Blake stated that he had read and annotated Bacon's Advancement of Learning when he was young - probably a teenager. Then and later he "felt ...Contempt & Abhorrence" at what he read. Blake later wrote notes in another of Bacon's books, Essays Moral, Economical and Political. Although Blake's annotations for the first book are lost, those for the second are recorded in Erdman's, The Complete Poerty and Prose of William Blake.
Annotations to Reynolds, (E 660)
"I read
Burkes Treatise when very Young at the same time I read Locke on
Human Understanding & Bacons Advancement of Learning on Every
one of these Books I wrote my Opinions & on looking them over
find that my Notes on Reynolds in this Book are exactly Similar.
I felt the Same Contempt & Abhorrence then; that I do now. They
mock Inspiration & Vision Inspiration & Vision was then & now
is & I hope will
always Remain my Element my Eternal Dwelling place. how can I
then hear it Contemnd without returning Scorn for Scorn" 
Yale Center for British Art
Jerusalem
Plate 41
Jerusalem, Plate 41 [46], (E 188)
"Thou art in Error Albion, the Land of Ulro:
One Error not remov'd, will destroy a human Soul
Repose in Beulahs night, till the Error is remov'd
Reason not on both sides. Repose upon our bosoms
Till the Plow of Jehovah, and the Harrow of Shaddai
Have passed over the Dead, to awake the Dead to Judgment.
But Albion turn'd away refusing comfort.
Jerusalem, Plate 37 [41], (E 184)
[mirror writing on scroll]
Each Man is in his Spectre's power
Untill the arrival of that hour,
When his Humanity awake
And cast his Spectre into the Lake"
The fault that Blake found in Bacon's book is not obvious but here are a few quotes which seem to diverge from Blake's understanding of the nature of God and Man.
Francis Bacon, Advancement of Learning, (1893)
"As for the knowledge which induced the fall, it was, as was touched before, not the natural knowledge of creatures, but the moral knowledge of good and evil; wherein the supposition was, that God’s commandments or prohibitions were not the originals of good and evil, but that they had other beginnings, which man aspired to know, to the end to make a total defection from God and to depend wholly upon himself.
But yet the commandment of knowledge is yet higher than the commandment over the will; for it is a commandment over the reason, belief, and understanding of man, which is the highest part of the mind, and giveth law to the will itself. For there is no power on earth which setteth up a throne or chair of estate in the spirits and souls of men, and in their cogitations, imaginations, opinions, and beliefs, but knowledge and learning.
which science whether I should report as deficient or no, I stand doubtful. For I find a certain rhapsody of natural theology, and of divers parts of logic; and of that part of natural philosophy which concerneth the principles, and of that other part of natural philosophy which concerneth the soul or spirit—all these strangely commixed and confused; but being examined, it seemeth to me rather a depredation of other sciences, advanced and exalted unto some height of terms, than anything solid or substantive of itself.
So, in like manner, although our persons live in the view of heaven, yet our spirits are included in the caves of our own complexions and customs, which minister unto us infinite errors and vain opinions if they be not recalled to examination.
But out of these two do result and issue four main branches of divinity: faith, manners, liturgy, and government."
Here are some of Blake's notes in his copy of Essays Moral, Economical and Political
Annotations to Bacon, (E 619-632)
"Self Evident Truth is one Thing and Truth the result of
Reasoning is another Thing Rational Truth is not the Truth of
Christ but of Pilate It is the Tree of the Knowledge of Good &
Evil
_________
What Bacon calls Lies is Truth itself
_________
Pretence to Religion to destroy Religion
_________
Bacon put an End to Faith
_________
What do these Knaves mean by Virtue Do they mean War & its
horrors & its Heroic Villains
_________
Thought is Act. Christs Acts were Nothing to Caesars if
this is not so
_________
When the Reverence of Government is Lost it is better than
when it is found Reverence is all For Reverence
_________
A Tyrant is the Worst disease & the Cause of all others
_________
Bacon has no notion of any thing but Mammon
_________
The Devil is the Mind of the Natural Frame
_________
There is no Such Thing as a Second Cause nor as a Natural
Cause for any Thing in any Way
He who says there are Second Causes has already denied a
First The Word Cause is a foolish Word
_________
An Atheist pretending to talk against Atheism
_________
What a Cursed Fool is this Ill Shapen are Infants or
small Plants ill shapen because they are not yet come to their
maturity What a contemptible Fool is This Bacon
_________
a Lord Chancellor's opinions as different from Christ as
those of Caiphas or Pilate or Herod what such Men call Great is
indeed detestable
_________
Bacon calls Intellectual Arts Unmanly Poetry Painting
Music are in his opinion Useless & so they are for Kings & Wars &
shall in the End Annihilate them
_________
Bacons Business is not Intellect or Art
_________
King James was Bacon's Primum Mobile"
_________
As Oliver Sacks reminded me, when we see a reflection in a mirror, we
have lost a dimension of
the image. A three dimensional image has been reduced to two
dimensions: there is no depth. This was Blake's complaint about
Bacon. In order to see the world empirically, Bacon eliminated the
dimension of spirit. Although the world included a channel for
receiving information from the non-material world Bacon
recommended that man ignore
communication through that channel in order to focus on
measurements, theories, experiments and proofs. I remember as a
high school student learning to adopt the methods of science and
mathematics in order to view the world in terms of qualities and
quantities. The dimension of myth, music, art, and meaning was
neglected in order to focus on physical descriptions, theoretical
constructions, objective analysis. Bacon was admired for being the
father of the scientific method which introduced the line of reasoning
which emphasized empiricism and inductive logic. Jerusalem, Plate 15, (E 159)
"O Divine Spirit sustain me on thy wings!.
