In recent weeks, I've written about protecting data stored locally on a hard drive, against both people with physical access and potential remote attacks. But your data is much more vulnerable in transit, as it passes between end points or via servers.
This problem is effectively solved for instant messages with iMessage, which uses strong end-to-end encryption designed in such a way that--Apple says--not even they can decrypt your messages. This is accomplished by creating local encryption keys through a process that can't be reverse-engineered on their side. Even though iMessages pass through intermediate points on the Internet, there's no opportunity for others to grab the plain text, images, and audio within. (The same is true with FaceTime audio and video.)
But it's still a mess for email, whether Mail in iOS or OS X, or third-party email software. The problem arises from email protocols working too well. Yes, I know how that sounds, as Apple's Mail app frustrates on both its platforms. But the diversity of what you can choose among native and Web apps has to do with no company or organization controlling how email works. iMessage is entirely Apple's ecosystem, which is the case for most messaging systems, including Facebook's WhatsApp and the messaging component of Microsoft's Skype. In contrast, there are thousands of native email programs across all platforms and all time, and hundreds remain in wide use.
The problem with email
The email protocols comprise POP3 (ancient and still in use) and IMAP for email retrieval and synchronization, while SMTP handles sending. Because they emerged from the dawn of Internet, they have evolved in fits and starts with weird vestigial pieces. Email continues to function because of compromises and a tacit agreement that nobody can break or refuse to support major components--partly because no one controls a big enough piece to force change.
One of the biggest problems past and present in Apple's Mail.app is, in fact, because Google has an odd setup for its IMAP service, and Apple dances around fully embracing it. Google can't break IMAP entirely, because then millions of users who pull in Gmail messages through Outlook or other software would be out in the cold, and potentially switch away. (Android has three separate email apps, in fact: two that work with Gmail in different ways, and third for "regular" email accounts.) Likewise, Apple can't invent a new, superior way to send email because every mail server in the world would need to be updated to receive it.
In the last few years, enough standardization and upgrading have taken place that one aspect is well secured: the connection between an email client and an email server. Email flows from a client to a server run by your ISP or company or email host, and from there typically directly to the recipient's corresponding email server. By default, Apple's mail clients and those of other companies try to set up a new account to use SSL/TLS, the same session-based encryption technology used for secure Web interactions.
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