February 1, 2011 (Vol. 31, No. 3)

Electrical engineer Owen Piette at Integrated DNA Technologies provided the winning answer to GEN’s latest “Cryptogram Challenge: qPCR.” Owen, who with the help of a colleague also won the first GEN contest, “Microarray Challenge,” two years ago, figured out that the answer to the current puzzle was “counting equals knowing.”

GEN, along with partner, Scintellix, and sponsor, Bio-Rad, congratulate Owen on his accomplishment. In addition to winning a $1,500 cash prize, Owen also won Bio-Rad’s MyCyclerTM personal thermal cycler, which he plans to donate to a research laboratory.

Owen works on electrical designs for new machinery for IDT’s manufacturing environment. He also develops special software for data collection and analysis to increase performance in the company’s manufacturing operations. IDT is a leading supplier of synthetic DNA.

“I find these kinds of contests challenging and fun,” says Owen. “On first look the puzzle seems abstract with lots of gibberish. But almost simultaneously I realize that there is something in the cryptogram that makes sense.”

Owen added that the fact that a lot of IDT’s oligos are used in PCR reactions helped draw him into tackling the qPCR cryptogram challenge. “PCR is closely tied into our business and is very applicable to our work,” he noted.

While contest clue 5, “biological specificity is important,” led Owen to start thinking about adenine, guanine, cytosine, and thymine, clue 10 (“The clue on the web page in clue six is the inventor of PCR, Kary Mullis”) and clue 11 (“In the encoded alphabet the letters in his last name add up to 50”), set him on the road to solving the cryptogram challenge.

“Of course, the real key was the last clue, about Mullis equaling 50,” continued Owen. “Not only did it imply that I was on the right track, for example, that there was a directly encoded alphabet, but it also gave me the mapping, which I will explain later. I had thought the mapping of letters to numbers was going to be more complex, and while there was a twist, it wasn’t arbitrary.

“When clue 11 came up, I had already been scratching my head for a week or two trying to find the information about the letter sequence. But I already knew there were 21 letters.”

Owen Piette

Online Anagram Solver

Ultimately, Owen used an online anagram solver. It gave him hundreds of words, but he iterated through them until he found the answer. Owen’s actual strategy for solving the challenge follows.

He drew lines between AT and GC bases to find midpoint cells. He gave those cells a cycle number and a log-plotted number. The log numbers ran as 1,2,3,4,5,6,7,8,9,10,20,30,40,50,60,70,80,90,100.

“That took a long time to figure out. I feel stupid for overcomplicating it,” Owen says. “I was using y=0.1*10^(N/9) for a long time.”

He then multiplied the cycle number and log number together and plotted them, noticing they had 26 discrete values. He divided the products by 50, because that gave him the numbers 1–26.

“Realizing quickly that a straight 1=A didn’t work, I stewed until I got MULLIS=50. I tried every one (of 26) possibilities of simple mapping, which I thought was too simple, until I got MULLIS=50.”

Owen then found a jumble of letters that “didn’t make any sense,” and subsequently reversed the alphabet and tried again. He came up with LKIIGGECAWUUTSQOONNNN.

Owen later went online, Googled for an “online anagram solver,” typed in the sequence, and received many results. He finally figured out that the answer was “counting equals knowing.”

Owen remarked that the enthusiasm at his company regarding those who saw or took on the cryptogram challenge was “remarkable.” He was pleasantly surprised when it was pointed out to him that a number of cryptogram challenge winners, such as himself, decided to donate the cash prize and/or the scientific instrument prize to a laboratory, hospital, or research facility.

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