Much nonsense is talked about Shakespeare not writing his plays, but more interesting questions remain: who edited the First Folio? And were substantial changes made?

Sometime in 1623, seven years after Shakespeare's death, the actors John Heminges and Henry Condell published Mr William Shakespeares Comedies, Histories, & Tragedies – what we now know as the First Folio. It was the literary event of the century, recording for all time the sound of Shakespeare's English and the sweep of his imagination: Elsinore, Egypt and the Forest of Arden; a balcony, a spotted handkerchief and a skull.

Yet despite this shrine to Shakespeare's memory, erected by those who knew him, sceptics have continued to doubt his authorship of the plays. He was, they insist, inadequately educated, insufficiently travelled, and didn't know how to spell his own name. A range of alternative candidates have come and gone over the centuries, including Anne Hathaway, the Jesuits, and more recently Edward de Vere, the 17th Earl of Oxford, the subject of Roland Emmerich's film Anonymous. As always, conspiracy is more fun than consensus, and the doubters have the internet on their side. Shakespeare has thus become the focus of a global conspiracy industry, joining company with reptilian elites, self-destructing lightbulbs and skeletons on the moon.

Scholars have recently fought back against this scepticism, however. Books such as James Shapiro's Contested Will and Paul Edmondson and Stanley Wells's Shakespeare Beyond Doubt marshal facts, allusions and funeral monuments to prove that Shakespeare did indeed write the plays and poems attributed to him. Or as Iago says at the end of Othello: "what you know, you know."

So Shakespeare wrote "Shakespeare". The printing of the First Folio, however, raises another, ultimately more interesting, question. Without the Folio, Shakespeare's plays – scattered around in playscripts or in smaller quarto editions – might have been lost to posterity. But did Heminges and Condell edit the text?

Many of the plays existed in a number of versions: all needed to be edited and prepared for the press. Neither Heminges nor Condell had produced a book before, nor would they afterwards. And it is unlikely that the backers of the Folio, the printers Isaac Jaggard and Edward Blount, would have risked putting such an expensive project in their hands. As one expert puts it: "it is doubtful" whether they would be capable of such "exacting work".

Some have suggested that the scribe to the King's Men, Ralph Crane, may have been involved, or the bookkeeper, Edward Knight. But again, would they have been entrusted with such a long and complex undertaking?

New technology has changed scholarship. Whereas previous generations of experts have sought to reconcile the differences between quarto and Folio, current thinking highlights the difficult relationship between the various incarnations of Shakespeare's texts, something made easier by the availability of rare Shakespeare quartos in digital databases such as Early English Books Online.

The scholar Eleanor Prosser thus detects "considerable evidence" for the elimination of metrical and stylistic "irregularities" in the Folio: short lines are lengthened to 10 syllables, verbs agreed with subjects, double negatives resolved. In addition, a range of unusual words are added to the text, words not used elsewhere by Shakespeare. Prosser concludes: "somewhere behind the Folio … lies a conscientious and exacting editor with literary pretensions", albeit one "more experienced in the transcription of literary than of theatrical works". But who was it?

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Hamlet provides interesting reading on this question. In Act 5 scene 2 Hamlet taunts a pretentious "Courtier" (renamed "young Osricke" in the Folio):

HAMLET put your Bonet to his right vse, 'tis for the head.

OSRIC I thanke your Lordship, 'tis very hot …

HAMLET Mee thinkes it is very soultry, and hot for my Complexion.

OSRIC Exceedingly, my Lord, it is very soultry, as 'twere I cannot tell how …

HAMLET I beseech you remember. [pointing to his hat]

OSRIC Nay, in good faith, for mine ease …

As critics have noted, Hamlet's frustration with the courtier's over-formality recalls a dialogue from John Florio's Italian language manual, Florio's Second Fruits, printed in 1591:

G Why do you stand barehedded? you do your self wrong.

E Pardon me good sir. I doe it for my ease.

G I pray you be couered, you are too ceremonious.

E I am so well, that me thinks I am in heaven.

G If you loue me, put on your hat.

