Yeehawww. Just had two exams in an eight hour span. I’m dead tired but feeling pretty spiffy. One exam on Friday left. The last exam ever! Hooboy. On my kitchen table I found an old schedule outlining all the assignments, projects, presentations and exams I had to get done through the last few weeks and I involuntarily cringed at the unfathomable horribleness of it. I still don’t know how I pulled it all off.

You know, it’s looking like I’m going to be the first ever Bioinformatics grad from my university. There are a couple others in the same stream but they don’t have all the credits they need yet. It’s going to be funny if they give me a gold medal for the highest mark of my program. I totally don’t deserve one with what will likely be a low seventies average. The injustice is sweet, my friends. Haha!

Oh so sleep deprived. I’m excited though. I’m starting to feel real excited about my coming metamorphosis from a dull and lowly undergrad into a beautiful and elegant butte– graduate. I am looking forward to starting fresh somewhere, a new job, new city, new place. New new new. Maybe I’ll even earn some money that isn’t spent on rent or food. Even in the worse case scenario of not finding a job this summer, the idea of going back home to T. Bay in September is exciting. I’ll reconnect with old friends who’ve probably written me off, enjoy the doting attention of a mom who hasn’t had her son in the house since he was eighteen, buy some new skates and a stick with which I will unleash an incomprehensible torrent of furious hockey skill and prowess upon the unsuspecting patrons of the outdoor rinks of my childhood neighbourhood! Ohhh yes!

I think I’m going to renew my campus recreation membership and locker for the summer. Preparation starts now!

Hmm. Good comments, good comments. I think I’ve actually mustered up the necessary resolve. I’ve written enough on it for now. It’s coming though.

Yawn yawn yawn. Always so sluggish on Sunday. Last week I had my last day of class ever. It was a representative microcosm of all others. I slept in through the first three hours and walked in late to the last two. Three more exams and I’m done. I’m having trouble maintaining motivation to study though…

More boringly, I finished the last lecture of my ancient near eastern mythology audio book series. It was on wisdom. Hopefully, I osmosed at least some of it. The lecture was, in part, a reminder of how trivial my current problems are. I have no right to complain when I’m in such a privileged position. There are many who are better off but the amount of people suffering with much more serious problems dwarfs that. I’m pretty good at keeping things in context but sometimes it does slip away.

I started another series on classical mythology for continuity. I’m about two hours in. As a bonus, I found some supplemental material on TV last night at 5am. It was a Robin Hood cartoon, where for some inexplicable reason, Robin and Little John were traveling through outer space. They landed on a planet where they needed to help Jason, of Argonaut fame, obtain the Golden Fleece and get past a Hydra. Holy shit, I hit the jackpot! Roman mythology and Medieval legend combined with a sci-fi twist. And in cartoon format too! I was transfixed and mesmerized by this amusing amalgamation.

Ahhuuh, Girlfriend in a Coma is such a perfect song for my mood right now. Mellow, lazy and sublimely evil. I just found out the other day that Morrissey was the lead singer for The Smiths. Who knew? Everyone but me apparently.

You know, even though I’m basically a biology grad, whenever I hear “osmosis”, it only summons up a mental image of Garfield where he’s got books strapped to his feet and head.

I’m often glib when I refer to Merle but the truth is that I really do care about her and am searching for a way to end things in a way that doesn’t cause a destructive explosion. Some things she has said in the past regarding what would happen if we break up have been pretty scary. I really do believe that she has a mild case of borderline personality disorder and there is a significant danger of suicide. I talk about running away as a solution but I’m not serious. I know this is something I’m going to have to face very soon. Due to our respective U.S. citizenship issues she recently talked to a lawyer about her green card/naturalization situation as well as what I need to do to obtain a work permit (it will be easy if I find a willing employer). She asked about marriage and the lawyer strongly advised against it. When she told me this she was crying but I felt relief. Her visit after my last exam on the 15th is now in question too because of her green card expiration. There is a danger that when she crosses the border, she’ll be nabbed and deported to France. That would be funny! (no it wouldn’t. no it wouldn’t.)

