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Nelson's signal at Trafalgar shows some of the shortcomings Howe's code. The first eight words were each signaled with a three flag hoist. Even the two letter word "do" needed a hoist of three flags. Nelson had wanted to send "confides", but the word was not in the code book so he settled for "expects" which was. The last word "duty" was also not in the code book, and the closest words that were, "best" and "utmost" were not considered appropriate. "Duty" therefore had to be spelt letter by letter which took seven flags. Because illustrations of the signal show all the flags at once it is sometimes thought that this was how the signal was sent. Actually of course it was sent in a succession of hoists over a period of four minutes.
To avoid the code being deciphered, in time of war the actual meaning of each flag in Howe's code would change periodically (every six
months(?)). Hence, would one expect Popham's code to change with it. Thus to resend Nelson's signal six months later, it appears one would have
needed different flags.)
  It used to be thought that Nelson's signal had been sent using the 1803 code.  In about 1912 Perrin, the Admiralty Librarian who wrote
"British Flags", discovered that a
1799 code book had been captured by the French in August 1803, and that consequently the code had been changed before Trafalgar in
October 1805.  Illustrations of Nelson's signal before between 1885 and 1908 show the
correct flags in the wrong arrangement.
David Prothero, 4 December 2001
One possible representation of the sequence of flags can be seen in this set of poles.
The 1799 code was changed by an Admiralty Circular of 4th November 1803. Nelson's Trafalgar signal was shown correctly until 1885. In that year it was pointed out that the Signal Book of 1799 was not replaced until 1808, and that the signal made at Trafalgar in 1805 must have used the 1799 code. The Admiralty were persuaded that this was correct and a coloured leaflet was issued illustrating the signal according to the numerary code in the 1799 Signal Book.
In 1908 Perrin found a book of the numerary code, corresponding to that in the
1808 Signal Book, that had been authorised and signed by three admirals, who were in office together in the Admiralty only between 21st January and 15th May,
1804.  This convinced the Admiralty that the original sequence of flags was correct, and a circular was issued admitting that the leaflet of 1885 was wrong.
Remembering that the numerary code was only a part of the complete Signal Book, the sequence of events
was:
1780, ca.: Howe's code, partly table-based, partly positional.
1788: An officer of the Navy published a numerical code system.
1790: New signal book by Howe, using a numerical code system.     Signals: Must have changed, since they are no longer positional.
Still included sail-signals.              260 entries.     Numbers: may or may not have been equal to 1788.     Was gradually expanded until: 
1799.  New Signal Book.     Signals: Sail signaling was dropped.              340 entries.     Numbers: Unchanged?
   1800: Popham introduces his 'Telegraphic Signals of Marine Vocabulary'
   1803: Popham's code officially adopted by British Royal Navy.              3000 entries.
1803.  August.  Code book captured.
1803.  November.  Instruction to change the numbers that had been assigned to the numerary flags in the 1799 Signal Book.
1804.  Revised code book.
1805, September: 50 Popham code-books issued to British fleet at Cadiz.
1805, October.  Trafalgar; Nelson's signal made in revised code.
1808.  Revised version of 1799 Signal Book.     Numbers: Unchanged (from 1804).     Signals: ? Depends on what was actually changed. The need to add
directly coded signals would probably have lessened due to       those being
codable with Popham's code as well.
   1813: Expanded version of Popham's dictionary, to 6000 phrases     and 60,000 words (one sources has
"30,000 words"). 
1885.  Assumption that Nelson's signal must have been made in the code shown in the 1799 Signal Book.
1908.  Discovery of 1804 code book and recognition that Nelson's signal was made
in the revised code.
Due to a peculiarity of that part of the code used to send the letters of the alphabet, the word "duty" appears to be mis-spelt.
"T" the 20th letter of the alphabet was signalled "19", because the alphabet had
been reduced to 25 letters and "I" and "J" were both signalled by "9". This moved all subsequent letters up one number.
However "U", the 21st letter was signalled "21", because in the alphabet it was listed after "V".
