(March 27, 2025) The Reformation only challenged the Catholic Church's thought control, it did not challenge using the Bible as the main source for community knowledge. Seeing nature as such a community knowledge source only came about during the Enlightenment.

A well stated overview of the Enlightenment published in 1966:

• "To call the Enlightenment Pagan is to conjure up the most delightfully irresponsible sexual license: a lazy sun-drenched summer afternoon, fauns and nymphs cavorting to sensual music and lascivious paintings, preferably by Boucher. There is some reality to this fantasy: the philosophes argued for a positive appreciation of sensuality and despised asceticism.... In speaking of the Enlightenment as pagan therefore, I am referring not to sensuality but to the affinity of the enlightenment to classical thought. Words other than pagan - Augustan, Classical, Humanist - have all served as epithets to capture this affinity ...." (Peter Gay 1966)

The first battle between nature and the Bible would be over the question of whether the earth moved. The Christians viewed the earth as immovable because the Bible said so: 

• (Psalm 104:5, NIV) He (God) set the earth on its foundations; it can never be moved.

Also 1 Chronicles 16:30, Psalm 93:1, Psalm 96:10.

Yet developing observations and theories about nature indicated that the earth moved.

References

(March 27, 2025) Any claim that the earth moved was viewed as Pythagorean and heretical. Christians got most of their information about the Pythagoreans from Aristotle. He wrote:

• It remains to speak of the earth, of its position, of the question whether it is at rest or in motion, and of its shape. As to its position there is some difference of opinion. Most people-all, in fact, who regard the whole heaven as finite-say it lies at the center. But the Italian philosophers known as Pythagoreans take the contrary view. At the center, they say, is fire, and the earth is one of the stars (heavenly bodies), creating night and day by its circular motion about the center. They further construct another earth in opposition to ours to which they give the name counter-earth. (1)

"Star" is the Greek word ἀστήρ ("aster" as in astronomy) which means any heavenly body. 

"Fire is the Greek word φωτιά ("fotia" as in photograph) which has been traditionally translated as either fire or light.

The most complete statement about the Pythagorean conception of the universe is found in a surviving summation of old Greek texts done by Joannes Stobaeus around 400 CE. It says:

• Philolaus (first Pythagorean author) says that there is a fire (emanating glow) in the middle (of the world) at the center; he calls it: Hestia (Greek equivelent of Selu/Selene),  the All, the Guard-post of Zeus, the Mother of the gods, the Altar, the Link, and the Measure of Nature. Besides, he locates a second fire, quite at the top surrounding the world. The center, he says, is by its nature the first, around it, the ten different bodies carry out their choral dance. These are: the heavens, the planets, lower is the sun, and below that the moon, lower the earth, and beneath this, the counter-earth, then beneath these bodies is Hestia, in the center, where it maintains order. The highest part of the covering, in which he asserts that the elements exist in a perfectly pure condition, is called Olympus; the space beneath the revolution-circle of Olympus, and where in order are disposed the five planets, the sun, and the moon, forms the cosmos; finally, beneath the latter is the sublunar region which surround the earth where are the generative things susceptible to change. (1)

References

(1) Aristotle (350 BCE) On the Heavens, Book 2, Part 13. Online at https://classics.mit.edu/Aristotle/heavens.2.ii.html

(2) Original in Stobaeus, Eclogarum Physicarum, translated by August Meinekie (ed) Ioannis Stobaei Eclogarum Physicarum et Ethicarum, vol. 1 (1860). I found it in: Phythagoras or Christ by Alberto A. Martinez (2022) Saltshadow Castle, Cambridge, Massachusetts, USA

(March 25, 2025)  The Pythagoreans were devoted to the celestial light fate powers of  Selu/Selene because they did not think the emotion class of motion powers were pure enough (Selene means "powers of Selu" in Akkadian). This is a consequence of their contact with Zoroastrian Dualism. Her male complement was the dark, new moon and eye pupil god Su who represented the emotion sources magic including that aimed at affecting fate  (astrology magic).

