Category Archives: commentary

DNA as data storage

What’s the oldest data format in the world? It’s not any of the ones that computer engineers developed in the 20th century, or even ones that telegraph engineers created in the 19th. Far older than those — by billions of years — is the DNA nucleotide sequence. We can think of it as a simple base-4 encoding of arbitrary length.

DNA double helix According to the usual, somewhat simplified, description, a DNA molecule is a double helix, with its backbone made of phosphates and sugars, and four types of nucleotides forming the sequence. They are adenine, guanine, thymine, and cytosine, or A, G, T, and C for short. They’re always found in pairs connecting the two strands of the helix. Adenine and thymine connect together, as do guanine and cytosine.

DNA for data encoding

That’s as deep as I care to go, since biochemistry is far away from my areas of expertise. What DNA does is fantastically complicated; change of few bits and you can get a human or a chimpanzee. But as a data model, it’s fantastically simple.
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When sloppy redaction fails, resort to censorship

The Broward County School Board used an idiot’s form of “redaction” on a PDF before sending it to the media. The Sun Sentinel removed the blackout layer from the file and found newsworthy information on shooter Nikolas Cruz. They published it. Judge Elizabeth Scherer flew into a rage. She decreed, “From now on if I have to specifically write word for word exactly what you are and are not permitted to print… then I’ll do that.”

That’s called prior restraint, or censorship.
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PDF or HTML for public documents?

Should official online documents be PDF files? Many institutions say they obviously should, but the format has some clear disadvantages. An article on the UK’s Government Digital Service site argues that HTML, not PDF, is the right format for UK government documents. Its arguments, to the extent that they’re valid, apply to lots of other documents.

It makes a plausible case against PDF. The trouble is that the case against HTML is even stronger in some ways.
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The “Zip Slip” vulnerability

Sometimes my reaction to a story is “Wait, are they saying someone was that dumb? … No one could be that dumb! … Oh, gods, they were that dumb!” Naked Security’s account of the Zip Slip vulnerability is just such a story.

The article starts with a fair warning that the vulnerability is “so simple you’ll need to put a cushion on your desk before you read any further (in case of involuntary headdesk injury).” It explains that because of the coding mistake called “Zip Slip,” “attackers can create Zip archives that use path traversal to overwrite important files on affected systems, either destroying them or replacing them with malicious alternatives.” This is where I started to suspect.

The vulnerability isn’t in the Zip format as such, but in bad coding found in some of the zillion ad hoc pieces of software written to unpack Zip files. Have you figured it out yet? I’ll put the cut here to give you a chance to think…
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Flash in the Library of Congress’s online archives

Everybody recognizes that Adobe Flash is on the way out. It takes effort to convert existing websites, though, and some sites aren’t maintained, so it won’t disappear from the Web in the next few decades.

When it’s minor or abandoned sites, it doesn’t matter so much, but even the Library of Congress has the issue. Its National Jukebox currently requires a browser with Flash enabled to be useful. Turning on Flash for reliable sites such as the Library of Congress should be safe, at least as long as those sites don’t include third-party ads from dubious sources. Not everyone has that option, though. If you’re using iOS, you’re stuck.

I came across the National Jukebox while doing research for my book project Yesterday’s Songs Transformed, and it’s frustrating that I can’t currently use it without taking steps which I’d rather avoid. The good news is that this is a temporary situation and work is already underway to eliminate the Flash dependency. David Sager of the National Jukebox Team replied to my email inquiry:
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“Mad” file formats

There really are some file formats that have “mad” in their name or extension. Some people may find this blog when trying to learn about them, so I suppose I should provide some information about them.
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The Joy Reid case and the fragility of archives

The exposure of old, embarrassing posts by MSNBC columnist Joy Ann Reid has provoked a lot of heated discussion. It’s also revealed the difficulty of retaining reliable information about old material on the Web.

When these old posts came to public attention through Twitter, she asserted that there had been one or more unauthorized break-ins altering her articles to add offensive content.

In December I learned that an unknown, external party accessed and manipulated material from my now-defunct blog, The Reid Report, to include offensive and hateful references that are fabricated and run counter to my personal beliefs and ideology.

I began working with a cyber-security expert who first identified the unauthorized activity, and we notified federal law enforcement officials of the breach. The manipulated material seems to be part of an effort to taint my character with false information by distorting a blog that ended a decade ago.

Now that the site has been compromised I can state unequivocally that it does not represent the original entries.

The “altered” material, however, also was found on the Internet Archive’s Wayback Machine with the same content. If Reid’s statement is true, the alterations must have taken place shortly after their publication and yet not been noticed, or else the Internet Archive must also have been compromised.

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PDF in three dimensions

There are two ways to put 3D models into a PDF file. Neither of them is an extension of the two-dimensional PDF model. Rather, they’re technologies which were developed independently, which can be wrapped into a PDF, and which software such as Adobe Acrobat can work with.

PDF has become a container format as much as a representational format. It can hold anything, and some of the things it holds have more or less official status, but there are no common architectural principles. The two formats used with PDF are U3D and PRC. Both are actually independent file formats which a PDF can embed.
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Apple hides attachments in malformed multipart mail

Recently I got a PDF of a filk songbook which I had contributed to. More precisely, the email said I was getting it, but there was no sign of an attachment. I wrote back to the editor who’d sent it, and she insisted it was there. Digging it out of the message revealed to me a whole new way of messing up email formats.

A quick look at the message source showed that there really was an attachment with Content-Type of “application/pdf” which took up well over 90% of the message. The question was why Thunderbird didn’t show it to me.
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