Better Living With Computer Science

A bubbling frothy mass got me wondering

Why do so many people still think that "Computer Science" means fixing a broken computer? 

Why do so many people think that teaching "Computer Science" is the same thing as teaching keyboarding (e.g. typing on a keyboard) or word processing? 

Why do so many people not understand the significance of the questions? 

Sigh...

After all this time, I still get looked at with disbelief and dismay when I say I am not the best person to upgrade someone's neighbor's friend's relative's new operating system or that I'm not the most qualified person to take apart your printer. I mean sure, I'll be happy to take apart your printer.  But you may not be happy with me doing so. Assuming you want the problem, whatever it is, guaranteed fixed and all parts back in their correct places and functioning properly.

I willingly throw myself upon the mercy of the repair guy or gal when my motherboard pukes or my external drive locks up or my video controller goes psychedelic. I do have an advantage in that I can generally figure out what is going on ("oh crap, the xyz controller has gone belly up"), but that doesn't mean I am going to put my sticky fingers in there to mess with it. With or without a magnetic screwdriver. I want everything back in one place and better than functional at the end of the day. Instead, I call in the pros.

But I'd never ask that same repair whiz to develop a pedagogically sound online tutorial, or lay out the requirements for an enterprise software system, or develop an effective computational biology DNA algorithm. The repair whiz would likely think me slightly deranged for asking.  

We go through high school classes in chemistry, physics and biology and we come out understanding a few distinctions between chemists, physicists and biologists. For the most part we have at least a basic understanding of what chemistry, physics and biology are because we have taken classes in those topics.

I was watching a strange concoction burbling on the stove the other day. I pondered that I was watching chemistry and physics in action: burble burble the molecules interact in order to boil in a certain way, the electrons bounce around, the foam develops and slithers around.The Pyrex nicely distributing heat from the element is the result of some darned smart chemists. I recognize the relationship between chemistry and physics in front of my eyes. And the biology involved with my quivering nostrils and soon to be activated taste buds.

I am a Computer Scientist. Also at times a Mad Scientist (and proud of it). I'm not a Chemist or Physicist even though I can cook. Doesn't it sound crazy to even suggest that?

Perhaps we need to teach Computer Science in high school along with Chemistry, Physics and Biology?

Genetic Sequencing, Bio-Informatics and Computing

Today I obtained a new view into the world of bio-informatics when I had a chance to speak with someone who works in the field. This person is not a computing professional but was able to explain to me some of the interesting work in the field that relies on computing. With her assistance I located a company that does some of this work (link coming below). I gathered much of this information over a breakfast meeting and sometimes my coffee, granola parfait and egg (separate plate) got cold as I scribbled notes like mad on the seat next to me. On the other hand my freezing orange juice warmed up while I was writing chewing and talking.

There are many different areas of bio-informatics - huge field. Interestingly (perhaps not surprising) the medium to large sized companies employ many computing professionals who are cross-over people. For example, in one major company my breakfast colleague knows about there are three computing groups under the umbrella of a Vice President: "traditional" IS/IT support, a bio-informatics group and a software development group.

For a company that studies or supports the study of genomes, there are lots and lots of data to manipulate and crunch. Typical customers of such a company are academic researchers in a hospital setting, researchers in federal agencies such as the CDC or NIH, and corporate entities including pharmaceutical companies, bio-tech companies and diagnostic companies.

What do they want to accomplish? One angle is to study a gene, or a biomarker, to try and understand better how it works. The researchers may want to cause a particular gene to do more of what it naturally does or to turn off a particular gene (cause it to stop doing its job). The term used a lot in this type of work is Polymerase Chain Reaction (PCR) which, very simply put, means to amplify a region of a genetic sequence so that it can be detected and manipulated. Another angle of research has as its goal to figure out if a specific gene has an error in a particular (living) population - related to a pathology perhaps. Cancer is a classic example. There is a lot of bio-informatics terminology that I am trying to avoid using, but to use the official terminology as it was explained to me in this instance, people in the line of work we are discussing are trying to identify what the nucleotides are in a particular region of a gene, which will then be used as primers in sequencing. Yes, a mouthful if that isn't your field. If you are still with me you get brownie points.

Computing is the backbone that allows this kind of work to take place, because the clients referred to above want to order specific sequences of DNA for analysis. A company such as Integrated DNA Technologies (the example company I located) supports researchers who are studying genomes by (among other things) providing the genetic sequences needed by those researchers. It has been a loooong time since this was done by hand - with what we know now and the data volume we have it is unimaginable. Forget the row of people in white suits pouring things in and out of test tubes (they may exist, but not for this task). There is an entire computer driven manufacturing process to synthesize desired genetic sequences in the most efficient manner possible. These sequences may need to be highly customized.

Let's say an order comes in for 100 oligonucleotides (a short sequence of nucleotides, which are the basic building blocks of DNA and RNA). Each of the 100 requested oligonucleotides is 20-200 nucleotides long and each one is different. There are banks of computers that have programs to synthesize (create) these oligonucleotides. Not only must the software determine the correct chemicals, the timing of their use and the stability of the result, but the software must also recognize that load balancing is required; the heavily customized sequences slow down the process and are generally forked off to another process along with other similar desired sequences. This can lead to orders from several clients being created together on one "plate". There might be 5 orders of 100 oligonucleotides that are distributed across the system at the same time in order to provide accurate and timely creation.

Eventually the software must take the end results and regroup them for the appropriate customer. Every step of the process involves complex algorithms, timing, QA checking, load balancing and rebalancing and did I say LOTS of quality control? Heaven forbid a customer received a different genetic sequence than they asked for. Someone (lots of someones) has to know their software system optimization techniques as well as their chemistry.