"Nay, in good faith, for mine ease"; "I doe it for my ease". The

similarities of the passages, as well as the mention of "complexion" suggest a desire to satirise not only the stereotypical courtier, but Florio himself, who had become a groom of the privy chamber in August 1604 (Hamlet was published later the same year) and who was known for his "fiery" – possibly acned – complexion.

And in the following lines the satire of Florio's ornate linguistic register, with its alliteration and invented words, becomes more overt:

OSRIC Sir there is newly come to Court Laertes, belieue me an absolute gentleman, ful of most excellent differences, of very soft society, and great showing: in-deede to speake fellingly of him, hee is the card or kalender of gentry …

HAMLET Sir, his definement suffers no perdition in you, though I know to deuide him inuentorially, would dazzle th'arithmaticke of memory …

OSRIC Sir …

HORATIO His purse is empty already, all's golden words are spent.

Horatio's words offer a reminder of the full title of John Florio's first book: Florio's First Fruits, which yield Familiar Speech, Merry Proverbs, Witty Sentences, and Golden Sayings (1578).

Shakespeare's "Courtier" may therefore be a satirical portrait of Florio, with whom Shakespeare had shared a patron in Henry Wriothesley. But what is especially interesting is that all the lines in this second quotation from Hamlet are deleted from the 1623 Folio. There are two, equally uncertain, possibilities as to why. The first is that, thinking he had overdone the satire of Florio, and perhaps needing to make a theatrical cut, Shakespeare erased the passage from the play. The major – although not conclusive – problem with this theory is that Shakespeare was long dead before the text was edited in its Folio form.

The other possibility is more disturbing – that alongside Jaggard and Blount there worked an experienced editor who had a particular reason to cut it, someone used to seeing long and inguistically demanding works through the press. And in that sense, one acquaintance of theirs was uniquely qualified.

Editor in chief? John Florio was an accomplished linguist and lexicographer. Photograph: Culture Club/Getty Images

John Florio was born in 1553, 11 years before Shakespeare. His father, Michaelangelo Florio, was an Italian Protestant refugee who served as preacher to the Italian Church in London. On the restoration of Catholicism under Mary, the family fled, settling in the Italian Alps. But sometime in the 1570s, the young Florio returned to England and began to make his mark as a scholar and translator. He wrote his pair of pioneering language manuals, the First Fruits of 1578 and the Second Fruits of 1591, and edited the 1590 edition of Sir Philip Sidney's Arcadia. His career culminated in his monumental translations of the Essays of Montaigne in 1603, Boccaccio's Decameron in 1620, and his Italian-English dictionaries – A World of Wordes (1598) and Queen Anna's New World of Words (1611). In all, the OED ascribes 1,224 first usages to Florio – words such as "judicious", "management" and "transcription", but also "masturbation" and "fucker". In this, he is matched only by Chaucer and Shakespeare.

What is important for this story is how Florio's career brought him into close contact with the printers of the First Folio. Blount had published Florio's translation of Montaigne, as well as his dictionaries. Jaggard had printed his translation of the Decameron. The Shakespeare First Folio was dedicated to William and Philip Herbert, patrons with whom Florio had links going back to his father's day.

If Jaggard and Blount were looking for someone to edit Shakespeare, Florio was an obvious choice. He was an indefatigable editor and wrote dialogue and verse, contributing a dedicatory poem to Ben Jonson's Volpone. And he was seasoned in the pitfalls of book production. He describes how books may "misse their ayme, by the escape of Errors and Mistakes, either in sense or matter, the one fault ensuing by a ragged Written Copy; and the other through want of wary Correction".

What's more, Florio had known Shakespeare. They had shared a patron, and both knew Jonson. But whether the relationship between them was entirely amicable is unclear. Shakespeare may have mocked Florio not only in Osric, but also in the pedantic Holofernes in Love's Labour's Lost, as well as perhaps even Malvolio and Shylock (Florio's father was originally of Jewish descent). And such animosity may have been mutual. The biographer Jonathan Bate suggests that the "Dark Lady" of the Sonnets may well have been Florio's wife.

But Shakespeare had died in 1616, and Florio was hard up: a pension promised to him by James I had failed to materialise. The opportunity to improve Shakespeare's "ragged written copy", and further ingratiate himself with the Herberts may have come as a welcome opportunity.