She told me in our second year together that she wanted to marry me. I figured it was just infatuation and would pass but it didn’t. Since then I’ve done an incredible job of resisting marriage or engagement but even the most resolute rocks erode. Last year she threw a serious proposal at me which I rejected in the most delicate way possible. Still, she was deeply hurt and is still bitter about it. She won’t move on though. Personality attributes that I don’t like about myself I think she finds desirable. She is an intensely jealous creature and therefore likes my introversion. She is social, bombastic and steals my few friends. I know that if we broke up, if she felt like it, she could find someone else with much more ease. She had two previous boyfriends before me that threw flower petals at her feet and she dominated them. I observed from a distance as she unceremoniously ripped out one poor young man’s heart and stomped on it like a tomato. This coincided with her decision to aggressively pursue me. Maybe it’s retribution or karma that I’m the one she fell for. Anyway, my independent nature prevents bullying from Merle and often sparks spectacular fights. In one of the most oddly satisfying things she’s told me, she said that she likes how I keep her “in line”. That was so fucking bizarre to hear coming from her.

There is a psychology professor at my university that I know on a somewhat personal level. He is intelligent, well spoken, witty and thoughtful. I have a lot of respect for him. I once looked up his student evaluation records and wasn’t surprised at all to find that his students absolutely adore him. He tends to be very busy but I enjoy our occasional conversations. He is a fifty something who went through a divorce about two years ago and now lives with his teenage daughter. He has demanded I stop by for a visit before fleeing London in search of fame and fortune. The reason I am writing about him is that he is so incredibly soured on the idea of marriage and living with women. I don’t have any knowledge about how he was scorched by his ex-wife but I sense that he was really miserable. It gives me real pause when Merle says that she wants to marry me. I’m twenty five. Sometimes that feels old and I’m compelled to just throw in the towel and settle for Merle. Maybe I don’t love her, but I do care for her. Maybe that’s enough. I know she truly loves me. Then I think of this professor and how bad I fought with Merle when we lived together, how I believe she is incapable of change. Do I want my relationship to be a wild rollercoaster or something more fulfilling? I have serious doubts in my abilities to reach out and find someone else though.

I’m riding my bike again (yes the pedal kind, not the motor kind) and I don’t wear a helmet. I stubbornly refuse to. If I’m destined to die from a horrible bike related concussion than so be it. A little egg shell helmet isn’t going to save me. Merle gets very upset about this. Justifiably, I suppose. Still, she won’t let the issue die and it is one of our many regular fight topics. She doesn’t accept the reason I gave at the top of this post, so out of boredom I tend to come up with other less convincing arguments like, “they look dorky”, “It will mess up my beautiful hair” or, “the strap will give me chin rash”. The last time we talked on the phone I told her that when riding to work I dress all in black because I’m a bike ninja. And bike ninjas don’t wear helmets. We’re silent and swift and don’t obey traffic laws. And for purposes of stealth I was thinking of taking off all the reflectors. I’m rarely such a sarcastic ass but during times of high stress she can draw it out of me. The results were predictable and I felt bad after.

She’s coming for a week long visit on the 16th. I don’t even get to breathe after my last exam on the 15th before she pounces. I know I’m going to be turning down another marriage proposal that week. I no longer have the school excuse. I wish I had stronger friendship bonds. Maybe I’d be able to take the leap I’m tempted to if I had a cat for moral support.

She’s a resident alien and was denied U.S. citizenship last week. She let her green card lapse too. Soon she won’t be able to come into Canada for an indeterminate amount of time. Maybe Vancouver’s the place to be. My talented little sister is out there too. She’s going to an art school. I have a feeling she’s living a bohemian lifestyle.

A guard at my workplace called in sick tonight so I’m covering. I feel like a dark little troll. When the weather starts to get better it makes working night shifts incredibly unbearable. There was a time when I used to revel in the sun. Out in it all day long, everyday. Maybe if I got more sunshine I wouldn’t write bitter little posts like this at 4:30am

Implementing models for DNA computing: concerns from the lab

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http://computer.howstuffworks.com/dna-computer3.htm

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Even as you read this article, computer chip manufacturers are furiously racing to make the next microprocessor that will topple speed records. Sooner or later, though, this competition is bound to hit a wall. Microprocessors made of silicon will eventually reach their limits of speed and miniaturization. Chip makers need a new material to produce faster computing speeds.

You won’t believe where scientists have found the new material they need to build the next generation of microprocessors. Millions of natural supercomputers exist inside living organisms, including your body. DNA (deoxyribonucleic acid) molecules, the material our genes are made of, have the potential to perform calculations many times faster than the world’s most powerful human-built computers. DNA might one day be integrated into a computer chip to create a so-called biochip that will push computers even faster. DNA molecules have already been harnessed to perform complex mathematical problems.

