Wednesday, February 27, 2013

The Secret of DNA's Success is That It Carries Information

It has been said that, as humans, music is in our DNA. According to promising results published in the journal Nature by researchers at the European Bioinformatics Institute, practical, high-capacity, low-maintenance information storage in synthetic DNA may be feasible. What is the implication for music?

[Image credit: Janusz Kapusta. Title quote: Jonathan Wells.]

High-resolution digital audio (24-bit samples at 96KHz or higher) is big data. The transition of music from physical media to weightless high-resolution digital form is contributing to the forecasted 50-fold increase in global data by 2020, while hard drive capacity may only grow 15-fold in the same period [David Epstein]. There is a growing storage gap.
Enter DNA. Just as digital information can be encoded as arbitrarily long sequences of 1's and 0's, (bits) it is also possible to imagine the same information as arbitrarily long sequences of other characters, including 0's, 1's, and 2's (trits). EBI scientists Nick Goldman and Ewan Birney have devised a mapping from a string of trits to a DNA string with no repeated nucleotides {A, C, G, T}, as well as scheme for organizing arbitarily long DNA strings into overlapping fixed-lengths runs for sequencing with robust error-correction. The result is a method for encoding digital information in synthetic DNA, a volumetric (rather than planar) storage medium that requires no power and can last indefinitely.
Here's how it works (slightly simplified):
  1. Digital music is encoded as a String S0 of 24-bit samples.
  2. S0 is converted from binary to String S1 in base-3, transforming each 24-bit sample to a sequence of 18 trits.
  3. Add length information (20 trits) and zero-padding to produce a string S2 whose length N is a multiple of 25.
  4. Convert S3 to a DNA string S3 of nucleotide (nt) characters {A, C, G, T} according to a mapping based on the last character written and the next trit in the sequence, such that there are no repeated nt.
  5. Split S3 into overlapping segments of 100 nt, each offset from the previous by 25 nt. This step provides decoding redundancy for error correction. Each nt is contained in up to four segments. For a string S3 of length N, N/25 − 3 segments are produced.
Encoding high-resolution digital audio as a DNA string.

According to this method, 1 second of 24/96 digital audio comprising 576K bytes would generate a DNA string of more than 16 Million nt, a 28x size expansion that seems inefficient. (Digital aduio is typically compressed for storage, not expanded.) But DNA is incredibly dense. Even with the data size expansion, DNA encoding achieves a data density of 2.2 Million GB/gram, which translates to more than 1200 hours of high-definition digital stored in a single gram of DNA barely visible to the human eye. (That's twice the size of my entire library.)
Goldman and Birney proved the viability of their method by encoding digital files of all the Shakespearean sonnets into synthetic DNA, then using standard DNA sequencing software to recover the string for decoding to the original texts.
A media player based on DNA playback is not in our immediate future. The current price of DNA storage is estimated at $7.5 Million per GB, as opposed to $0.05 ("five cents") per GB for magnetic disc space. Furthermore, the speed of DNA sequencing and subsequent decoding to audio does not support real-time playback. The technology is on a 50-year horizon.
            Vinyl-to-Digital Restoration #53            

Artist: Dan Fogelberg & Tim Weisberg
Title: Twin Sons of Different Mothers
Genre: Rock
Year: 1978

You wouldn't have thought to put the late folk singer/songwriter Dan Fogelberg with jazz flutist Tim Weisberg, but the collaboration worked well, even producing the hit "Power of Gold." A fitting title for our discussion of DNA. 70's hair aside, the two musicians don't really look like twins, a fact they conceded on their followup 1995 release, No Resemblance Whatsoever.

© 2013 Thomas G. Dennehy. All rights reserved.

Wednesday, February 13, 2013

That Was the Day Before Love Came To Town

It's an established tradition at In Aurem A2D to use holidays as opportunities for Surface to Air Full Circle music challenges. Our last was on Thanksgiving.

[Photo credit: Yehia-elal​aily]

You know the drill. (Connection between our game and the WDET-FM Music Head fundraiser is in our first challenge.) Starting with a particular song, chart a path along associated metadata to create a connected playlist; but at some point, reverse course and return along a different metadata path to arrive full circle back at the starting song, in "about an hour" of running time. Bonus points if you only use songs from your personal library (as I always do).

