perfect example. She channels chakra into a firey form and applies it to her whip.
In this way, Magic seems very scientific and plausible, doesn't it?
Vital energies can replicate naturally physical things like fire and water. The results may be the same or simply act as physical illusions applied to reality. The research into how this works would be a great breakthrough in Science and even aid in finding the Fifth Fundamental Force.