David Prothero and Peter Hans van den Muijzenberg, 5 December 2001
Howe's code allowed only 1000 signals, but apparently the Popham code could send those 3000 entries by adding a separate flag for each of three tables of 1000 entries. This appears to be a rather cumbersome way of simply adding a fourth digit, which could have been done more consistently by adding a third repeater. I do wonder how this was for the eventual 66,000 entries. I doubt they used 66 flags merely to indicate the correct table. So there must have been a table of sorts to indicate the table with a more limited set of flags. Adding yet a fourth repeater would have given room for 100,000 signals. (All on the assumption there was room for four-flag resp. five-flag hoists.)
Further information can be found at The Early History of Data Networks - Mirrors and Flags and Signal Flags
Nelson's words were changed to numbers using Popham's Vocabulary Book. The numbers were
signaled with the flags of the 1790 Signal Book selected in accordance with the revised numbering of 1803, which also introduced a white
flag and removed the red flag. 
253 269 863 261 471 958 220 370 4 21 19 24
The first substitute (D) was used for the second 2 in 220.
The hoist 253 for "England" was preceded by the Telegraph Flag to show that succeeding hoists constituted one message.  If 253 had not been preceded by the
Telegraph Flag it would have had a different meaning.
David Prothero, 6 December 2001
The signals officer of the Victory at Trafalgar was Lt John Pascoe, who many 
years later wrote that Lord Nelson had originally asked for "England 'confides' 
that every man will do his duty", and that he had suggested "expects" in place 
of "confides" because it would take fewer signal flags. I have also seen it 
suggested that the signal was originally given as "Nelson confides etc.", but 
(whilst England would take very many fewer flags than 'Nelson') Pascoe's account 
appears to contradict this and I have been unable to confirm it elsewhere.
Christopher Southworth, 23 September 2003
The book by Captain Barry Kent entitled: Signal! 
- A history of Signalling in the Royal Navy describes the procedure of 
hoisting signals. On Plate I opposite page 100 he shows the Trafalgar signal in 
full colour flags as well as a diagram of a three masted ship of the line with 
the sequence in which the flag hoists are read. He states that the 
signal.......was of course sent as a series of separate hoists. He goes on to 
state that: The principle (of reading the hoists) is: main, fore, mizzen; 
starboard before port; upper yards before lower. In practice it would be unusual 
for more than two or three to be hoisted at the same time, and Nelson's signal 
would have been transmitted by a quick succession of hoists. According to the 
logs of the ships reading it, the whole signal took no more than about four 
minutes to transmit.
Each hoist was kept flying until all the ships addressed had hoisted the 
acknowledgment meaning that they have seen and understood the signal. With a 
large fleet like Nelson's at Trafalgar, this could take a long time and to 
facilitate signalling in such circumstances, frigates were stationed along the 
line to windward to repeat the signal for the benefit of the ships furthest 
away. The acknowledgements were in turn repeated by the frigates for the 
flagship's benefit. For all of Nelson's ships to have read and understood such a 
long signal in the space of only four minutes, reflects great credit on the 
competence of the signal officers and signalmen in that fleet.
Andre Burgers, 24 September 2003
The following information came from the Ministry of Defence, Admiralty 
Library:
The signal comprised eleven separate hoists to the mizzen masthead. HMS Victory 
was at the head of the fleet, the wind was aft, and the repeating ships were in 
their station, so the mizzen masthead was the most generally visible location as 
well as the most usual. The flagship's signals would have been bent onto the 
mizzen topgallant signal halyard.
David Prothero, 5 November 2003
All the more credit to Lt Pascoe's team of signallers to pass that long 
signal in only four minutes using only one halyard.
