In The Secret Doctrine, in volume I, stanza II, śloka 5-6 (SD I, 28), the Book of Dzyan speaks of a germ from which the universe is born:

5. THE SEVEN SONS WERE NOT YET BORN FROM THE WEB OF LIGHT. DARKNESS ALONE WAS FATHER-MOTHER, SVABHAVAT; AND SVABHAVAT WAS IN DARKNESS.

6. THESE TWO ARE THE GERM, AND THE GERM IS ONE. THE UNIVERSE WAS STILL CONCEALED IN THE DIVINE THOUGHT AND THE DIVINE BOSOM. . . .

In SD I, 1 we find an explanation of this twofold germ in terms of the symbols displayed on the palm leaves of the archaic document mentioned by HPB in the first lines of the Proem:

The point in the hitherto immaculate Disk, Space and Eternity in Pralaya, denotes the dawn of differentiation. It is the Point in the Mundane Egg […], the germ within the latter which will become the Universe, the ALL, the boundless, periodical Kosmos, this germ being latent and active, periodically and by turns.

The central point in the circle in the second archaic symbol represents the eternal germ. This germ is one of the fundamental aspects of the unmanifested universe. In SD I, 379 we find another important clue as to the nature of the germ:

The spirit of Fire (or Heat), which stirs up, fructifies, and develops into concrete form everything (from its ideal prototype), which is born of WATER or primordial Earth, evolved Brahma — with the Hindus. The lotus flower, represented as growing out of Vishnu’s navel — that God resting on the waters of space and his Serpent of Infinity — is the most graphic allegory ever made: the Universe evolving from the central Sun, the POINT, the ever-concealed germ.

The navel of Viṣṇu is symbolic for the eternal germ, the central point in the Mundane Egg.

From SD I, 381n we learn that we might look for this allegory, or creation story, “in Indian Puranas”:

* In Indian Puranas it is Vishnu, the first, and Brahma, the second logos, or the ideal and practical creators, who are respectively represented, one as manifesting the lotus, the other as issuing from it.

There are several versions of the story of the birth of Brahmā, for example one of these is found in Manusmṛti chapter I, verses 10-17 and another one in the Mahabhārata book III, section 270. The Manusmṛti version is referred to by HPB in SD I, 333. In the Viṣṇu Purāṇa the story is touched upon several times. In the Bhāgavata Purāṇa however, BhP III.8.10-17, we find a fairly detailed version of the story. In verse 10 in the French 1840 translation of Eugène Burnouf, the primordial state of of the universe is presented like this:

10. Au temps où l’univers tout entier était submergé par les eaux, celui dont les yeux ne se ferment s’abandonna au sommeil, couché sur un lit formé par le Roi des serpents, solitaire, inactif, et trouvant sa dans sa propre béatitude.

We may recognize the waters as the darkness or space from the Book of Dzyan, and the bed formed by the King of serpents, as eternal duration. The serpent in this version of the story is called Śeṣa, and in some other versions it is called Ānanta, meaning endless or eternal. In SD I, 73 we have:

Sesha or Ananta, ‘the couch of Vishnu,’ is an allegorical abstraction, symbolizing infinite Time in Space, which contains the germ and throws off periodically the efflorescence of this germ, the manifested Universe….”.

Viṣṇu’s state of sleep in verse 10 represents pralaya, the tamasic state, a state of inertia. Then there are three qualities attributed to the pralayic state of Viṣṇu: 1. solitaire, 2. inactif, and 3. trouvant sa dans sa propre béatitude. The Sanskrit (see GRETIL: Gaudiya Grantha Mandira) terms here are 1. eka, 2. kṛtakṣaṇa and 3. svātmaratau nirīha:

10. udāplutaṃ viśvam idaṃ tadāsīd yan nidrayāmīlitadṛṅ nyamīlayat
ahīndratalpe ‘dhiśayāna ekaḥ kṛtakṣaṇaḥ svātmaratau nirīhaḥ

The term eka simply means “one”, a term we come across very frequently in volume I of The Secret Doctrine. It is slightly different from Burnouf’s “solitaire”, as it is a more philosophical term indicating primordial unity, rather than isolation or separateness.

Kṛtakṣaṇa would be something like “waiting for the right moment”, composed of kṛta, “done”, and kṣaṇa, “moment”. (Monier-Williams) An alternative “in leisure time”, “waiting”, “pausing”, as opposed to “inactif”, would incorporate the element of time, which is important in subsequent verses. (kāla)

Svātmaratau means “both his own self and delighting”, and nirīha is “indifferent”, “without desire”, “effortless”, or “motionless”, so svātmaratau nirīhaḥ might be translated as “remaining in unity, delighting, without effort”.

In BhP III.8.13-14 the lotus is produced from the navel of Viṣṇu:

13. L’essence subtile, renfermée au sein de celui dont le regard pénètre les molécules élémentaires des choses, agitée par la qualité de la Passion qui s’était développée sous l’influence du temps, sortit, pour créer, de la région de son nombril.

14. Elle s’éleva rapidement sous la forme d’une tige de lotus, par l’action du temps qui réveille les œuvres; ce lotus dont l’Esprit [suprême] est la matrice, éclairait, comme le soleil, de sa splendeur la vaste étendue des eaux.

The corresponding Sanskrit is:

13. tasyārthasūkṣmābhiniviṣṭadṛṣṭer antargato ‘rtho rajasā tanīyān
guṇena kālānugatena viddhaḥ sūṣyaṃs tadābhidyata nābhideśāt

14. sa padmakośaḥ sahasodatiṣṭhat kālena karmapratibodhanena
svarociṣā tat salilaṃ viśālaṃ vidyotayann arka ivātmayoniḥ

The quality of Passion, rajas, stimulates primordial matter, which rises up through the navel taking the form of the bud or stalk of a lotus. (padmakośa)

In verse 13 we have kālānugatena, which is kāla + anugata + -ena, “through acquirement with time” (cf. Monier-Williams), corresponding to Burnouf’s “qui s’était développée sous l’influence du temps”. An alternative would be “after a certain period”, “at a certain time/moment”. In verse 14 we have kālena, “by time”, or “through the workings of time”, “par l’action du temps”, and again an alternative would be the instrumental of time: “in time”, “at a certain moment” or perhaps even HPB’s more poetic “when the hour has struck”.

No. 47.110/60 1 in The National Museum, New Delhi

Returning to the enigmatic quotation from the “Occult Catechism” in SD I, 11:

“What is it that ever is?” “Space, the eternal Anupadaka.”* “What is it that ever was?” “The Germ in the Root.” “What is it that is ever coming and going?” “The Great Breath.” [..]

The eternal germ is the principle “that ever was” because it is at any time the origin of the current world process. It is the First Logos, or as we have seen, in terms of the Bhāgavata Purāṇa, Viṣṇu, or more specifically the navel of Viṣṇu.