Greek ἑστία (Estia, Hestia) is the Akkadian phrase ES.T meaning "Spiritual-fluids of astrology magic." Spiritual fluids were emanations such as the light and heat from hot coals and the sun. Emanations are not the same as the "expulsions" which are the actual flames of a fire.

Selu/Selene was called "Vesta" in Latin. Vesta is the Akkadian phrase US.T meaning "Binders of Astrology-magic." This word has the essentially the same meaning as Estia/Hestia. She was the goddess of fate for family and society and was guardian of the family hearth which protected the family. This hearth fire was not the element of fire/flame. In Rome, her main priestesses were the state sponsored Vestal Virgins. Being virgins they had nothing to do with fertility and life powers. 

(July 7, 2022, updated March 26, 2025) Perhaps everyone has heard of the time-space continuum from Einstein's Relativity Theory. This is the foundation of both the universe and mathematics because it has the property that some smaller interval always exists. If a system needs it then it can pop into existence. The classic example of a continuum is the mathematical curve defined by 1/x shown to the left. Because the curve is symmetric around the point (1,1) as many points can exist between 0 and 1 as between 1 and infinity.

With no hard minimum length, lengths can only be defined in a relative fashion by ratios from geometry or from wave functions (musical harmonics, quantum mechanics). That is, by comparison of a reference length to another. The reference length can be called 1. All other numbers can then be defined by a ratio making process. Mathematics can thus be used to approximately describe the workings of continuums.

Historically, this insight was first made by the Pythagoreans. The first Pythagorean who wrote anything down was the Greek Philolaus who began his book (only now exists in small fragments) with a bold statement about this insight:

• Nature (physis) in the world-order (cosmos) was fitted together out of things which are unlimited and out of things which are limiting, both the world-order as a whole and everything in it. (Stanford Encyclopedia of Philosophy) 

Here the continuum is called an "unlimited" and the "limiting" processes were the ratios defined from geometry and musical harmonics.

In regards to the Pythagorean theorem assigned to them, they may or may not have invented it but its use of geometric ratios would naturally have associated it with the Pythagoreans.

References

Stanford Encyclopedia of Philosophy - Philolaus (Sept 2003, revised September 2024). Online at: https://plato.stanford.edu/entries/philolaus/

(March 30, 2025) 

Bruno was born in 1548 in the town of Nola near Naples. At the age of 17, he entered the Dominican Order at the monastery of San Domenico Maggiore in Naples, taking the name Giordano, after Giordano Crispo, his metaphysics tutor. He continued his studies there, completing his novitiate, and ordained a priest in 1572 at age 24. During his time in Naples, he became known for his skill with the art of memory and on one occasion traveled to Rome to demonstrate his mnemonic system before Pope Pius V and Cardinal Rebiba. His great memory is what initially gained him attention.

He later became known for his cosmological theories which incorporated the sun centric model of Copernicus. He forced this model to its logical conclusions suggesting that stars were distant suns surrounded by their own planets. He even raised the possibility that these planets might foster life of their own. He also insisted that the universe is infinite and could have no center. 

An invitation in 1592 to go to Venice to teach Count Giovanni Mocenigo the science of memory led to his downfall. Mocenigo in short order turned him over to the Inquisition on a charge of heresy.

After a nine-month trial, the Venice court sent him to Rome where he was imprisoned and underwent another trial that lasted seven years. He was convicted with the Pope's approval and sentenced to death by burning on Feb. 9, 1600.

The inquisition cardinals who judged Giordano Bruno were Cardinal Bellarmino (Bellarmine), Cardinal Madruzzo (Madruzzi), Camillo Cardinal Borghese (later Pope Paul V), Domenico Cardinal Pinelli, Pompeio Cardinal Arrigoni, Cardinal Sfondrati, Pedro Cardinal De Deza Manuel and Cardinal Santorio (Archbishop of Santa Severina, Cardinal-Bishop of Palestrina). Many of these would also be involved in the later trial of Galileo.

