Google books search shows that "A Disciple", in an article entitled "Emerson's Essays" which appeared in the June 1845 issue of United States magazine and Democratic review, wrote

... as a recent critic on the "Teutonic Metaphysics or American Transcendentalism" has satirically expressed it, "everything is everything, and everything else is everything, and everything is everything else."

I have no idea who this critic was. The expression is simple enough that it might have been coined independently several times, but if this was the original coinage, it cannot have been earlier than American Transcendentalism itself, which puts it 1836 or later.

Note that it's easy for an expression like this to change from a negative to a positive meaning. For instance, "the Big Bang" and "abstract nonsense" were originally expressions meant to slight the Big Bang theory and certain types of argument in mathematics, respectively, but which are now used positively by people in their respective fields.

Dictionary discussions of 'boning up'

J.E. Lighter, Random House Historical Dictionary of American Slang (1994) reports that "bone up" emerged from an earlier student term "bone," which was in use by 1859:

bone v. ... 4.a. Stu. to study (a subject) intently.—Also (esp. in 20th C.) constr. with up.—Also intrans. Hence boning, boner, n. [First three cited instances:] 1859 in O.E. Wood West Point Scrapbook 88: Much study, ... you call it boning, is quite weary to the flesh. 1862 in [Mathews,] D[ictionary of] A[mericanisms]: Not unfrequently I took the liberty to suggest to him that if he did not leave poetry and bone math more than he was doing we should be deprived ere long of his excellent society. 1887 E. Custer Tenting 181 {ref. to 1860's}: I have known the General to "bone up," as his West Point phrase expressed, on the smallest details of some question at issue.

The 1859 example that Lighter cites is from a long poem titled "West Point Life." At the point where "boning" appears, the poem has devolved into a series of punning couplets. Thus:

Much study too you must admit, when starting out afresh,

Although you call it "boning," is quite weary to the flesh.

Mitford Mathews, A Dictionary of Americanisms on Historic Principles (1951) has the following entry for bone as a verb in the relevant sense:

bone v. ... 2. tr. and intr. To study hard, to prepare (a subject), or get well acquainted with it by close study. Colloq. or slang. [Sylvia] Clapin, [A New Dictionary of Americanisms (1902)] 64, implies that this sense is derived from Bohn [n.], q.v. No evidence other than that in Clapin, has been found for Bohn, v.

Mathews gives as its citation for this meaning the 1862 quotation cited by Lighter above, but identifies it as coming from "G. C. Strong, Cadet Life West Point 198." Hence, all three of Lighter's earliest citations are explicitly connected to the U.S. Military Academy in West Point, New York, which makes a strong initial case for the notion that "bone up" originated as military academy slang.

With regard to the noun Bohn, Mathews has this entry:

Bohn, n. (See quot. 1856.) Slang. Obs. — 1855 Songs of Yale (1860) 40 'Twas plenty of skin with a good deal of Bohn. 1856 Hall, College Words (ed. 2) 32 Bohn, a translation; a pony. The volumes of Bohn's Classic Library are in such general use among undergraduates in American colleges, that Bohn has come to be a common name for a translation.

As for the word pony in Hall's definition of Bohn, Benjamin Hall, A Collection of College Words and Customs, first edition (1851) has this definition:

PONY. A translation. So called, it may be, from the fleetness and ease with which a skillful rider is enabled to pass over places which to a common plodder present many obstacles.

Though the second edition (1856) of Hall has the entry for Bohn cited above, the first edition (1851) does not; neither edition has an entry for bone in any sense.

Mathews is incorrect in supposing that Sylvia Clapin was the first investigator of slang to draw the connection between bone (in the sense of "to study") and Bohn (the slang noun). J.S. Farmer & W.E. Henley, Slang and Its Analogues, volume 1 (1890) has this relevant entry for bone as a verb:

BONE ... Verb ... 3. (American cadets'.) To study hard. {From BOHN (q.v.).})

Farmer & Henley's entry for Bohn reproduces Hall's definition word for word. John Bartlett, A Dictionary of Americanisms, fourth edition (1877) has this brief entry for "To bone":

To bone. To apply one's self closely. "To bone into it."

No such entry for bone appears in the third edition (1861) of Bartlett; and it's interesting that the preposition Bartlett chooses here is into not up.

Robert Hendrikson, The Facts on File Encyclopedia of Word and Phrase Origins, fourth edition (2008) has this entry for the term:

bone; bone up on. Bones were once used to polish shoes, and some scholars have attempted to link such bones to the expression to bone up on a subject, to study it hard and thoroughly, especially for an exam. One would then "polish up" his knowledge, presumably, but bones probably have nothing to do with this term. It was first used in the 1860s by collegians, and they apparently first spelled the bone in the phrase Bohn, probably referring to the Bohn translations of the classics, or "trots," that they used in studying. British scholar Henry George Bohm (1796–1884) was the author and publisher of many books, including the "Classical Library."

