Of course, there is the black stone at the Kaaba in Mecca that the Muslims hold as sacred. It is called in their language “Hadschar al Aswad.” It is believed to be a meteor. According to legend, it was given to Abraham by the Angel Gabriel. It comes from a tradition far older than Islam and so venerated by Muslims that they say Mohammed himself inserted the stone into the corner of the Kaaba.

The Black Stone of the Kaaba in its silver frame.

The Black Stone is seen in the circular white spot near the base of the structure.
Mithra was said to be born from a stone fully grown. Here, he carries a torch and trowel. The rock is flint and the torch represents the spark that springs from it. The trowel links Mithra to Masonic secrets.
Mining is, of course, done underground and the word for infernal or underworld deities as “chthonic.” Alchemists placed great emphasis on the mining of ores and gems and considered it a sacred, esoteric trade. Mithraists met in underground temples. Today, we refer to anything secret, esoteric or non-commercial as “underground.” We generally think of secrets as being buried. Gems and ores simply represent those secrets from the hidden source or simply put—the occult.
Lovecraft’s mythos could simply be seen as a metaphor for the human consciousness: We know that our brain has evolved up from the earlier animals and that we do, in fact, have a reptilian brain that stretches back a good 500 million years. There must be a tremendous amount of knowledge and instinct stored in our brains no longer accessible to us at least in any conscious fashion but instead have been consigned to the basement, i.e. the subconscious or the collective unconscious. What terrible, dark secrets are lurking down there trying to signal to us? Jung called them archetypes—universal, archaic patterns and images buried in the murky depths of the collective unconscious that function as the psychic equivalent of instinct. They enter the conscious mind to be expressed in a certain fashion by cultures all over the globe (remember the unconscious is collective) such as the Mother, the Trickster, the Flood. But the conscious symbolism is based on a particular culture. For example, all of us can access the Trickster archetype but people of different cultures express it differently—the Sioux Indians called it Iktome the spider while the Norse saw it as Loki, etc. Oddly, in most cultures, the Trickster gives fire to man.
Another archetype is the Shadow which contains all our darkest desires as well as all our creative power. Its physical aspect finds form in our reptilian brain. Like a reptile, the Shadow cannot be tamed, cajoled, seduced or reasoned with. Ancient humanity learned to control it imperfectly through ritual and ceremonial magic. Without the rituals, humanity would have long ago destroyed itself and today it is still a struggle but we have somehow managed.
Dreams are very important in Jungian psychology as they are in Lovecraft’s mythos. Both Lovecraft and Jung saw dreams as a form of communication. Jung saw dreams as communication from the collective unconscious while Lovecraft saw them as communication from Cthulhu. But then sunken R’lyeh could be a metaphor for the unconscious where everything is different from the everyday world if not the opposite of it and dead Cthulhu is the Shadow archetype lurking deep down there communicating to us in our dreams. He is the One that knows where all our skeletons are buried, so to speak, concerning our evolution and survival. The One whose truths would drive us mad.
The very opening paragraph of Lovecraft’s “The Call of Cthulhu” reads:
“The most merciful thing in the world, I think, is the inability of the human mind to correlate all its contents. We live on a placid island of ignorance in the midst of black seas of infinity, and it was not meant that we should voyage far. The sciences, each straining in its own direction, have hitherto harmed us little; but some day the piecing together of dissociated knowledge will open up such terrifying vistas of reality, and of our frightful position therein, that we shall either go mad from the revelation or flee from the deadly light into the peace and safety of a new dark age.”
In fact, Lovecraft prefaces his story with the following quote by British horror author Algernon Blackwood:
“Of such great powers or beings there may be conceivably a survival . . . a survival of a hugely remote period when . . . consciousness was manifested, perhaps, in shapes and forms long since withdrawn before the tide of advancing humanity . . . forms of which poetry and legend alone have caught a flying memory and called them gods, monsters, mythical beings of all sorts and kinds. . . .”
From these two quotes we can see that while science-fiction often anticipated real science, horror fiction anticipated depth psychology (which has replaced ritual for most of humanity). Blackwood, as you may know, was also a member of the Victorian British magical society called The Hermetic Order of the Golden Dawn to which Crowley also belonged. And so perhaps we get a glimpse into what these societies believed about human nature and the human consciousness concerning our ancient past. They know or believe they know who and what we really are.

Einstein explains his Special Theory of R’lyehtivity.
Other strange Lovecraftian coincidences:
Lovecraft said that R'lyeh is located at 47°9′S, 126°43′W in the southern Pacific Ocean.[4] August Derleth, however, placed R'lyeh at 49°51′S, 128°34′W in his own writings.[5] Both locations are close to the Pacific pole of inaccessibility, the point in the ocean farthest from any land. Derleth's coordinates place the city approximately 5100 nautical miles (5900 statute miles or 9500 kilometers), or about ten days journey for a fast ship, from Pohnpei (Ponape), an actual island of the area. Ponape also plays a part in the Cthulhu Mythos as the place where the "Ponape Scripture", a text describing Cthulhu, was found.
In summer 1997, the U. S. National Oceanic and Atmospheric Administration’s autonomous hydrophone array in the Equatorial Pacific Ocean repeatedly recorded a peculiar sound of a nature suggesting its biological origin. Yet, the sound’s amplitude was too large to be produced by any known animal species, and its source remains a mystery. According to NOAA, the readings yield a general location of the sound’s source “near 50° S 100° W”. The sound was given the name “Bloop”.
R'lyeh - Wikipedia, the free encyclopedia
An audio file of "Bloop" at this site:
Acoustics Monitoring Program - Icequakes (Bloop)
The NOAA now believes that Bloop is an icequake—part of an iceberg breaking off another. They provide an audio clip of Bloop and one of an icequake (their third clip has been disabled). Aside from the fact that the two clips sound really nothing alike (even though they tell us they do), I find it hard to believe that the NOAA never heard the sound of an iceberg breaking apart before 1997. Even stranger after insisting that Bloop had a biological origin. It's Cthulhu, damn you, man!
In "Shadow Over Innsmouth" which he wrote in 1931, Lovecraft mentions some kind of intelligent marine creatures in the South Seas that resembled fish that came up on land to talk with humans, give them knowledge and make deals with them. This was a couple of decades before two Frenchmen published a paper about the Dogon tribe of Timbuctu who have a secret society where they teach about a being called Nommo that came from Sirius and landed on earth and jumped into the ocean and swam around because he resembled a dolphin. Then he came up on land to talk to the humans and give them knowledge. The two Frenchmen lived with the tribe for years before being allowed to join the secret society. They first came in contact with the Dogon in 1931:
The Nommo are ancestral spirits (sometimes referred to as deities) worshipped by the Dogon tribe of Mali. The word Nommos is derived from a Dogon word meaning, "to make one drink," The Nommos are usually described as amphibious, hermaphroditic, fish-like creatures. Folk art depictions of the Nommos show creatures with humanoid upper torsos, legs/feet, and a fish-like lower torso and tail. The Nommos are also referred to as “Masters of the Water”, “the Monitors”, and "the Teachers”. Nommo can be a proper name of an individual, or can refer to the group of spirits as a whole. For purposes of this article “Nommo” refers to a specific individual and “Nommos” is used to reference the group of beings.
Nommo - Wikipedia, the free encyclopedia
The Greek “Nomos” also means “law.”