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So much is speculation. But a close reading of the Folio reveals some fascinating evidence.

If we look at Hamlet, for instance, we notice that the editor of the Folio introduces a number of unusual words to the text. Thus in Act 1 scene 5, Hamlet instructs his sinews to bear him "swiftly up" to revenge. The Folio changes the quarto's "swiftly" to "stiffely", a word never used elsewhere by Shakespeare but familiar to Florio, who uses it four times. In Act 5 scene 2, "breed" is changed to "beauy" (bevy), again a word never used elsewhere by Shakespeare but which Florio uses three times. And the same can be said of a number of unusual additions to the play – words such as "pratlings", "checking", "detecting", "quicknesse", "diddest", "daintier", "hurling" and "roaming". In Act 2 scene 2, Polonius tells how Hamlet was "repell'd" (rejected) by Ophelia. The Folio changes "repell'd" to "repulsed", the latter a familiar word now, but one never used elsewhere by Shakespeare, or Marlowe or Jonson. But such a substitution would occur naturally to Florio, who uses "repulsed" four times, defining the Italian Ripulso as "repulsed, repelled".

This pattern of rather recondite substitution can be seen across the Folio. In Henry V, Exeter presents the French king with a copy of Henry's family tree, describing it as "In every branch truly demonstrated". The Folio changes "demonstrated" to "demonstratiue", a word never used elsewhere by Shakespeare, Marlowe or Jonson. However, while Florio used "demonstrated" only once, he uses "demonstratiue" 20 times. In Henry IV, Part One, "intemperence" is replaced by "intemperature", again never used by Shakespeare, Marlowe or Jonson, but again familiar to Florio. And in Henry VI, Part Two, the Folio version has the King enter "on the Tarras", a somewhat redundant elaboration on the King's entrance in the quarto. But whereas Shakespeare was never to use the word again, Florio used it 13 times in his translation of the Decameron, published three years before.

Time to put it down? ... an open book. Photograph: Jan Stromme/Getty Images

Further comparison of the quartos to the Folio reveals a number of words in passages added to the plays that are again uncharacteristic of Shakespeare but familiar to Florio, among them "abutting", "blabbing" and "bungle" (there are lots more). And in the Folio-only plays there are several very rare words that again are familiar to Florio: "longly", "mothy", "queasines", "roynish". And some words from the Folio can only be found in Florio and not in any other writer – "enfoldings", "swaruer".

Even more interesting is where the editor of the Folio feels entitled to not only correct but supplement Shakespeare's text. In King Lear (a play so differing in its quarto and Folio versions that it is often printed as two texts), Gloucester has been fooled into thinking that Edgar has conspired against him, and laments the treachery of the times (the words in italics show the Folio additions):

In Cities, mutinies, Countries, discord; in Pallaces, Treason; and the Bond crack'd, 'twixt Sonne and Father. This villaine of mine comes vnder the prediction; there's Son against Father, the King fals from byas of Nature, there's Father against Childe. We haue seene the best of our time. Machinations, hollownesse, treacherie, and all ruinous disorders follow vs disquietly to our Graues. Find out this Villain, Edmond, it shall lose thee nothing …

The words added include some not used by Shakespeare anywhere else, such as "disquietly", but also the word "machinations" – never used elsewhere by Shakespeare but used five times by Florio in singular and plural forms and also added to Edgar's speech in Act 5 scene 1.

And while it might seem gratuitous scepticism to doubt the integrity of Shakespeare's text, it is clear that someone edited the Folio. It is Florio's linguistic inventiveness – as well as his links to Jaggard and Blount – that would seem to single him out as the most likely contender. Indeed, in King Lear we might almost fancy we can see the lexicographer Florio at work – as Edmond expresses his worship of "nature" rather than nurture:

well the legitimate Edgar, I must haue your land, our Fathers loue is to the bastard Edmund, as to the legitimate: fine word: Legitimate. Well my legitimate, if this letter speede, and my inuention thriue, Edmund the base shall to'th'legitimate.

It seems odd that the nefarious Edmond should pause to admire the word "legitimate". But it is almost as if Florio stops to afford Shakespeare some credit, adding "fine word: Legitimate" to the Folio text.