'Bohned' and 'bohning'

Mathews (above) suggests that (as of 1951) no early instances of Bohn as a verb had been adduced. But Google Books searches find a number of matches for bohn as a verb and for bohning as a gerund, in a seemingly relevant sense, going back to at least 1874.

One is from "Alma Mater's Lament," in The University Palladium (1874):

Never again will any class bring so many honors to its Alma Mater. In athletic contests they have always borne off the victor's palm. They are lords of the contentious campus. Shall mine eyes ever again behold such intellectual giants? What class ever excelled them in Bohning through the intricacies of Cicero and Isocrates? What class has ever been so ready at imbibing the spirit of the German language? Why, they are as fluent as though they had been brought up on beer, sauer-kraut und scweitzerkäse; and when you tackle them on metaphysics, you experientially perceive that they are on their native heath.

From "Inter Nos" in Hamilton Literary Monthly (October 1885), discussing "lack of support to college athletics and college publications":

The fact is that reputation in athletics and college matters bring a college before the people full as much as the curriculum, and Williams, Harvard and Yale draw many in that way. What we desire, is that each one of us will "bohn in," sympathetically, financially and intellectually, and make not only a reputation for scholarship, but also for energy and activity in student matters.

From Addenda to Memorabilia of the [Hillsdale College] Class of 1887 (1947) [combined snippets]:

Well do I remember the summer of 1886, when Fred Dewey, later F. N. Dewey, M.D., and I boned out the orations of Demosthenes, or at least some of them, under the tutelage of Professor Parsons. (The word "boned," as used here, is a shortened form of "Bohned," a student's derivative from Bohn's Library of Translations from the ancient classics ; but we did not Bohn in that sense at all, for our translation work, me judice, was strictly all wool and a yard wide.)

From "Some Points for Young Engineers," in The [Rensselaer Polytechnic Institute] Polytechnic (May 19, 1888):

During his course in the Institute a student looks forward to graduation as the time when he shall have finished the routine of "bohning" and reciting; when, leaving the college world with all its cares and works, he shall at last be free. Of course he will continue his studies, and he calculates to review some of the subjects through which he has rushed in the limited time allowed in the Institute course; but he will be free from the irksome thought that he must learn what he studies sufficiently well to make a "rush" before some curious professor or assistant.

From Nine Members of the Saturday Night Club, The Seventh Son: A Story (1888):

He always got his lessons at the last hour, with a wet towel on his head like Sidney Carton, and always got them well. He did not study like the other boys — he never "bohned." He never read by words or even sentences, but seemed to take in whole paragraphs at a glance. He was the favorite of professor and student and was altogether a "jolly good fellow."

From Hamilton Literary Monthly (April 1890):

The past term was one of hard work. It seemed as if the members of the Faculty vied with one another in attempting to get the most work from the students. The majority of the students were ill at one time or another during the term and therefore had much work to make up. The result was that all were "bohned out" after the strain of examinations, and were in need of more rest and relaxation than could be gained in a vacation of one week.

From an item titled "In the Museum," in The Harvard Lampoon (May 12, 1892):

ALICE — Oh look at that ossified man. What ails him?

REGINALD (who is perfectly safe) — Oh, he probably Bohned too much.

From "A Senior's Soliloquy," in The [Cornell University] Cornellian (1893):

My bills are legion and my assets nil,/There's scarce a mail but brings me in a bill/For clothes that long ago my uncle owned,/Or books, that as a sophomore bold I bohned.

From "The Marking System," in Hamilton Literary Monthly (April 1893):

"Bohning for marks" and all that it implies has become in some respects a term of reproach. To our marking system we often hear attributed all the evils of cribbing, which is to such an extent practiced by the students ; it is frequently asserted that owing to the influence of this system men neglect in college much that is essential to a thorough education, and that owing to considerations growing out of the struggle for marks they are often induced to pursue subjects which are relatively of less importance to them than others which they feel compelled to drop.

From an ode to calculus, in The [Lehigh University] Epitome (1897) [combined snippets]:

For six long months beneath thy thrall/We've labored, toiled and "bohned;"/Thy cruelty, thy cussedness,/Can never be condoned.

From W.M.W., "A Notable Reform," in Michigensian, Volume 3 (1899):

"...I found I cared a sight more for her opinion than I thought, and I determined to show her I could do as well as the rest of you. I have a theory, you know, that a fellow could pass any course in the 'Varsity if he bohned hard enough for a week or two. And maybe I didn't bohn! I've sweated over math and pol ec till I was ashamed of myself. Why, I didn't get to bed any night last week before one o'clock."