That I may awake Albion from His long & cold repose.
For Bacon & Newton sheathd in dismal steel, their terrors hang
Like iron scourges over Albion, Reasonings like vast Serpents
Infold around my limbs, bruising my minute articulations
I turn my eyes to the Schools & Universities of Europe
And there behold the Loom of Locke whose Woof rages dire
Washd by the Water-wheels of Newton. black the cloth
In heavy wreathes folds over every Nation; cruel Works
Of many Wheels I View, wheel without wheel, with cogs tyrannic
Moving by compulsion each other: not as those in Eden: which
Wheel within Wheel in freedom revolve in harmony & peace."
Jerusalem, Plate 54, (E 203)
"But the Spectre like a hoar frost & a Mildew rose over Albion
Saying, I am God O Sons of Men! I am your Rational Power!
Am I not Bacon & Newton & Locke who teach Humility to Man!
Who teach Doubt & Experiment & my two Wings Voltaire: Rousseau.
Where is that Friend of Sinners! that Rebel against my Laws!
Who teaches Belief to the Nations, & an unknown Eternal Life
Come hither into the Desart & turn these stones to bread.
Vain foolish Man! wilt thou believe without Experiment?
And build a World of Phantasy upon my Great Abyss!
A World of Shapes in craving Lust & devouring appetite
So spoke the hard cold constrictive Spectre"
Jerusalem, Plate 92, (E 253)
"Then Los again took up his speech as Enitharmon ceast
Fear not my Sons this Waking Death. he is become One with me
Behold him here! We shall not Die! we shall be united in Jesus.
Will you suffer this Satan this Body of Doubt that Seems but Is Not
To occupy the very threshold of Eternal Life. if Bacon, Newton, Locke,
Deny a Conscience in Man & the Communion of Saints & Angels
Contemning the Divine Vision & Fruition, Worshiping the Deus
Of the Heathen, The God of This World, & the Goddess Nature
Mystery Babylon the Great, The Druid Dragon & hidden Harlot
Is it not that Signal of the Morning which was told us in the Beginning"
Annotations to Spurzheim, (E 663)
"Cowper came to me & said. O that I
were insane always I will never rest. Can you not make me truly
insane. I will never rest till I am so. O that in the bosom of
God I was hid. You retain health & yet are as mad as any of us
all--over us all--mad as a refuge from unbelief--from Bacon
Newton & Locke"
Letters, To trusler, (E 702)
"Why is the Bible more
Entertaining & Instructive than any other book. Is it not
because they are addressed to the Imagination which is Spiritual
Sensation & but mediately to the Understanding or Reason Such is
True Painting and such was alone valued by the Greeks & the
best modern Artists. Consider what Lord Bacon says "Sense sends
over to Imagination before Reason have judged & Reason sends over
to Imagination before the Decree can be acted." See Advancemt of
Learning Part 2 P 47 of first Edition"
Letters, To Butts, (E 716)
"This I endeavour
to prevent & with my whole might chain my feet to the world of
Duty & Reality. but in vain! the faster I bind the better is the
Ballast for I so far from being bound down take the world with me
in my flights & often it seems lighter than a ball of wool rolled
by the wind Bacon & Newton would prescribe ways of making the
world heavier to me & Pitt would prescribe distress for a
medicinal potion. but as none on Earth can give me Mental
Distress, & I know that all Distress inflicted by Heaven is a
Mercy. a Fig for all Corporeal Such Distress is My mock & scorn."
Letters, To linnell, (E 775)
"Sr Francis Bacon would say it is
want of Discipline in Mountainous Places. Sr Francis Bacon is a
Liar. No discipline will turn one Man into another even in the
least particle. & such Discipline I call Presumption & Folly I
have tried it too much not to know this & am very sorry for all
such who may be led to such ostentatious Exertion against their
Eternal Existence itself because it is Mental Rebellion against
the Holy Spirit & fit only for a Soldier of Satan to perform"
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