Tuesday, May 31, 2011

Journalism Meets Computing - In A Big Way

"You should go talk to that guy over there, Jonathan Stray, he is really interesting". That was all I needed to hear to set my feet zipping across the room where I plunked myself down on the floor next to Jonathan and, telling him he came highly recommended, asked if I could interview him for my blog. A momentary look of surprise crossed his face but he said yes. That was in March, during the Interdisciplinary Computing meeting I wrote about. Computational journalism was a hot topic and my source had told me Jonathan was a computer scientist who had entered the field of journalism. Cool. Very cool. So with little ado, we exchanged contact information and I happily planned for our conversation. We had that conversation a few days ago. Surprises awaited me.

I had a fairly standard set of  "get to know you" questions lined up until I started doing a little background investigation. I tossed out my original questions. I hadn't really paid attention to the affiliation on his name badge, but at some point it dawned on me (duh) that "ap" stood for Associated Press. Small moment of anxiety as I realized I had asked a Journalist (note the capital J) if I could interview him. I got over it. I started reading Jonathan's blog (link at end of this post) and realized this guy really is a computer scientist too. On one end of the spectrum he writes about such things as experimenting with putting his iPhone in the freezer to reset the WiFi (it worked - sort of) complete with technical explanation. I was right with him through the whole fascinating story. How often does someone write well enough to suck you into wanting to know the nitty gritty details of how to ice a phone? On the other hand, Jonathan also writes in his blog about about some pretty deep and serious cultural issues, describing what he sees so realistically that is almost creepy. I can't shake off one entry from Jakarta that juxtaposed prostitutes, people digging through garbage and blow dart sellers (blow dart sellers???) against fast paced sales of skin whitening creme by those (presumably with income) who wish they were White. I have traveled a lot, yet I was still stopped in my tracks several times by the implications of Jonathan's blog entries.

I guess I neglected to mention that Jonathan oversees a group of developers (yes, as in computer programming developers) at the AP who produce "interactives". I went and took a look and found the AP Economic Stress Index for the US. I was able to zero right in on San Diego County. This month, the Overall Stress Index is 13.79, the Unemployment Rate is 10.2% (ow!), Foreclosure Rate is 2.2% and the Bankruptcy Rate is 1.84%. At least it is worse in Los Angeles: Stress Index is 15.93%. The oveall rate in California is 16.9%. The only state to have it worse is Nevada, at a crushing stress index of 20.67%.

You can zoom all around the country and check out what is going on back to 2007 when the recession began. There is information to explain what it all means if you want to read it. What a way to tell a story.

How did this all come to be? 

It all started out like a "typical" computer kid story: the movie Tron was a pivotal moment, reading computer graphics textbooks in high school for fun, getting a degree in CS and Physics....an MS in CS...a developer job at Adobe....challenging, cutting edge technological work. Good money, good hours, good exposure.

Then Jonathan took some time off and went backpacking in Asia. He described to me that it seemed an "almost impossibly different reality" - how could such different cultures exist on the same planet? He started writing.

Came back to Adobe...then went backpacking overseas again. More writing ensued. It turned out that at the time, at the University of Hong Kong Rebecca MacKinnon was on the journalism faculty studying global online media policy, specifically, Chinese censorship of the Internet. That was too good to pass up: Jonathan enrolled in an MA program.

Cultural study, writing and developing information for the public good, technology.....

As if on cue, a job almost tailor made for him appeared at the Associated Press. What does Jonathan like best about his job?   The job requires he be right on the edge of what is possible in the constant evolution of technology and journalism.

There is a lot more to say about this. So I'm going to pause here, and pick up in the next post. Even if I did not feel compelled to share more about what I learned from speaking with Jonathan about the integration of computing and journalism, he himself said something that tells me I must. Sound bites. We live in a world of soundbites and too often all we get are soundbites. Not the full story. So... to be continued.

Jonathan Stray's Personal Blog

Wednesday, May 25, 2011

Surviving the Challenges of Personal and Professional Volunteering

I volunteer for a few organizations, one of which allows me to get into the mountains on a regular basis. I am a weekend host at a mountain lodge. Absolutely lovely and worth the occasional hassle. This past weekend I had hassle in larger numbers than usual. Dead mice played a part as did several people who felt they did not have to pay to use the facilities. We are not talking big bucks here. In fact, "extremely inexpensive" would be most accurate.

Spending several days in the woods, even when unexpectedly called upon to become a plumber, electrician, random trouble shooter or occasional Tough Guy (Gal), leads to regular introspection. This weekend I found myself thinking about the process we use to choose to take on "extra" activities, and how we decide when we have achieved a good balance. Taking on innovative professional projects often starts off as "volunteer service". We come up with an idea we just can't put down and we run with it. Eventually, if all goes well, the project blossoms, and becomes part of our portfolio of acknowledged and rewarded activities.

