Since 2x4's and other timbers are cut from trees, people think of tree trunks as just being wood. After all they say, how can you hurt a board? ....it's just wood! While the center of the trunk is usually "just wood" (Heartwood), the inner bark consists of living tissue. These layers are known as the Phloem and the Cambium, with the cambium being the growth layer.
The xylem transports water and nutrients up the tree, and phloem transports products of photosynthesis back down. Because these layers of tissue are just inside the outer bark, it's important to protect this area from wounds, since these trunk wounds provide an excellent opportunity for disease pathogens.
Cross section of a tree trunk showing the xylem, cambium, phloem and outer bark
Trees have a different way of "healing" wounds. Unlike skin wounds, where our skin cells regenerate and we heal tissue, trees work to "wall off" or "compartmentalize" their wounds. Anything you can do to encourage rapid compartmentalization will surely help a tree.
When branches are removed, a tree forms callus tissue over the opening and compartmentalizes the wound. The speed with which a wound is compartmentalized often indicates the vigor of the tree. Below is a photo of callus tissue forming on the trunk of an oak tree where a branch was removed during a previous year.
It's desirable to see good buttressing (flaring-out) all the way around the base of a tree trunk. However, when you see a flat side on a tree trunk at the base of the tree, you should suspect a girdling root. Girdling roots grow across the side of the trunk instead of growing outward, and away from the tree trunk.
Usually, the leaves are smaller on the side of the tree with the offending root. It's often necessary to remove the root, by carefully excavating the soil around the trunk, and cutting it out. Root cuts, unlike branch cuts, should be painted or sealed with tree paint. Maple trees are the most common suspects when it comes girdling roots.
In the event a tree trunk is damaged by heavy equipment, it's best to cut loose bark away, back to where it is solidly connected to the tree trunk. The old recommendation was to shape the surgical cut into the shape of a canoe (with pointed tips aimed up and down the trunk) but current recommendations indicate that a circular shaped area is just as good. Following surgery, exposed bark tissue around the edges should be painted with orange shellac. The large area of trunk in the middle (heartwood) should be left unpainted.
Below we see the desired response to a surgically repaired bark area, with callus tissue beginning to grow over the trunk wound. Eventually, this tree will compartmentalize the wound, even though it could take as long as ten years.
Conks are usually hard shelf-like fruiting bodies (of a Fungus) which grow on tree trunks.
They should serve as 'red flags' indicating that something more may be wrong with the tree. These areas can extend well beyond the spot where you actually see the conk.
The fungus could actually extend throughout much of the tree trunk serving to weaken the trunk.