February 1, 2009 (Vol. 29, No. 3)

IDT Engineers Follow the Clues to Take Home the $1,500 Prize

Two scientists from Integrated DNA Technologies (IDT) successfully solved GEN’s online MicroArray Challenge. Owen Piette, electrical engineer III, and Ryan Witt, system engineer I, shared the winner’s prize of $1,500.

The hidden message of the MicroArray Challenge (MC), which ran from the middle of November through the end of December, was: “In the beginning was the code.”

The IDT scientists, who used a poster of the MC in the company’s cafeteria to work on over lunch, agreed that the seventh and last clue to solving the puzzle was the one that allowed them to make some headway. The seventh clue was: “In the triplet code, three adjacent dots code for each letter, which should be placed at the site of the center dot. Words are created from abutting triplet-coded letters. The code for the letter ‘e’ is ‘yellow green green’ and the code for the letter ‘n’ is ‘green red green.’”

Peter C. Johnson, M.D., artist, and president and CEO of Scintellix, created the MC and embedded a cipher (algorithm for performing encryption and decryption) based on the dots in the pastel. The image used in the MC also appears in part on the cover of Dr. Johnson’s poetry collection (also known as MicroArray, Scintellix Publishing, 2008).

“I conceived of using the pastel painting, MicroArray, to convey a cryptogram, because at the time I painted it (in 2001), I was reading Simon Singh’s The Code Book that discusses the history and methods of cryptography,” notes Dr. Johnson. “When I painted MicroArray, the field of bioinformatics was just beginning to accelerate. Since it was essentially a code-breaking science I thought it would be interesting to exemplify the role of the gene-expression microarray as a manifestation of the code of life that demanded to be deciphered.”

Owen Piette (left) and Ryan Witt (right), scientists from Integrated DNA Technologies, were the winners of GEN’s Microarray Challenge contest.

One Way to Interpret the Code

In creating the code, Dr. Johnson explains that he chose a single pad key code, meaning that there was only one way to interpret the code, and that it would be very difficult to break. “I enhanced the difficulty by making it a triplet code (that is, three dots needed to act together to specify one letter),” he continues.

“This was done to create an analogy to the three bases of RNA required to code for a single amino acid. Finally, I used a `family of colors’ concept that allowed for many hues to be used in the image (such as various shades of the red family) but which needed to be combined into specific color families that would be considered equivalent to allow the code to be broken.”

For eight years, although many made attempts to break the code, it was never broken. In running the MicroArray challenge, then, it became imperative to provide clues to allow the cryptogram to be solved, according to Dr. Johnson. These clues were graded in value from the necessary but least valuable first clue (regarding the reading direction) to the most important clues regarding grouping of families of colors and ultimately, the provision of the codes for several of the letters in the message. In the end, a single pad key code is usually only breakable when some of the latter information is given.

“Since the contest was due to run only until December 31, we chose to provide that information in the last week of the contest. This information, combined with the information in all of the previous clues, was designed to enable those who had been ardent about the solution to reach the proper conclusion most rapidly. This is exactly what occurred when Witt and Piette submitted the winning entry.”

“The critical problems we had were over which colors merged into other colors and which were independent colors,” notes Piette. “The key clues were those that had to do with naming specific colors. Ultimately, it was the final clue that led to our breakthrough.”

“The seventh clue, which helped us figure out what two of the letters actually were, allowed us to recognize some patterns that could form words. I think it was the letter N more than anything that helped us since that occurred so often in the code,” says Witt.

Piette and Witt believe that their academic training and job skills played a role in helping to figure out the MC, although Piette admits that his background in science almost made it more difficult for him to solve the puzzle.

“I was much too analytical and looked at the MC not so much as a word problem, which it turned out to be, but more of a clustering, grouping, data analysis, and segmentation problem,” he says.

“My focus was on trying to find patterns within it,” adds Witt.

Both scientists hold bachelor’s degrees in electrical engineering. Piette has carried out research on cation uptake in the melting and forming of the DNA double helix. He also has experience in bioinformatics, microarrays, and image analysis and currently works on the electrical systems of robotics instrumentation in IDT’s production facility.

Witt designs embedded control systems  as well as software for data analysis and robotics control.

Agilent Technologies sponsored the MC.  “We really liked the concept behind the MicroArray Challenge as it’s a fun way to highlight what the arrays really do in the lab: present patterns of data that the scientists then must interpret,” says Renee Zuckerman, senior genomics marketing manager.

“At Agilent, we always try to look at problems from multiple perspectives, and the MicroArray Challenge is a fresh approach for engaging the readers of GEN. Fortunately, cryptograms are much simpler to solve than biological pathways.”

Watch for Future Challenges!

Check out the Microarray painting and clues that we released during the challenge!

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