Andre Burgers, 24 September 2003
Under the influence of the military historian John Keegan, I would wonder 
whether the question is whether the achievement is creditable or rather whether 
it is credible. Here's why:
I've always understood the message to be 12 hoists, not 11, but even for eleven 
hoists four minutes seems improbably fast. If we assume that Pascoe timed the 
signal from the moment the first word started moving up the halyard until the 
letter "Y" of "duty" was closed-up (which omits the time taken to bend on the 
flags for the first signal and the time to haul down the last "Y", as well as 
the time to hoist the ensuing signal for close action), we have 21 trips up and 
down the mast. Besides the time to physically raise and lower the flags, we have 
to take account of the time needed to replace one signal with another in between 
hoists, plus the time each signal had to remain flying while the rest of the 
fleet acknowledged it. Even if we allow two seconds to make each of the 10 
changes after "England," and ten seconds for each acknowledgement through the 
letter "t"--both of which strike me as unbelievably fast--that leaves only 120 
seconds in which to make those 11 haulings-up and 10 haulings-down, or 5 2/3 
seconds for each. The mizzenmast of HMS Victory measures 152 feet (46.3 meters) 
from the waterline; let's guess 115 feet from the deck. Could Pascoe's signalmen 
really move the flags up and down at a rate of 20 feet per second? 
Andre's the former signal officer, so if he says it's possible, I'll accept it, 
but it sounds like Pascoe's memory may have exaggerated what was undoubtedly a 
remarkable performance, my nitpicking questions notwithstanding.
Joe McMillan, 7 November 2003
I am inclined to follow Barry Kent on the question of the hoisting of the 
famous signal. I am also doubtful that the eleven hoists could have been done in 
four minutes using only one halyard and here I speak with some experience having 
been a Signals officer myself and having participated in and conducted numerous 
signal hoisting exercises. And we were using flag lockers while I believe in 
Nelson's time they were still using flag bags to pull and stow the flags. Barry 
Kent, in his book Signal! on Plate 1 following page 100, shows the signal and 
alongside it, a sketch of a ship of the line with all the hoisting positions on 
the various masts numbered in the order that the signals should be read. He does 
not actually state that this was the manner of hoisting the Trafalgar signal, 
but the implication is clear.
David, what is the source of your Admiralty Librarian for the statement that 
only the mizzenmast in Victory was used for signalling? The team of bunting-tossers 
also seems to have been a bit too small for such fast work on such a long 
signal. Seamen Aslet, Heaver and Roome plus the two boys and the Middy, would 
have been scarcely enough to serve the mizzen signal halyard. If we remember 
that two further signals were made, the last, for close action, at 1220, this 
small team must have been very busy indeed over that period.
Joe, the four minutes are mentioned also by Barry Kent on page 7 of his book, 
taken from the signal logs of several ships reading the signal, and the first 
hoist having gone up at 1156. 
Andre Burgers, 7 November 2003
I checked with the Admiralty Library. It was a mistake; twelve hoists not 
eleven. 
Four minutes was thought to be a reasonable time for a signal of twelve hoists 
bearing in mind -
1. The time of four minutes was derived from log entries which were not timed to 
the second. It might have been nearer five than four.
2. This was the flagship; the signal party would have been very experienced.
3. Hoists were not acknowledged. Each went straight up and straight down, with 
no pause at the masthead.
David Prothero, 10 November 2003
The source? I don't know. The Gordon and 
Wheeler-Holohan editions of Flags of the World say that the signal was "sent up 
in succession to the main topgallantmast-head". This may have been an assumption 
based on the fact that the signal 'engage the enemy more closely' was hoisted 
there.
David Prothero, 11 November 2003
Can I add a bit, the movements before, etc, the Battle itself was fought 
using the 1799 code book with the signals 1804 "tip in" issued by the admiralty. 
Pophams Telegraphic Signals or Marine Vocabulary was used for other traffic and 
"England Expects..","I intend to go through the enemy's line to prevent them 
getting into Cadiz", etc. The book you refer to in the NNM, allegedly the 
Victory's copy is a 1799 work, it only says examined TM Hardy and the signature 
page and has Nelson's signature on the front. 
Interestingly you do not mention signal 501, the Breaking the Line Signal which 
is closely related to the Secret memorandum written shortly before the battle on 
October 9th which includes Nelsons four master ideas for the battle plan.