If Florio was indeed involved in the Folio, a number of other passages may well be his work. It is well known that Gonzalo's utopian vision in The Tempest is lifted from Florio's translation of Montaigne's essay "Of Cannibals". The standard view has been that this represents Shakespeare's borrowing from Montaigne; the alternative is that it might represent Florio borrowing from himself.

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There is no reason to assume, of course, that Florio was responsible for every change made between quarto and Folio. Nor should we assume that Shakespeare's quartos represent "pure", unadulterated texts. On the other hand, it is possible that Shakespeare made changes to his plays after their quarto publication. In other words, uncertainties abound.

Yet there are three pages of the Folio that we know for a fact were not written by Shakespeare: the "Dedicatorie Epistle", and the address "To the great Variety of Readers" at the beginning. They are signed by Heminges and Condell, but the cost of the project suggests they were written by a more experienced hand. The obvious candidate would seem to be Ben Jonson: but if he did write them, why didn't he sign them?

These pages feature a number of unusual words and phrases – "exposed", "leauened", "imitator", "ouerseen", "most bounden" – most of which are unfamiliar to Jonson or his contemporaries, but which are familiar to Florio. Other evidence exists, too, not least that calling the preface an "Epistle Dedicatorie" is almost a Florio trademark: he includes them in his Second Fruites (1591), his World of Wordes (1598) and his translation of Montaigne's Essayes (1603), as well as defining the Italian Dedicatória, in his dictionary, as "a dedicatorie Epistle".

Of course, objections remain. Why is Florio's name not on the title page? One response is that Florio had published his translation of the Decameron anonymously, and might have thought it best to lie low, especially if his relationship with Shakespeare had been less than amicable. Secondly, if Florio "censored" a possible allusion to himself in Hamlet, might he not have removed other possible slights elsewhere – in relation to Shylock, perhaps, or Malvolio in Twelfth Night? Here one might say that he could not sabotage the whole project: the scenes involving Malvolio, then as now, were some of the most celebrated in the play. Yet the other simple answer is that we don't know he didn't.

Perhaps the most disturbing aspect of Florio's possible involvement with the Folio is that we may never know its true extent. As Othello says in lines added to the Folio: "I thinke my Wife be honest, and thinke she is not." While with plays such as Hamlet, Othello and King Lear we can compare the Folio against the quarto, for other plays – such as Antony and Cleopatra, The Tempest and Macbeth – we cannot. Half of Shakespeare's works were published for the first time in the Folio; the question remains whether they were subject to Florio's "wary correction". Our knowledge of changes made to the quartos, as well as Florio's treatment of Boccaccio and Montaigne, suggests that there is a strong chance that they were. And yet we have no sure way of knowing. We cannot tell for certain whether the words were written by John Florio or by William Shakespeare.

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In the final scene of Twelfth Night, a play published only in the Folio, Fabian reveals the tricks that have been played on the puritanical Malvolio, but pleads "sportful malice", in the hope that it may "pluck on laughter than reuenge". The clown Feste joins in, quoting from the letter that had duped Malvolio into believing Olivia loved him – "Why some are borne great, some atchieue greatnesse, and some haue greatnesse throwne vpon them" – adding: "and thus the whirlegigge of time brings in his reuenges".

What is interesting is that Feste was not on stage when Malvolio read the letter, nor when he repeated its contents to Olivia. Moreover, the original letter read: "Some are become great, some atcheeues greatnesse, and some haue greatnesse thrust vppon em." In Feste's lines the words and spellings have changed: "atcheeues" is spelt "atchieue", and made to agree with the pronoun, "thrust" becomes "throwne", and "them" used for "em". The word "whirlegigge" is also interesting, meaning a children's top, but is not used anywhere else by Shakespeare.

But both the words and the spellings and the grammar are familiar to Florio, whose verbs always agree with their pronouns, who never writes "atcheeue", always "atchieue", who disdains the use of "em", and who uses the word "whirlegigge" five times. Malvolio's response is his final utterance in the play and receives no reply: "Ile be reueng'd on the whole packe of you."

• Saul Frampton's When I Am Playing With My Cat, How Do I Know She Is Not Playing With Me? – about Montaigne – is published by Faber. He is writing a book about John Florio and Shakespeare.