While still in their infancy, DNA computers will be capable of storing billions of times more data than your personal computer. In this article, you’ll learn how scientists are using genetic material to create nano-computers that might take the place of silicon-based computers in the next decade.

A Fledgling Technology

DNA computers can’t be found at your local electronics store yet. The technology is still in development, and didn’t even exist as a concept a decade ago. In 1994, Leonard Adleman introduced the idea of using DNA to solve complex mathematical problems. Adleman, a computer scientist at the University of Southern California, came to the conclusion that DNA had computational potential after reading the book “Molecular Biology of the Gene,” written by James Watson, who co-discovered the structure of DNA in 1953. In fact, DNA is very similar to a computer hard drive in how it stores permanent information about your genes.

Adleman is often called the inventor of DNA computers. His article in a 1994 issue of the journal Science outlined how to use DNA to solve a well-known mathematical problem, called the directed Hamilton Path problem, also known as the “traveling salesman” problem. The goal of the problem is to find the shortest route between a number of cities, going through each city only once. As you add more cities to the problem, the problem becomes more difficult. Adleman chose to find the shortest route between seven cities. You could probably draw this problem out on paper and come to a solution faster than Adleman did using his DNA test-tube computer. Here are the steps taken in the Adleman DNA computer experiment:

1. Strands of DNA represent the seven cities. In genes, genetic coding is represented by the letters A, T, C and G. Some sequence of these four letters represented each city and possible flight path.
2. These molecules are then mixed in a test tube, with some of these DNA strands sticking together. A chain of these strands represents a possible answer.
3. Within a few seconds, all of the possible combinations of DNA strands, which represent answers, are created in the test tube.
4. Adleman eliminates the wrong molecules through chemical reactions, which leaves behind only the flight paths that connect all seven cities.

The success of the Adleman DNA computer proves that DNA can be used to calculate complex mathematical problems. However, this early DNA computer is far from challenging silicon-based computers in terms of speed. The Adleman DNA computer created a group of possible answers very quickly, but it took days for Adleman to narrow down the possibilities. Another drawback of his DNA computer is that it requires human assistance. The goal of the DNA computing field is to create a device that can work independent of human involvement.

Three years after Adleman’s experiment, researchers at the University of Rochester developed logic gates made of DNA. Logic gates are a vital part of how your computer carries out functions that you command it to do. These gates convert binary code moving through the computer into a series of signals that the computer uses to perform operations. Currently, logic gates interpret input signals from silicon transistors, and convert those signals into an output signal that allows the computer to perform complex functions.

The Rochester team’s DNA logic gates are the first step toward creating a computer that has a structure similar to that of an electronic PC. Instead of using electrical signals to perform logical operations, these DNA logic gates rely on DNA code. They detect fragments of genetic material as input, splice together these fragments and form a single output. For instance, a genetic gate called the “And gate” links two DNA inputs by chemically binding them so they’re locked in an end-to-end structure, similar to the way two Legos might be fastened by a third Lego between them. The researchers believe that these logic gates might be combined with DNA microchips to create a breakthrough in DNA computing.

DNA computer components — logic gates and biochips — will take years to develop into a practical, workable DNA computer. If such a computer is ever built, scientists say that it will be more compact, accurate and efficient than conventional computers. In the next section, we’ll look at how DNA computers could surpass their silicon-based predecessors, and what tasks these computers would perform.

A Successor to Silicon

Silicon microprocessors have been the heart of the computing world for more than 40 years. In that time, manufacturers have crammed more and more electronic devices onto their microprocessors. In accordance with Moore’s Law, the number of electronic devices put on a microprocessor has doubled every 18 months. Moore’s Law is named after Intel founder Gordon Moore, who predicted in 1965 that microprocessors would double in complexity every two years. Many have predicted that Moore’s Law will soon reach its end, because of the physical speed and miniaturization limitations of silicon microprocessors.

DNA computers have the potential to take computing to new levels, picking up where Moore’s Law leaves off. There are several advantages to using DNA instead of silicon:

• As long as there are cellular organisms, there will always be a supply of DNA.
• The large supply of DNA makes it a cheap resource.
• Unlike the toxic materials used to make traditional microprocessors, DNA biochips can be made cleanly.
• DNA computers are many times smaller than today’s computers.