A different computing dependent activity IDT is involved in is providing the software to help customers design the oligonuclotides they want. Double stranded DNA can be several thousand base pairs long and the customer wants to determine where in that genetic sequence is the best place to make and attach (or detach) an oligonucletide. Software provides the ability to evaluate the characteristics of a given oligonucleotide (there are many factors involved). The software can predict the specificity, the stability and the cross-reactivity / structure of potential candidates (I'm getting tired of typing out the "o" word - I'm bound to mis-type it if I haven't already). The customers can use IDT's SciTools to help them decide what request to submit for manufacture.

These tools have to have all the hallmarks of any well designed and constructed s/w application - an easy to use UI for the target customer, efficient processing and logical functionality. The inner guts have to have the usual features including: bug free, flexible, sufficient, robust and responsive. Who is most qualified to design these applications? You guessed it - (interdisciplinary) computer scientists.

IFF Computing == Cabbage

I am periodically asked "what is it like to write a book?" If you have written a book you may be having a small laugh to yourself all of a sudden. A sort of evil chuckle. Because you know, .... well, I don't need to tell you. It takes you over in strange and wonderful and unexpected ways.

You probably also know that no matter what you say it may not convince the conversant that conceiving cognitively comprehensible and convivial concepts takes considered concentration. Even if you say "it is Computer Science!" (people often assume fiction for reasons I know not why) there is ofttimes a clinging to the concept that you must spend much of your time continuously cavorting. Come again? If we waited to compose for when we felt suitably inspired by The Muse ... my Editor could conceivably consider calling out the Costa Nostra (uh, just kidding...right, Randi and John?)

Perhaps my more-often-than-usual far away look, prompted not by my new glasses so much as by a looming deadline, brings on the question with greater frequency lately. However, I find myself contemplating a different question: "How do you know when you are really and truly becoming one with interdisciplinary computing?" (with which topic my book most certainly is concerned).

I have the answer. It came to me this evening as I took a break and sat looking out over a neighborhood canyon just breathing calmly. Even in stillness, everywhere I looked I saw things that reminded me of a computer. "Canyon - how lovely...oh, Canyon starts with the same letter as Computer." "Critter poo on the sidewalk leading up to the bench....Critter reminds me of Computer". "I Cannot see the stars because there are Clouds in the sky. Clouds? Computer!" "Concentrate on your breathing ...Concentrate. Concentrate. Computer Computer Computer".

A Colleague gave me a red Cabbage from their garden. Oh my gosh that was good - a fresh Cabbage tastes like Candy Compared to Cabbage from the grocery store". Candy? Compared? More "C" words! Cabbage. Is an excellent source of Vitamin C and beta-Carotene. Consuming large amounts of Cabbage reduces the Chances of getting Colon Cancer because it Contains Chemicals that protect Cells against free radicals. All those words Commence with the same letter as COMPUTER! Perhaps I have passed the threshold and am now officially (Crazy?) Coalescing with interdisciplinary Computing and Computer science and Computational thinking.

The Cabbage Convinced me. Computers are truly everywhere. All you have to do is Consider it.

Software and Art Authentication

I spent a few days up in the mountains unplugged. However, technology has an interesting way of creeping in even with the cellphone turned off (reception is unreliable anyway) and the laptop stowed. And I'm not going to talk about the visiting electrician who suggested that I test a 9V battery by licking it (he found this quite amusing, but I declined).

First, I was reading one of my alumni magazines and there was a story about a physicist who used software to examine highly controversial paintings that might or might not have been newly discovered Jackson Pollack works (full story here). The physicist, Richard Taylor, uses software to discover the presence of fractal patterns. Apparently, according to his research, true Pollack paintings are fractal filled. Benoit Mandelbrot agreed. Taylor also determined that fractal patterns reduce our stress levels. Interesting. (Has anyone investigated the effects of meditation while looking at fractals?)

There was a lot of money on the line in this particular situation, and apparently the politicking and public flame throwing were severe. As Taylor said in his article: "For the first time, computers were playing a significant role in determining the fate of artworks". The project was kept secret in order to protect its objectivity as well as Taylor himself. The full story reads a bit like a spy thriller. At one point he was advised not to go outdoors in case a bird dive bomb his head; at another point he was advised to he leave the country for a short while! Eventually his analysis, later supported by other evidence, determined the paintings were fakes. (This was about the time he was told to flee to New Zealand). The process of using software to analyse fractals in artwork is now legitimized and used by many researchers.

Reading this article caused me to think of a similar activity on a smaller scale and closer to home. My father (who passed away in 2009) was an archaeological chemist and spent hours on end sitting at his computer developing FORTRAN code to analyse art. Over the years, he was called upon to authenticate ancient ceramics, paintings from the Middle Ages, and was always glued to stamps (he'd appreciate the little joke). Although the culture of ceramics and artwork is interesting, it was his analysis of stamp forgeries that was most unique as far as I (in my admittedly biased position) could tell. He was always programming programming programming and peering at these little bits of lines and ink. I never got to see his code, and I suspect it is now lost, but I'd give a lot to know more about what he was doing. Over the years I would periodically be ordered off on a mission to obtain some obscure piece of software that he wanted to use, or to locate a specific piece of share-ware that he had somehow learned about. Fortunately he published more articles than I could ever read and a few books, so I can read his results even if I cannot see the code that produced it. If those subjects interest you too, here are a few books: on ceramics (here and here), stamps (here and here)