Many of the interesting interdisciplinary computing projects I come across start off as an idea that pops into someone's head and they run with it. The projects I hear about are usually the successful ones - difficult people were dealt with, project goals were achieved, peers, subordinates and supervisors are enthusiastically on board, and academic or business objectives are aligned.

But there are great projects that never gain traction.  In several recent cases I heard about, a critical reason for failure was "volunteer overload and burnout".  You have probably noticed that some of the most creative people take on more than their share of projects - because they have the ideas and energy. There is a delicate balance needed between taking on many exciting projects and not being driven to pull your hair out all at once.

Successful entrepreneurial and adventuresome types know their personal limitations: physical and emotional. They know when enough is enough and how to say "no more".  They know how to deal with annoying people who want to suck the lifeblood out of them. They have patience and are able to emotionally let go of the annoying lifeblood sucking people. They know when to ask for help: we can't simultaneously be spontaneous plumbers, electricians, maintenance personnel, stackers of wood, and gatherers of litter. We know when to call in reinforcements, or at least someone who knows how to stop the mystery leak.

Sometimes we have to catch mice. I had to remove 4 dead mice upon my arrival in the mountains this weekend, and do it before the guests arrived. Then I had to listen to the "snap" in the middle of the night as the mousetraps caught more mice - which I had to get rid of before everyone got up in the morning. I'm not a big fan of killing mice. In fact I'd rather not. This weekend, with the large number of dead rodents to deal with, and the couple of people who were determined to take advantage of my being a "volunteer", I thought about the importance of setting scope, fixing boundaries, goal setting and knowing when to let go of what is not really that important for the sake of the bigger picture. Just like my professional projects. No different.

Thursday, May 19, 2011

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.

Friday, May 13, 2011

Challenges That Should Not Be Challenges

An interlude....

Earlier this week, I dropped in on someone I know well who, along with another person, was using a business application. Both are "typical" users in the sense that they use software to accomplish business tasks and that is the extent of their interaction with the computer.

As I walked in the room, one of them pointed in the general direction of the printer and told me they had been having trouble getting "that" back in place - I couldn't quite see what they were pointing at and in a light hearted way I said "Have you tried closing your eyes, giving it a kick and hoping that nothing snaps?". The reply was an amused comment about how that just might have to be the next step.  But there was an underlying frustration there. A short while later they finished up their work and took off. After taking care of what I needed to do I took a look and the problem was that the top cover of the printer paper feed was out of the printer and they were having trouble putting it back in place. It was a matter of a second or two and I popped it back in. That same day I was labeled the "go-to" person.

This got me thinking...we have been having some serious conversations here about interdisciplinary applications of computing, yet there remains a huge gap of basic .... something. I'm not sure it is knowledge. I'm not sure what exactly it is...I have been searching for the right phrase. I'm still working on it.

But there is a connection here and I'm grasping for it. I'm thinking....when we talk about interdisciplinary computing...when we talk about helping people...I'm wondering....what can we do in an interdisciplinary collaboration that will make computer systems and their basic (to many of us) operation less confusing to those who live in very different worlds? Popping the paper feed cover on was trivial to me; I knew instinctively the angle and direction to hold it. The operation was certainly not trivial for them - and they run a very successful business - smart, educated, thoughtful, savvy people.

First we (I) need to get a handle on how to describe the issue. It isn't "computer literacy" or "digital literacy". I think it is something different. But I'm convinced there is something here, very fundamental, that needs to be tackled - for adults. Adults who have their productivity disrupted by challenges that should not be challenges.

My antennae are vibrating all over the place that there is something important ...

Monday, May 9, 2011

Interdisciplinary Computing Meeting Number 2: Day 2, Part 2

This is my last direct report post about the meeting, although I hope to follow up with some interesting related posts that came out of this meeting. In this post I'm going to list some of the "hard questions" that stakeholders could ask about Interdisciplinary Computing (IC) development. These questions came out of one of our breakout sessions. I have several pages of questions, so I'll pick some representative interesting, challenging or just plain important ones.

Our group was trying to come up with the toughest questions that anyone considering IC development should be prepared to answer. In a few cases I will suggest starting points for answers, but in most cases I leave it to you to ponder. The answers will need to be tailored to who is asking the question and in what type of institution the IC program/course is being considered. I hope that if you grapple with these questions you will be inspired to think outside the box and feel inspired.

I will end with a few reading recommendations given to me at the meeting. I have not read these books yet, but they are high up there on the list; I'll share them now and we'll see how they turn out. If anyone has read these books and has comments, I'd love to hear them.