DNA’s key advantage is that it will make computers smaller than any computer that has come before them, while at the same time holding more data. One pound of DNA has the capacity to store more information than all the electronic computers ever built; and the computing power of a teardrop-sized DNA computer, using the DNA logic gates, will be more powerful than the world’s most powerful supercomputer. More than 10 trillion DNA molecules can fit into an area no larger than 1 cubic centimeter (0.06 cubic inches). With this small amount of DNA, a computer would be able to hold 10 terabytes of data, and perform 10 trillion calculations at a time. By adding more DNA, more calculations could be performed.

Unlike conventional computers, DNA computers perform calculations parallel to other calculations. Conventional computers operate linearly, taking on tasks one at a time. It is parallel computing that allows DNA to solve complex mathematical problems in hours, whereas it might take electrical computers hundreds of years to complete them.

The first DNA computers are unlikely to feature word processing, e-mailing and solitaire programs. Instead, their powerful computing power will be used by national governments for cracking secret codes, or by airlines wanting to map more efficient routes. Studying DNA computers may also lead us to a better understanding of a more complex computer — the human brain.

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DNA computing is a form of computing which uses DNA and molecular biology, instead of the
traditional silicon-based computer technologies. A single gram of DNA about the size of half inch cube can hold as much information as a trillion compact disks.

This field was initially developed by Leonard Adleman of the University of Southern California. In 1994, Adleman demonstrated a proof-of-concept use of DNA as form of computation which was used to solve the traveling salesman problem. In addition, Bernhard Yurke (Bell Labs) has developed DNA motors. Since the initial Adleman experiments advances have been made, and various Turing machines has been proved to be constructable.

There are works over one dimensional lengths, bidimensional tiles, and even three dimensional DNA graphs processing.

On April 28, 2004, Ehud Shapiro and researchers at the Weizmann Institute announced in the journal Nature that they had constructed a DNA computer from biomatter extracted from human feces. This was coupled with an input and output module and is capable of diagnosing cancerous activity within a cell, and then releasing an anti-cancer drug upon diagnosis.

DNA computing is fundamentally similar to parallel computing — we take advantage of the many different molecules of DNA to try many different possibilities at once. The number of possible solutions to a problem grows very quickly with the size of the problem, exhibiting exponential growth. For very large problems, the amount of DNA required will be too large to be practical. Thus, DNA computing does not provide any new capabilities from the standpoint of computational complexity theory, the study of which computational problems are difficult.

DUE  April 8, 2005

Overview of DNA computing applications (’98).
Implementing models for DNA computing: concerns from the lab
Implementing addition with DNA computation
A mathematical interpretation of DNA operations
A comparison between DNA computing and quantum computing.
DNA computing by splicing.
DNA computing by self-assembly.
Cryptography using DNA
Complexity measures of DNA computing.
The sticker model for DNA computation.
Computing Boolean formulas with molecules.
Design a DNA algorithm for a computational problem of your
choice.
Aqueous Computing
Watson Crick Automata

Instructions for Final Exam Report:

Your final essay should be of 1500 words. It should be of essay type(not just  title headings). No pictures necessary. The exam should be written in your own words . You should not use sentences taken from published papers or online resources. Failure to do so , it  is considered to be plaigirism and the penalty for that is a failing grade in the course and a possible expulsion from the university. You should also include the list of references(published articles) you used for the report. No online references are allowed.

Submission :
Please print your paper and put it in my mail box by Friday April  8 before Noon. NO online submission. Any submission after noon will not be accepted or graded.  Best to give it to me during class hours on Thursday if you have it ready.

I satirized myself in that last post. It sounds like a nightmare scenario but there is a lot of it that I find desirable.

5:00am on Tuesday morning. Frustrated with an overdue assignment that I thought would be simple. It is like a little pebble I am tripping over after climbing mountains. There are a bunch of complex, half-formed ideas and sentiments in my head that want to be expressed and purged but I’m too fried to explore them. I wouldn’t say my life is out of control right now but it’s moving at supersonic speed. When I came home today after my last presentation I loved the way my apartment looked. The vibrant, chaotic beauty of it. I wanted to savour and remember that image because I know I’ll miss it. I love the person I am now. I have truly surprised myself, back in January I really thought I was dead meat. I’ve achieved so much more than I thought I could.