References

https://en.wikipedia.org/wiki/Giordano_Bruno

Alberto A. Martinez (2022) Pythagoras or Christ? Saltshadow Castle, Cambridge, MA,USA

(March 31, 2025) Interestingly, the Vatican records, normally so voluminous and complete are missing the pages listing his alleged heresies. But we happen to have such a list from a German witness to the events in Rome named Gaspar Schoppe, who was visiting Cardinal Madruzzi at the time. His list was found in a letter to a friend. The most important 2 according to Martinez (2022) were:

1. Worlds are innumerable

2. The Holy Spirit is the soul of the world (that is what caused it to move)

Multiple worlds are were a heresy because that implies that Christ must have visited them all, died, and then have been repeatedly resurrected to save them. This goes against Christian teachings even today (which is why even the modern Catholic church has never officially forgiven him). 

Claiming a moving earth had a soul causing it to move is a heresy for 2 reasons, first the Bible says the earth is stationary (Psalms 104:5), second the Bible says the Holy Spirit is God's power to comfort, guide, and generally empower Christians, not change anything. Bruno and many other saw Aristotle's theory was flawed, especially in regards to natural motion. Wood rose in water but fell in air. What was its real natural motion? If that was imposed motion then all things falling in air was imposed motion so things did not have a natural resting place (like the center of the earth) which they sought. So the only alternative was to claim the Holy Spirit moved things but this was Pythagorean and thus Pagan.

Paradigms matter.

References

https://en.wikipedia.org/wiki/Giordano_Bruno

Alberto A. Martinez (2022) Pythagoras or Christ? Saltshadow Castle, Cambridge, MA,USA

(March 30, 2025) Yet the real proof that the physics of earth extended into the heavens was only seen by those who could understand the astronomical mathematics in Kepler's 650 page book published in 1609 entitled: 

• New Astronomy, Based upon Causes, or Celestial Physics, Treated by Means of Commentaries on the Motions of the Star Mars, from the Observations of Tycho Brahe, Gent.

Kepler made the claim that planets moved in elliptical orbits subject to physical forces and did not move magically in perfect circles. Additionally he put the sun at one focus of the ellipse. To make this claim he had to replace the classical era Aristotelian physics which placed the earth at the center of the universe where it attracted all physical bodies. 

Yet Kepler was still partly trapped by the old divine power source paradigm. While he was the first to define gravity as a force similar to the force of magnetism by saying this:

• Gravity is a mutual corporeal disposition among kindred bodies to unite or join together; thus the earth attracts a stone much more than the stone seeks the earth. (The magnetic faculty is another example of this sort).... For it follows that if the earth's power of attraction will be much more likely to extend to the moon and far beyond, and accordingly, that nothing that consists to any extent whatever of terrestrial material, carried up on high, ever escapes the grasp of this mighty power of attraction .... 

He want on to say in chapter 33 that the sun somehow moves the planets laterally. He claimed the Sun emitted a physical something, analogous to light, which pushed the planets along. And this was still a Catholic Christian heresy.

References

(July 6, 2022) Two discoveries started the expansion of physical nature into heavens which ultimately ended up forcing a paradigm change about motion. 

Galileo built himself this telescope in 1609 after he heard about Kepler's laws and the invention of the telescope in the Netherlands. His first telescope demonstration was for the Venetian military which gained him a life time appointment as a professor and raised his salary to 1000 florins a year. In the fall he turned an even better telescope towards the heavens. He confirmed that planets orbited the sun by seeing that planets had phases. He also saw that the moon's surface was imperfect and thus it belonged to the material realm.He published a book called the"Starry Messenger" describing and illustrating these discoveries in Venice on March 12, 1610. The book caused a sensation. Kepler was delighted because it confirmed his contention that physics extended to the heavens.  After this, Galileo's hometown of Padua offered him a professorship with terms better than those from Venice so Galileo moved back home. 

Galileo Galilee (1564 - 1642) was a professor of Mathematics at the University of Padua in the Republic of Venice where he specialized in instrument making. This included an irrigation device and an advanced drawing compass/slide-rule.

