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Yes, secret codes will be a part of the treasure hunts at times. Nothing too difficult, though, and here is a quick lesson on the subject to help you out.
Most secret codes simply replace a letter with another (w = a, x = b, d = c, ...), or they may use numbers as well (22 = a, 39 = b, ...). Periods and other punctuation may or may not be used. There are much more complicated codes, but these are the type I will stick to for our purposes.
Deciphering or "breaking" secret codes then, involves figuring out which letters or numbers were substituted for which. This is determined in part by understanding of how often certain letters normally appear in written language, also known as "letter frequency." A simple example: Since "e" is the most frequently used letter in English, if there are far more incidents of the number "34" in a message than any other, then "34" is probably substituting for the letter "e."
Of course, there is no guarantee that this is correct. A short message, for example, is less likely to conform to the normal frequency distributions, and letter frequency varies by language, topic, and dialect. Suppose a message is about kayaks and cake. It would use the letter "k" far more often than normal. And here's an example of dialect differences: the ending "ise" is more common in Britain, while "ize" is used more in America. Thus, the use of "z" is more common in secret messages written by Americans.
Also, everyone writes differently. Interestingly,, this fact is sometimes used to prove or disprove authorship. The average sentence length, word length, and letter frequencies can be determined for each author, and a forger can rarely forge an authors "style," as determined in part by these measurements. During World War Two, British code breakers used analysis of this kind to identify not just what a secret message said, but who was sending it as well.
Average Letter Frequency In English (Source: Wikipedia):
a 8.167%
b 1.492%
c 2.782%
d 4.253%
e 12.702%
f 2.228%
g 2.015%
h 6.094%
i 6.966%
j 0.153%
k 0.772%
l 4.025%
m 2.406%
n 6.749%
o 7.507%
p 1.929%
q 0.095%
r 5.987%
s 6.327%
t 9.056%
u 2.758%
v 0.978%
w 2.360%
x 0.150%
y 1.974%
z 0.074%
You can see that the letter "e" is by far the most frequent, followed by "t" and "a." Of course, the frequency of letters in a given message will never perfectly fall in line with that chart above, but once you determine the most common letters or numbers, one will likely be an "e" or "t."
Now that you know a bit about codes and breaking them (there is more coming), you may want to try deciphering the following message, written in a simple secret code.
qt mak xgb gbxcqwr hpqi, eawrgxhkyxhqawi! qt mak exw sgbxz hpqi eacb, mak xgb gbxcm tag hpb eacb sgbxzgwr epxyybwrbi qw hpb rgbxh eayagxca hgbxikgb pkwh. wal mak sbhhbg rbh skim xwc tqwc x hgbxikgb!
For the deciphered version, and to learn the basics of how to decipher secret messages, see the page, Basic Code Breaking.