Summer Reading
Back in the day, I used to go to the library, pick out, check out, and read books during summer vacation. I had not done that in many, many years, but this summer I decided that I would.
Although nothing like The Boxcar Children, the books I have read so far are: Parts and Places: The Structures of Spatial Representation by Casati and Varzi, The Process of Communication: An Introduction to Theory and Practice by Berlo, Digital Mantras: The Language of Abstract and Virtual Worlds by Holtzman, and On Intelligence by Hawkins with Blakeslee. I also listened to the audiobook of The Da Vinci Code by Brown. Casati and Varzi is logical and philosophical, Berlo is old school, Holtzman is new age, Hawkins is scientific, and Brown is fictional and mystical, but what is common to these books is their emphasis on patterns, structures, hierarchies, and language.
In our weekly grouplet meetings, many times Alan prefaces a comment by saying that his synapses just fired; according to my fellow Cornell electrical engineer Jeff Hawkins, it is the hierarchical organization of the cortex of the brain that leads to the following effect: "A dinner conversation with friends follows a circuitous route of associations. The talk may start with the food in front of you, but the salad evokes an associated memory of your mother's salad at your wedding, which leads to a memory of someone else's wedding, which leads to a memory of where they went on their honeymoon, to the political problems in that part of the world, and so on." He continues that, "We call this chain of memories thought, and although its path is not deterministic, we are not fully in control of it either."
They say that you are not really into your research unless you're thinking about it in the shower, when eating, walking, and doing just about anything.
In addition to reading books, I also lowered the stack of accumulated magazines sitting on my bedside table. When going through the May issue of IEEE Spectrum, I was reminded of the following email that made the rounds a few years ago: "Aoccdrnig to rscheearch at Cmabrigde uinervtisy, it deosn’t mttaer waht oredr the ltteers in a wrod are, the olny iprmoetnt tihng is taht the frist and lsat ltteres are at the rghit pclae. The rset can be a tatol mses and you can sitll raed it wouthit a porbelm." My synapses fired, and I realized that this effect is a good analogy to the stochastic, but structured nature of regulatory motifs in genomes, also known as cis-regulatory elements and as transcription factor binding sites. (I have been spending some time recently looking at modeling regulatory motifs with graphical models and doing empirical Bayes parameter estimation.)
Regulatory motifs are short patterns in DNA to which proteins known as transcription factors bind. The binding or non-binding of transcription factors controls the expression of downstream genes. However, there is some allowable ambiguity or randomness in the pattern. For example, the ABF1 transcription factor binds to both TCTCTCGCAACG and TCACGTCACACG. Just as the English-speaker can read both uinervtisy and university, the transcription factor can bind to both patterns. The randomness is structured; there is more allowable ambiguity in the middle than the ends in these two examples.
As genomics keeps popping up in my posts, let me give a shout out to my friend Krish Eswaran, another fellow Cornell electrical engineer, who is at the Broad Institute for the summer. He gave an interesting talk to us yesterday about his preliminary work on operon prediction in bacterial genomes.
