99% of the human genome is, as far as scientists can tell, Junk DNA. I would however like to suggest that some is not junk but simply redundant troglomorphic DNA.
It is well accepted that early man dwelt in caves. The high radioactive levels present in these caves may have led to high mutation rates in germ line (reproducing) cells.
Development is known to be under the control of master switch mechanisms (evidence from experiments on mutations in fruit flies). Should one of these switches be mutated, the course of development could be radically altered in a single generation.
Human embryos can be seen to pass through fish and reptile like stages. A mutation could conceivably cause arrest at one of these stages. Born into the pools deep in caves (French style) these young might survive, using their external gills and feeding on garbage and other cave inhabitants. Should sexual maturity be reached they would be fully functional 'neotenous humans' (Neoteny is a common troglomorphic characteristic, seen in the newt like cave fish which are neotenous lizards (or other species)).
The neotenous forms that were able to mate with humans would spread their DNA between caves, therefore the humanoid part of the life cycle developed.
[graphic - awaiting webeditor attention]
Advantages of switch to/from humanoid form:
1) Allows colonisation of other unconnected subterranean sites.
2) Homo Sapiens could regenerate from cave form after hard winters etc.
T = dominant troglomorphic switch gene
t = recessive 'do not switch' gene
Homo Troglodytus genotypes: TT and Tt
Homo Sapiens genotype: tt
Homo Trog may breed like this:
TT & TT -> TT
TT & Tt -> Tt+TT
Tt & Tt -> TT + 2Tt +tt
Note if mother is in troglomorph form tt embryos die as can't switch and mother unable to support development to humanoid form.
TT & tt -> Tt only
Tt & tt -> Tt + tt
If mother is Homo Sapiens:
tt are born normally (? explanation of virgin births in history)
Tt are 'miscarried' or so the doctors inform the unfortunate mother.
1) Pheromones produced by troglomorphs may be the reason cavers go caving. Just because you have never heard tales of it does not mean that it does not occur. After all many women only discover after leaving school that they are not the only mutant female masturbator.
2) Modern men prefer to mate in the dark
3) Cave names such as Grey Wife, Batty Wife, (CUCC's own) Tatham Wife, Valentine Hole, Levit Hag Hole, Devil's Parlour (many indulgers believe they are dabbling with the devil)
Also the Gill holes (Gaping Gill, Sell Gill): A gill being a measure of alcohol used by troglomorphs to attract cavers
4) What Americans mean by spelunking
5) Poetry such as..
In Xanadu did Kublai Khan A stately pleasure dome decree Where alph the sacred river ran Through caverns measureless to man Down to a sunless sea
But oh! That deep romantic chasm.