That bonus may get harder to achieve over time, if the trend continues away from music ownership and personal libraries to music access and personal playlists via streaming services.

To celebrate Valentine's Day in the USA, our starting/ending song is U2's "When Love Comes to Town" (featuring B. B. King).

Full-Size table here. Annotated table with metadata associations here.

A worthy effort at almost exactly an hour (within the margin of error on the published running times). However, it makes more use of direct song title to song title transitions than previous lists, something to watch in the future. Previous lists can be found in the Surface to Air 2012 Retrospective.

While you listen to any or all of the tracks along our journey, check out this Brain Pickings thought piece,  Calculating the Odds of Finding Your Soulmate. Happy Valentine's Day!

            Vinyl-to-Digital Restoration #52            

Artist: U2
Title: Rattle and Hum
Genre: Rock
Year: 1988

Music buyers who only know an industry dominated by iTunes can't imagine a time when you needed to buy an entire double LP set just to get the one or two tracks you really wanted. The feature film Rattle and Hum may have been negatively characterized by some critics as "an accidental mockumentary," but the performances are solid. For me, the highlights are "When Love Comes to Town," a hard-charging blues duet with B. B. King, and the equal-parts plaintive and haunting "All I Want Is You."

© 2013 Thomas G. Dennehy. All rights reserved.

Wednesday, February 6, 2013

A Funky Space Reincarnation

High resolution digital audio is big data. For any sizeable collection, we aren't talking gigabytes of data, more like terabytes (1 TB = 1,000 GB = 1,000,000 MB). Where do you store it all, and is your solution reliable?

I'll admit to hard drive paranoia — too many moving parts, too many failure modes Flash drives are my preferred storage solution.

But the 1TB flash drive housing my WAV library of nearly 1,000 full-length titles is nearly full, and my other drives are also maxing out. What's next?

Enter the LaCie Blade Runner, a 4TB USB 3.0 hard drive in a physical package by designer Phillipe Starck that is both beautiful and practical. (See photo, above.) The series of ribs will be immediately recognizable to anyone in the automotive audio business. They serve as a heat sink, dissipating the heat generated by the internal mechanism over a large surface area, eliminating the need for a cooling fan. The sealed enclosure also dampens vibration, and the raised rubber feet prevent vibration from being transferred to the desktop. The result is cool and quiet operation at state-of-the art transfer speed.
Where does all the space go? CD-quality WAV audio (16-bit/44.1 KHz) consumes 1GB for every 95 minutes of material. High-resolution lossless (24-bit/96 KHz) will cost you 1GB for every 29 minutes of audio. (Lossless compression — e.g. FLAC — will cut down the storage requirement, but not all media players support it as a native format and decompression is an additional step in the playback pipeline for those that do.) I prefer keeping material uncompressed.
In my weightless digital library I have 677 titles (600 hours) of 16/44.1 audio, and 300 titles (212 hours) in 24/96. The former is, not surpisingly, source from CD. The latter is almost entirely mastered from vinyl. Together they occupy more than 800 GB of disc space. Factor in album art and miscellaneous other audio and you can see that a 1TB drive will run out of space before I can add ten new 24/96 titles. The 2 TB drive holding the backup copies of mastering projects and FLAC downloads (compression is good for transport) is nearly full as well.
I see a Blade Runner in my future.  
            Vinyl-to-Digital Restoration #51            

Artist: Marvin Gaye
Title: Here, My Dear
Genre: Soul and R&B
Year: 1978

Ordered by a judge to turn over the profits from two albums to the first wife he'd left, Marvin Gaye produced this bitter, sad, bewildered masterwork. [N.B. The album includes the track used as the title of this piece.] Over sprawling funk tracks, he questions her, himself, love, family, and, of course,  asks, "Why do I have to pay attorney fees?" Both incomparably smooth and incontrovertibly twisted, Here, My Dear is Gaye with the mask off: even the multiple vocal overdubs can't hide his pain and his weariness. — Rickey Wright

© 2013 Thomas G. Dennehy. All rights reserved.