The importance of his father, Vincenzio, on Galileo's  anti-authoritarian views should not be over looked. Vincenzio was a musician and mathematician and part of the group which invented the opera as a musical revival of Greek tragedy. He invented a more refined musical scale for the lute based on the actual harmonies of sound instead of the traditional mathematical Pythagorean ratios. He wrote a book describing and defending this new approach called Dialog of Ancient and Modern Music.  In it he states:

• "they who in proof of any assertion rely simply on the weight of authority, without adducing any argument in support of it, act very absurdly. (page 17 Sobel 2000)

In 1608 or early 1609 Galileo heard about the invention of the telescope in Flanders which had came about because eye glasses had been invented making lenses more common. Because he was an instrument maker and designer he was one of the few who could build it sight unseen and keep on improving its magnification and clarity. His first telescope used standard eye glass lenses but Galileo soon went beyond that with lenses of greater power and clarity.

Reference

Sobel, Dana (2000) Galileo's Daughter, Penguin Books, New York

(March 31, 2025) 

For Galileo the simplest explanation of his new findings was that the earth had to move around the sun. Yet, as he would be told, this directly contradicted Psalm 104 verse 5: 

• Thou (God) fixed the earth upon its foundation, not to be moved forever.

Galileo's answer to this is found in a 1613 letter to a friend who was reporting this growing opposition to him:

• The Holy Scripture cannot err and the decrees contained therein are absolutely true and inviolable. I should only have added that, though the Scripture cannot err, its expounders and interpreters are able to err in so many ways. ( Sobel page 63)

He went on to say that many statements about nature were put into the Bible in order to keep it simple for the masses because the main purpose of the Bible was teaching salvation.  

Overt public attacks on Galileo began on December 21, 1614 with a sermon by a Dominican priest in Florence named Tommaso Caccini. He stated that all of Galileo's followers and indeed, all mathematicians in general were "practitioners of diabolical arts and ... the enemies of true religion." After this and the Catholic inquisition condemned heliocentrism again in 1615, Galileo went silent.

When a friend of his (Cardiinal Maffeo Vincenzo Barberini) became Pope Urban VIII from 1623 to 1644 Galileo was emboldened once again. In 1632 he published his sun centric astronomical views in a book entitled Dialogue Concerning the Two Chief World Systems. He framed it as a debate and not as his own views so he managed to get it approved by the church. But what he did not know was that his anti-sun centered proponent named Simplico just happened to hold the same views as Pope Urban VIII who was insulted and wanted revenge. He at age 68 and ill was tried by the Inquisition, found guilty of heresy, and forced to recant. He spent the rest of his life under house arrest until he died in 1642.

Yet some still naively hoped that a more proper reasoning methodology would somehow reconcile nature with the Bible and/or Catholic theology. This was never to occur but Protestant Francis Bacon (1561–1626) and Catholic Descartes (1596-1650) made the most  famous attempts. 

(March 30, 2025) The change of paradigm from a single realm in which all change was governed by divine powers to a binary realm with each realm having their own sources of change (Divine = occult change, Physical = mechanical change) was completed by Isaac Newton (1643–1727) of England in his 1687 book Mathematical Principles of Natural Philosophy. He wrote:

• "Since the ancients (as we are told by Pappus), made great account of the science of mechanics in the investigation of natural things; and the moderns, laying aside substantial forms and occult qualities, have endeavoured to subject the phænomena of nature to the laws of mathematics, I have in this treatise cultivated mathematics so far as it regards philosophy. The ancients considered mechanics in a twofold respect; as rational, which proceeds accurately by demonstration: and practical. To practical mechanics all the manual arts belong, from which mechanics took its name."

Reference

(July 6, 2022) Christian Europe was dualist. Truth was either true or false, people were either saved or unsaved.  The physical world was either evil and corruptible while the divine was good and  perfect. This dualism originated with the Zoroastrian religion of the Persian Achaemenid Empire (550-330 BCE) which made its way into Judaism during the Babylonian exile and then into Christianity. The ancient past was not dualist.

John Locke was the first person to attack dualism although he was not aware he was doing so. He was simply trying to understand the how humans could come to know things. The result was the first description of what moderns would call "Decision Theory." He took the new ideas of mathematical probability developed within the context gambling and commercial insurance and applied them to knowledge. Christiaan Huygens published his book on the subject in 1657 entitled On reasoning in games of chance.