Earlier I was taking a break in my dark apartment. It was raining outside and I felt drained and phased from all the work I’ve been doing lately. A kind of crash down from operating at such a high level for such a long time. I was just lying in my bowl chair in the dark and listening to good music that was accentuating my mellow mood. A large shadow shifted behind me and I knew something had just entered my apartment. I didn’t feel like moving to look though. And I know it was something very unusual. Maybe it sensed I wasn’t in the mood to pay attention to it.

My April calendar monkey is a vervet. He has a big furry white chest and a little black face. This one looks much different than the March Japanese Macaque who had a solemn, rundown look. Unlike the macaque, the vervet isn’t looking into the camera with sad eyes, he’s gazing off into the distance with an alert, focused expression. There is newly gained wisdom in his eyes and a determined set to his jaw. You can tell this monkey has been through a lot of shit and there is still more on the horizon. He can handle it though. He has a quiet confidence and passionate core that give him strength to persevere.

http://24.103.166.19:8888/Protein-Secondary-Structure-Display.ppt

Protein-Secondary-Structure-Display.ppt

I hate when the weather starts to get better. It makes working night shifts incredibly unbearable. I feel like a dark little troll. I used to revel in the sun. I used to be out in it all day long, everyday. l;kfjgkldgjoieguwoiugb

Since I know everyone wants to hear about it, I’m going to write about my haircut. I’ve been looking a little too much like Megaman lately. Sporting a large unkept mass of thick black locks that blows majestically in the wind. Like just about everything else, Megaman can pull it off (and with incredibly sexy results too). I needed something a little cleaner for my upcoming presentations though.

I went to the Gentleman’s Barber. The woman who did it is my least favorite on staff but she did a passable job. I like the Italian guys (if there’s one thing Italian guys know, it’s hair). My favorite woman wasn’t there. Too bad. I go there because it’s obvious that they take pride in what they do, only doing men’s cuts and really taking their time to do a fine job. They warm up the shaving cream and shave your neck and around the ears with a metal razor too. That’s the best. So much better than the place on campus where they shave you down in about five minutes and hustle you out the door.

Blah.. I can’t believe I actually broadcasted that I was listening to Chesney Hawkes on my last post. I like the hook but the soft synth interludes are cheesey beyond belief. I think it’s on my best of 1992 list. Some people have comfort food, I have comfort music that I retreat into during times of high stress. I’ll listen to club tracks with wicked hooks and the best tracks of 1980-1997, as previously and painstakingly chosen by me. I’ve decided that 1998 was the year that pop music got really crummy. 1999 was the worst year ever.

I think my posts are probably going to be pretty lame for a while. Burn out city. I coded most of the day. Still, I’m feeling fairly decent. I took the bike out for the first time of 2005, worked out and despite having some amusing quirks, my protein structure prediction program has actually started to work.

Happy Easter. No bunny trail this year unfortunately. No Easter chocolate either. My apartment is looking a lot like I am. Disheveled. Messy. Toasted. Sunday afternoon detox. Wicked headache. Likely due to stress and copious amounts of sugar and caffeine. Maybe it’s just dehydration. I was flying last night though. I’ll be ok, there be a brimming giant coffee right hurr.

I worked a crazy shift last night. I got some odd requests from the residents.  My favorite was received from a drunk first floor buisnessman calling from a bar. It was a panicked request to enter his unit and move all the beer from freezer to fridge to prevent explosion. He’s a nice guy, I didn’t mind helping him out. It was Sleeman’s Clear if you’re curious, wouldn’t have been my choice. Anyway, the supervisor is away and I’m being an even worse employee than usual. I wasn’t even pretending to do my job. I locked myself in (and everyone else out of) the exercise room and watched boxing. I flagrantly listened to Luna at the front desk. I neglected to do other more boring stuff (this has the potential to land me in a lot more trouble). Some school work got accomplished though.

Upon awakening yesterday, I was angry at myself for deleting Ms. Pacman. It’s good that I seized that moment of clarity and personal conviction because I wanted to play bad. What else. I hurt my vocal chords yesterday singing Just a Friend by Biz Markie in the shower. I’m enjoying my near eastern mythology lectures. The cannonites aren’t all that bad. They’ve got some funky gods and goddesses. Fallible sexual pagan gods are where it’s at. Hepcat.

My Thursday presentation weighs heavy on my mind cause the program I’m presenting still isn’t working. It’s reflective of its creator, there are some nice extra features but it still doesn’t do what its supposed to.