The primary signal book used at Trafalgar was the 1799, with many additions. My 
source for this is Naval Warfare in the age of Sail, and Collingswood's copy of 
the 1799 Signals and Fighting instructions which is in my possession, and has 
signal 501 in it, plus many additional signals added on the orders of Nelson, 
and pencil annotations as ordered by Lord Nelson.
Martin, 12 October 2005
Introduction re Signals and Fighting Instructions:
During the whole of the sailing era the command control of battle fleets by 
commanders and the transfer of information and intelligence, between ships, 
presented many challenges to local commanders. In addition, there were the 
nuances of ships only using sail, and the advantage that the windward position 
gave in battle. Secret Code Books were produced, called "Signals and Fighting 
Instructions", which not only covered signals but also had had Articles to go 
with the signals that covered the whole conduct of the fleet. In short, they 
were the distillation of the naval tactics up until that period and represented 
the only viable method of communication. Until the first Admiralty edition in 
1799 the production of local Signals and Fighting instructions was done by the 
local commander, such as Lord Howes 1790's version, which was the last private 
edition.
The contents of the1799 edition give an understanding of the breadth of the 
Signal Book:
Comprehensive Indexes
Indented Thumb indexes
Explanatory Instructions and explanatory instructions on the use of triangular 
flags
The numbered flags 0-9 – coloured drawing
Additional flags – coloured drawing
Main Admiral Day Signals including the Battle signals and blank spaces (and 
references to the articles)
Ships numbers
General Instructions for the Conduct of the Fleet – 34 articles
Instructions Respecting the Orders of Sailing – 17 articles
Instructions Relating to the Line of Battle – 4 articles
Instructions for Forming Line of Battle from the Orders of Sailing – 11 articles
Instructions for the Conduct of the Fleet, Preparatory to their
Engaging, and when Engaged with an Enemy – 31 Articles
Short table on the graduations of making and shortening sails for ships
Eleven plate illustrations for Orders of Sailing and other instructions
Instructions Relating to the Line of Battle – 4 articles
(Night Signals issued in separate volume but often bound or pencilled in, as per 
this copy)
Compass points and direction signals
Fog Signals
Signals and Fighting Instructions where often amended and added to as can be 
seen in the next section on the Admirals instructions, both in Pencil and Ink. 
This copy of Signals and Fighting Instructions 1799, the Nelson Touch and 
Nelsons Plan for Trafalgar.
This copy is believed to be Collingwood's, due to having HMS Excellent on the 
cover: this was Collingwood's ship at the time of issue (13th May 1799) and its 
content further supports this view. As such, this book was not just used in 
receiving orders but in addition issuing orders at Trafalgar. Only fourteen 
other copies have survived, showing how secret these documents where. All 
Nelson's and Collingwoods battles after The Nile where fought using the 1799 
version. This is the only known copy with all of the Nelson amendments.
Part of Nelson's genius was that he knew that signals during battle where hard 
to see and act upon, he knew that all the signalling had to be done before the 
battle, and had to be included in the signal book. This book has all these 
changes and one signal which is part of the Trafalgar battle plan, the Signal 
501 "Cut Through the Enemy's Line". At the battle he did give Captain Blackwood 
(HMS Euryalus) in command of his frigates the ability to issue signals in 
Nelson's name, such was his level of trust in his subordinates
In 1803 an unofficial copy of the Signal book was captured from a British 
Schooner off Toulon, and a tip revision of the signals was issued on the 4th of 
November 1803 coming in to force 16th January 1804. This copy has that tip in: 
this is probably the earliest version of modern flag signals in the world. (Page 
14)
In 1804, 82 new signals were issued to the British Navy in two sections by the 
Admiralty based upon Nelson's written ones: Signals from Junior to Senior 
Officers, and Signals from Senior to Senior Officers. This book contains the 
original manuscript ones, as they were issued by Lord Nelson, and 2 "in pencil" 
extant, not anywhere else in the world.