For Locke, all knowledge was uncertain. Only if the its probability was high enough could it be considered true. Certainty increases with:

1. The conformity of anything with our own knowledge, observation, and experience.
2. The testimony of others, vouching their observation and experience. In the testimony of others is to be considered : 1. The number. 2. The integrity. 3. The skill of the witnesses. 4. The design of the author, where it is a testimony out of a book cited. 5. The consistency of the parts, and circumstances of the relation. 6. Contrary testimonies. (book IV, Chapter XV: Of Probability)

Uncertainty in Knowledge Requires Tolerance

This weighing of evidence takes time therefore:

But in a contradictory nod the Biblical authority to prevent his book from being suppresses (a fear expressed in the books introduction) he says this:

Locke suddenly assumes the human receiver of knowledge is perfect, a perfection not seen anywhere else in his book.

The net result of his book was the falsification of the idea that knowledge was binary being either true or false. Knowledge could be gathered from nature over time with ever increasing certainty. It did not have to be suddenly revealed. He was certainly proved correct as evidenced by the existence of modern technology.

References

Locke, John (1689) Essay Concerning Human Understanding. Online at: https://en.wikisource.org/wiki/An_Essay_Concerning_Human_Understanding

Locke, John (1690) Essay Concerning Human Understanding (a second edition original) Online at: https://www.google.com/books/edition/An_Essay_Concerning_Human_Understanding/hGeKsjjtu6EC?hl=en&gbpv=1&dq=Essay+Concerning+Human+Understanding&printsec=frontcover

(April 3, 2025) During the Renaissance, reality became binary having both a material universe and a spiritual/divine universe. This led to the question of where were they and how were they related? Two possible answers emerged:

2. Binary Reality - The divine and material realms have different roles. This is the dominant paradigm of today. It is also the paradigm of Judaism, Christianity, Islam, and Buddhism. Yet how these 2 realms may interact is never explained by these dominant religions. That has been left to more recent philosophies which are:

1. Dimensionalism - The spiritual realm exists within a higher dimensional space. This makes the physical realm analogous to a sheet of paper floating in 3-D space representing the spiritual realm. This was popularized by the 1884 short story called "Flatland - A Romance of Many Dimensions" by Edwin Abbott Abbott. Online at: https://www.gutenberg.org/ebooks/45506.  The problem is that spaces higher than 3 dimensions cannot form complex structures like proteins. For example, knots in higher dimensions are not possible.  Stable orbits (atomic and planetary) are not possible. This was shown by the new mathematics of topology invented by that genius mathematician Leonhard Euler (1707 - 1783).
2. Pantheism - the divine and material realms exist "within" each other. But trying to use the word "within" is inaccurate and imprecise because that word is a spatially defined and the divine realm is not spatial in this case. Different definitions of "within" have led to  nebulous and imprecise definitions of pantheism as discussed by different authors. The most coherent definition of Pantheism is that space is an organized information processing network emerging out of a disorganized network representing the spiritual realm (see illustrations).

(March 8, 2025) Pantheism holds that the divine and material realms exist within each other but use different ways to separate causal events (that is, to change state).  

1. Material Realm's Spatial Separability: All events are governed by energy changes separated by space-time differences like material realm, therefore the spiritual realm exists in some higher dimensional space. Physical constants are unchanging.
2. Spiritual Realm's Quality Separability: All events are governed by quality ratio changes (same reasoning as Pythagorean ratios) like physical constant changes in the paddle ball example. In the material realm, each spatial dimension is a quality analogous to a primary color, just using spatial energy mixing rules instead of color mixing rules.

(July 6, 2022) Freemasonry was a Manifestation of the Freedom Stage of the Enlightenment. It was not meant to replace any existing religion but became popular because it was a place for free thinkers to associate in a private club atmosphere. Its popularity was due to doing ceremonial royal-like rituals together and working towards gaming-like level advancements in regards to those rituals. Its members were free to work out and choose their own religious path. This desire for freedom from the repressive state and religious authorities of the time led to most of its workings being secret.