"That's nothing, neither did I, and I haven't killed myself bohning that I know of," retorted Dick.

A much earlier instance of Bohned—with a significantly different meaning—appears in an item titled "American Rifling" in Punch, or the London Charivari (1851):

An ingenious correspondent in Notes and Queries, asks—

^{"Is there any one use for which an American rifle is to be preferred to an English one?"}

Punch makes answer for his pleasant and useful contemporary, and answers "Yes." Since the decision of LORD CAMPBELL, who, very properly, will not suffer foreign visitors to be Bohned, cost free,—the American rifle is superior to the British one; inasmuch as, in the hands of a Yankee bookseller, it inevitably brings down the English author.

The slang use of Bohned here is not entirely clear, but I think it may mean "translated into English-language editions for which they receive no royalties." The main joke here is the double sense of "bring down"—as in bagging the animal being hunted and as in "reducing or harming."

Early instances of 'bone up'

From "Things Chronicled," in The [University of Michigan] Chronicle (October 27, 1877):

A full professor of Mathematics from Hillsdale College spent a part of the past summer under Prof. Olney's instruction, "boning up" the identical General Geometry and Calculus which forms the work for students during the sophomore year, and we are informed that a professor (?) from the Fort Wayne Medical College (?), Fort Wayne, Ind., is at present in our Medical School. Who says we arn't a University!

From Henry Flipper, The Colored Cadet at West Point (1878):

At length, sure of my willingness to oblige him, he [a plebe] came to me, and, after expressing a desire to "bone up" a part of the fourth-class course, and the need he felt for such "boning," begged me to lend him my algebra. I of course readily consented, gave him my key, and sent him to my trunk in the trunk rooms to get it.

From "Things Chronicled," in The [University of Michigan] Chronicle (June 23, 1883):

Sam Schoyer "boned up" and went and passed off" some work in which he thought he had been "conditioned." Imagine his disgust when he learned he had previously passed all O. K.

From "American Aristocracy," in Life magazine (December 27, 1883):

Already it has been discovered that Agazzis, Miller, Faraday and Darwin recanted on their death-beds and died in the Faith, and it is well known that TYNDALL, HUXLEY and HOFFMANN have abandoned their shameful researches, and are boning up on the catechism with a view to becoming Jesuits.

From "Nemesis," in The Michigan Argonaut (January 23, 1886):

She was going to the Athens of the West to enter the freshman class, so was I, she was to be examined in several things for entrance, so was I. She had been boning up all summer, ditto I, and under such extenuating circumstances I could see nothing wrong in asking her to let me turn my seat over and sit vis-a-vis for the rest of the journey.

From "Annapolis Notes" (April 21, 1886), in The United States Army and Navy Journal (April 24, 1886):

The latter part of this week finds all hands "boning up" for the examinations. During the next month those cadets who are unsatisfactory will be "warned," and at the annual examinations in June, if unsatisfactory, they will be dropped from the rolls of the [Naval] Academy.

Conclusions

"Bone up" appears to have developed from the simpler verb form "bone," as J.E. Lighter, Random House Historical Dictionary of American Slang, reports. Several early instances of bone or boning in this sense are recorded from the U.S. Military Academy in West Point, New York, starting in 1859. The earliest match for "bone up" (or rather "boning up") is from 1877, from the University of Michigan.

The argument that "bone" as a verb with the meaning "study intensively" originated as "bohn," a verb alluding to the many volumes of the Bohn's Classics Library series, is less far-fetched than it might at first seem. Books in that series were extremely common in U.S. colleges and universities by 1850, and a number of references to bohned and bohning in the sense of intensive study appear between 1874 and the early 1900s.

Google Books search results show that students at some schools (notably the U.S. Military Academy and the University of Michigan) favored boned and boning, while students at others (notably Hamilton College and some Ivy League schools) favored bohned and bohning. Since the words were used in the same sense regardless of which spelling the writer adopted, it seems fair to view them as variants.

On the other hand, the recorded instance of boning in 1859—15 years before the first recorded instance of bohning, in 1874—raises the possibility that the pun on Bohn Classics was an afterthought attached to the existing bone of unknown origin. It is also noteworthy that an 1862 instance from the U.S. Military Academy uses bone in the context of studying mathematics—not a subject where Bohn translations would be likely to have much relevance.

At the very least, however, we can say that bohn was in fairly widespread use as a verb for several decades before bone (and bone up) won out in popular usage and rendered bohn obsolete. The connection between bone and bohn is much stronger than I had expected it to be.