Nelson evolved his battle plans through 1803, 1804 and 1805. It is through 
additions and amendments to the Signal Book 1799 that we can trace his ideas for 
the plan of attack at Trafalgar and communication of them. After rejoining the 
fleet on 25th September 1805, Nelson verbally briefed his captains at dinner of 
his plans,  which became know as the "Nelson Touch". On the 9th of October 
he produced the Secret Memorandum (much debated) and the following day his 
Battle Plan. Both refer to Signal 501:
Signal Flag Yellow with Blue Fly, Cut through the Emery's Line and engage them 
on the other side.
NB: This Signal is to be repeated by all the Ships. The Number of Enemy's ships 
under the Stern of which the Van Ship is to pass and engage will be pointed out 
by Signal counting from the Enemy's Rear. The Ships being prepared are to make 
all possible sail (keeping their relative Bearings and close order) so that the 
whole may pass thro' the Enemy's Line as quickly as possible and at the same 
time. It is recommended to cut away the Studding sails if set, to prevent 
confusion and fire. Each ship will of course pass under the Stern of the one she 
is to engage if the circumstances permit, otherwise to refer to the Instructions 
Page 160 Article 31 [for breaking the enemy's line]. The Admiral will probably 
advance his Fleet to the van of theirs before he makes the Signal in Order to 
deceive the Enemy by inducing them to suppose it is his intention to attack 
their Van.
The Memorandum covers four ideas: 1) Colligwood's separate role and attack, 2) 
the concentration of the attack on the rear, 3) the concealment of the direction 
until the very last moment, and 4) the crowding of sail to join battle as 
quickly as possible. All are in the Signal 501.
This book is opened at Signal 501, the only manuscript copy in the world. A 
printed version exists in the NMM and it has a copy with Signal 501 on page 17 
and shortened text, with 8 other signals. This could be, therefore, the original 
version. On the verso of it are Lord Nelson's Additional Rendezvous, issued for 
if the Combined Fleet escape, this exists only elsewhere with the printed copy 
of 501. Finally, following the Rendezvous signal are 5 pages of Lord Nelson's 
Additional Signals from Senior to Junior Officers and Lord Nelson's Additional 
Signals from Junior to Senior Officers. These do not exist anywhere else. It is 
very striking that all Lord Nelson's Additional Signals are about bringing the 
enemy to battle.
Finally the there are four amendments to the standard signals for breaking the 
line, Signal 27 Break through the line, and Article 160,  both in pencil, 
(Lord Nelson,) and Signal 36 and 37 referring to which Engagement side for 
battle. Both have substantial pencil additions about breaking the line and it 
has been suggested that these could be Lord Nelson's own.
On the morning of the 21st Nelson and Collingwood issued signals to get the 
British fleet into two lines and he did two very important course changes in the 
last hour before battle was joined. There were limitations with the 1799 Code, 
and a Naval Officer Sir Hugh Popham produced in 1803 the Marine Vocabulary or 
Telegraphic code. Nelson obtained 50 copies of this when he was last In England. 
This was used for "England Expects that every man will do his duty", not the 
1799 code. The battle and all the tactical manoeuvres were fought using the 
amended 1799 Signals and Fighting Instructions. All signalling ceased around 
midday after Nelson's favourite Signal 16 "Engage The Enemy More Closely", and 
"Prepare to Anchor".
Finally, when looking at this copy of Signals and Fighting Instructions one 
cannot but wonder at its survival, it being at Nelson's discussions for his 
battle plans with his best friend Collingwood and the "Band of Brothers", the 
amendments (especially those in pencil), the manuscript version of Signal 501 
"Cut through the Enemy line", and it being on the quarterdeck of HMS Royal 
Sovereign as Collingwood cut through the enemy's line, first at Trafalgar.
Reference:
Naval Warfare in the Age of Sail, The Evolution of Fighting Tactics
1650-1815, Brian Tunstall, Edited by Dr Nicholas Tracy
Nelson, Britannia's God of War, Andrew Lambert
The Campaign of Trafalgar, J Corbett
Naval Records Society Publications on Signals, J Corbett
Martin, 13 October 2005
According to Perrin (W.G.Perrin, 'British Flags', Cambridge University Press, 
1922) Page 178, the "preparitive" or "telegraph" flag in Popham's code was "a 
flag divided diagonally into white and red".