Freemasonry also provided much of the ritual structure for later Nature based magical practices. Many modern Nature Pagans still use the Freemasonry ritual practice of calling the cardinal directions, using its closing phrase of "so mote it be" and its original three degrees of advancement in education schemes. Also the 1950's founders of the British Wicca (Gerald Gardner) and the more nature based Order of Bards, Ovates, and Druids (Ross Nichols) were members of a Freemason inspired organization called the Ancient Druid Order.

Freemasonry's first informal lodges were formed in London starting around 1680. In 1717 the remaining members of these lodges came together and formally formed a grand lodge (Morris 2013). Consequently, their rise paralleled that of the 3rd and last stage of the Enlightenment which focused on social freedom. By joining a Freemason lodge its members were making more of a personal statement about being anti-authoritarian instead of seeking a nature based religion.

The ancient tradition most in line with freedom and which was adopted by these new Freemasons was that of stone-craft masonry which was in steep decline at the time due to the rise of brick as a building material. Brick had been of poor quality until the time of King Henry VIII (ruled 1509 to 1547) who build several palaces out of it. By the mid 1600's it was the building material of choice, especially for the conversions of old stone houses into houses having the new invention of fireplaces.

The governing guild charter of stone-craft masonry goes back to 1390 CE with the Regius Manuscript. It shows an egalitarian organization of traveling masons having a legendary ancient history. This fake history has the craft masons going back to the time of Babylon and then having the guild associated with Abraham and the Greek geometer Euclid in ancient Egypt at the same time.

Freemasonry invented "secrets" for itself. These secrets consist of passwords, various secret signal, and most of the rituals themselves. Over time most such secrets have been exposed. Why they did so can only be guessed. Perhaps it was to insure security against a misunderstanding and hostile world, perhaps it was to give it an aura of mystery and exclusivity. Yet by claiming to have these "secrets" Freemasonry has generated much hostility to itself. Many people think that they must be doing something nefarious if they have such deliberate secrets. 

Freemasonry's rituals in their temples (also called lodges) have been their most important gift to Nature Paganism. These rituals are done around a central altar.  The ritual room is orientated along the cardinal directions. Yet these rituals are done without the aim of generating feelings. They involve a lot of rote memorization. Often they are done to illustrate some ethical principle. While the initiation rituals can generate feelings that is not their goal. Instead, Freemason's seek to connect to the Divine with prayers thinking words are somehow transmitted across the veil (the material-spiritual barrier).

 Freemasonry is generally segregated by gender. It is also composed of many different organizations which are open to all Master Masons (3rd degree Masons) which belong to a Blue (Symbolic) Lodge. Some of these higher level male organizations are: York rites, Scottish Rites, Shriners, Grotto, Tall Cedars of Lebanon, and Knights Templar. The male African American Masonic orders are Prince Hall

The groups for the female relatives of male Masons are the Order of the Eastern Star, Order of the Amaranth, and the White Shrine of Jerusalem.

References

 Morris, S. Brent (2013) The Complete Idiot's Guide to Freemasonry (2nd edition) Alpha books

(July 6, 2022) The first attack on Freemasonry was a 1698 leaflet published in London. This attack occurred even before the formation of the Grand Lodge there. It is reproduced below:

The earliest Freemason statement on the religion of Freemasonry was made in 1723 by Freemason and Reverend James Anderson in his book Constitution of the Free-Masons. He imagined some common natural religious framework as the "religion which all men agree" with some natural "Moral Law" without stating what that was or how to find it. Beyond that all sectarian religious opinions were not to be discussed within Freemasonry. His important section of text is as follows:

The Catholic church under Pople Clement XII issued its first encyclical against Freemasonry in 1738 called "In Eminenti." The Catholic church did not argue against it on doctrinal grounds since that would mean promoting their own doctrine and condemning all other Christian denominations. Instead they seized upon it as being a secret society and assumed it like all secret societies was plotting against the state and the church. They also commanded the inquisition to go after all Catholic members:

This has continued to be the position of the Catholic church through it new Code of Canon Law of 1983:

Joseph Cardinal Ratzinger who soon became Pope Benedict XVI (2005-2013) issued a clarification on this:

The Southern Baptists also do not find Freemasonry compatible with Christianity. The following is a report from their missions board which was approved at the 1993 annual session of the Southern Baptist Convention. It's eight reasons of incompatibility are reproduced below:

1. The prevalent use of offensive concepts, titles, and terms such as "Worshipful Master" for the leader of the lodge; references to their buildings as "mosques," "shrines," or "temples;" and their use of words such as "Abaddon" and "Jah-bul-On" the so called secret name of God. To many these terms not only are offensive but sacrilegious.
2.  The use of archaic, offensive rituals and so called "bloody oaths" or "obligations" among these being that promised by the Entered Apprentice: "All this I most solemnly and sincerely promise and swear swear ... binding myself under no less penalty than that of having my throat cut from ear to ear, my tongue torn out by its roots ... should , in the least, knowingly or wittingly violate or transgress this my entered apprentice obligation." ... (more examples)
3.  The recommended readings in pursuance of advanced degrees, of religions and philosophies, which are undeniably Pagan and/or occultic, such as much of the writings of Albert Pike. Albert Mackey, Manley Hall, Rex Hutchins, W.L. Wilmshurst, and other such authors; along with their works such as Morals and Dogma, A Bridge to Light, An Encyclopedia of Freemasonry, and The Meaning of Masonry.
4.  The reference to the Bible placed on the altar of the lodge as the "furniture of the lodge" comparing it to the square and compass rather than giving it supreme place in the lodge
5.  The prevalent use of the term "light" which some may understand as a reference to salvation rather than knowledge and truth.
6.  The implication that salvation can be obtained through good works, implicit in the statement found in some Masonic writings that "Masonry is continually reminded of that purity of life and conduct which is necessary to Obtain admittance into the Celestial Lodge above where the Supreme Architect of the Universe presides." Even though many Masons understand that the "purity of life and conduct" can only be achieved through faith in Jesus Christ, others my be led to believe they can earn salvation by living a pure life with good conduct.
7.  The heresy of Universalism (the belief that all people will eventually be saved), which permeates the writings of many Masonic authors, which is a doctrine inconsistent with New Testament teaching.
8. The refusal of most lodges (but not all) to admit membership of African Americans. (https://www.chick.com/bc/2011/mason_report.pdf)

References

(July 6, 2022) The first phase of the Enlightenment challenged human created religious laws and institutions hiding behind a claimed divine sanction. The next phase will challenge was the divine right of kings to rule.

The Dawn of Freedom began in Britain in 1688  because that was the year of the "Glorious Revolution" in which constitutional limits were placed on monarchical power and religious toleration was made state policy. This phase had its roots in the philosophy of government from the classical era. This is why all the original government buildings in the United States look classical. 

The idea of liberty based upon natural rights only emerged during the Enlightenment. Freedom never emerged in nations having authorities not based upon nature.  

In this phase, the Enlightenment thinkers tried to separate the role of the state from the role of religion. Europe had seen too many religious wars and wars against heretics in its history. They concluded that the state would be responsible for material things while religion would be responsible for emotional/spiritual things. This first stated by John Locke  (1632-1704) who was also important in closing out the previous phase of Enlightenment. He wrote the following between 1689 and 1693:

Thomas Jefferson in the U.S Declaration of Independence shortened and generalized Locke's phase to "Life, Liberty, and the pursuit of Happiness."

The concept of happiness as used by Jefferson thus includes the right to health and the right to acquire and hold possessions. During the civil war Abraham Lincoln and the nation elevated in blood the Declaration of Independence above that of the constitution to justify the elimination of the property right of slavery. The Declaration as a statement of purpose trumped any legal document meant to implement that purpose. Freedom is Pagan.

References

Gay, Peter (1966)  The Enlightenment - The Rise of Modern Paganism 

Kramic, Isaac [editor] (1995)  The Portable Enlightenment Reader.  Penguin books