Christopher Southworth, 22 June 2004
According to W.J.Gordon in "Flags of the World" 1918 edition, the 'Telegraph 
flag' was hoisted at the yard-arm, while the twelve hoists of the message were 
hoisted in succession at the main topgallantmast-head. E.M.C.Barraclough in the 
1965 edition wrote of the telegraph flag; "It could remain in this [conspicuous] 
position throughout the period of the message, and then be hauled down to 
indicate that it had been completed, or, alternatively, hauled down before 
actually commencing to make the signal. In the latter case, provision was made 
for hoisting another special flag, called the "Message finished" flag [diagonal 
blue and yellow]. However as far as is known, the last mentioned was never 
used."
Its precise appearance is uncertain. Popham described it as "a diagonal red and 
white flag". It is, according to Barraclough, shown in contemporary signal books 
as a rising diagonal, sometimes red over white, and sometimes white over red, 
and that the actual flag used at Trafalgar is not known. T.Wilson in "Flags at 
Sea" shows red over white. Captain B.Kent in "Signal!" shows white over red.
David Prothero, 23 June 2004
The signal flown by the Victory at the beginning of the battle (and continued 
until shot away) was No. 16 (in Sir Hope Popham's extended code as revised 
January 1804 and used at Trafalgar) "engage the enemy more closely" which was 
flag No, 1 (a blue cross on a white field), over No.6 (divided horizontally 
blue-white-red). This would originally have been preceded by the 'Telegraph' or 
'Preparatory flag above the message (divided diagonally from the bottom left red 
over white) but this would have been hauled down prior to the battle. Nelson 
also intended to raise the signal for "prepare to anchor" after the battle, but 
due to circumstances his successor and former second in command, Collingwood, 
never used it. I do not, unfortunately have the full code, but the signal book 
reputedly used at Trafalgar is in the collection of the National Maritime Museum 
(NMM, SIG/B/76), and may be consulted by appointment (or at least could be when 
I last checked)..
Christopher Southworth, 11 February 2005
From https://www.theguardian.com/world/2018/jan/07/nelson-flag-battle-of-trafalgar-up-for-sale-sothebys:
A tattered panel of red, white and blue woollen fabric, an unusually large surviving piece of the union flag flown at Trafalgar from Lord Nelson’s ship Victory – one of hundreds of battle-stained souvenir fragments to which the flag was reduced by sailors grieving for their lost admiral – is to be auctioned by Sotheby’s at an estimated price of up to £100,000.On Nelson’s orders, his fleet flew the union flag as well as the white ensign at the battle against the French on 21 October 1805, which became his greatest victory but which cost him his life. The flags from HMS Victory came back to the UK with his body and were displayed as he lay in state in the Painted Hall at Greenwich, before being carried in his funeral procession to St Paul’s Cathedral in January 1806.
The ceremony was supposed to end with the sailors who carried the union flag folding it reverently and laying it on Nelson’s coffin before it was lowered into the grave. The Naval Chronicle recorded what actually happened: “These brave fellows, however, desirous of retaining some memorials of their great and favourite commander, had torn off a considerable part of the largest flag, of which most of them obtained a portion.”
Many of the surviving fragments are in museums, including the Maritime Museum at Greenwich, and sales from private collections are rare. This piece was apparently once even larger: it was owned by Capt William Hugh Dobbie – who was not at Trafalgar but serving with the East India Company – and was left by him to the museum of the Royal United Services Institute, which was broken up in the 1960s.
Collectors are avid for any Trafalgar memorabilia: the last complete flag from the fleet to be auctioned, from HMS Spartiate, went for almost £400,000 in 2009, 40 times the estimate. The Victory fragment will be sold with other Nelson items, including a cache of his letters, on 17 January.
Vexi-news, 13 January 2018