First. Who are those IC stakeholders? They include: Administrators (of various types), Industry, Parents, Faculty, Students, Alumni, Governance agencies (Legislators, Accreditors)

Possible Questions From Administration: 

Question: What is the impact on the department(s), major(s), what is the cost for equipment, resources of developing an IC course (not even a program)? Multiple questions rolled into one....

[Answer could center on this point (and data will need to be assembled to back it up): We will increase the enrollment to the institution. We will not just shift students from one area to another. This statement can then be expanded upon to address all the sub-questions (impact, costs etc)]

Question: How does IC fit into high stakes testing? How does it fit into existing standards, mandated or currently culturally accepted?

Question / Problem From Industry: What happens if an industry panel gets together and says "no, we aren't going to hire your students, we don't like what you are doing".

[The response would involve improved communication between those developing the program and industry and getting a handle on where this statement was coming from.]

Question from Parents: What is the ROI (Return On Investment)? What exactly is my child going to be when they graduate? What kind of job are they going to get? What is the time to graduation? [more multiple questions coming back to back but all centering on the first piece - ROI]

Question from new Faculty: How am I going to get tenure? Where will I publish?

Question that could come from a variety of sources: How does this contribute to workforce development? Prove it (the economic development the IC course/program will produce).

Problem / Question: IC programs are for people who can't hack it in either discipline.

[I personally have heard this one said. It represents an entrenched pov based not so much in any factual evidence but on personal opinion. That makes it challenging to address. But addressed it must be]

Things to chew on.

Now for the book recommendations. Uplifting, gets my intellectual bookworm instincts going full steam and a good way to finish this post:

"Innovator's Dilemma". Looks really interesting. There are two follow up books that look interesting as well: "Innovator's Solution" and "Crossing the Chasm". I'm looking forward to sinking my teeth into these. The orientation appears to be towards business rather than academia, but from perusing the first book quite a bit online, it looks like the principles could well be transferable. And check out the TOC - definitely not dull.

"Creating Interdisciplinary Campus Cultures". Now this one is definitely aimed at academia and looks like it might have some very practical suggestions. I can see reading Innovator's Dilemma and then this one. A possible interdisciplinary synthesis of perspectives and ideas.

Have a nice Tuesday.

Thursday, May 5, 2011

Interdisciplinary Computing Meeting Number 2: Day 2, Part 1

The second (and final) day of our meeting was jam packed. I need a giant suitcase to contain all the notes I could write about our discussions. So... I'll start again with some of the items that jumped out at me from the day.

  • Interdisciplinary need not be (as some have feared) a zero sum game. In fact, Interdisciplinary Computing (IC) can change the zero sum game (either you go into field X or field Y). With IC, one department does not lose students to another department ("student stealing"). Quite the opposite. Programs that implement IC programs, minors, (or the variety of forms I have discussed previously) often result in students having a foot in multiple departments. Depending upon how an institution calculates FTE  a student may be counted towards FTE in more than one department, thus giving "credit" to both departments - a good thing. (FTE = Full Time Equivalence, or to the layperson: a calculation of how many students are considered to be in class/department/division/school. FTE numbers often have a powerful effect on fund distribution, hiring etc.).
  • Here is an interesting observation: look at the National Science Foundation Discoveries site. This is a site where the NSF highlights innovation; most of the featured projects are IC - computing and another science. 
  • Big Science and Small Science. These terms were introduced and there was a bit of a discussion about what they mean and the implications. One table (I was not sitting there) later spent time discussing the topic in detail. But from the more general discussion, here is the gist I came away with. It started when someone posited the idea that computer science projects would more likely be "small science", i.e. local projects that produce a lot of data; "large science" (aka "long tail science") projects are large multi-institutional / multi-group / multi-person projects such as those conducted by NOAA (National Oceanic and Atmospheric Administration). The "problem" would be that larger projects are more likely to get large funding, and thus dissemination. What to do?
I'm not sure I totally buy this definition and the gloomy conclusion. There are certainly computing projects that obtain multi-million dollar funding - when I was working on my PhD some faculty I knew received that kind of funding. And even if we are talking smaller funding levels, I think multi-institutional grants of $500,000 or $1,000,000 are nothing to be sneezed at and can certainly produce results and wide dissemination. Those are available. I was recently one of several PIs on a grant in the first category. Sure it helps to be a government agency, but one does not have to be one in order to get your results "out there". You may have to work a little harder at dissemination, but there are channels. And in fact, sometimes, you know exactly who the groups are that have an interest in your type of work and can target them in a direct semi - personalized manner. And we haven't even mentioned the fact that Industry is working on IC projects and they have their own mechanisms for dissemination, sometimes working with academia, and other times going it alone.

But really, the question is: Why is "small" vs. "large" important for a discussion of IC? Our conversation turned to how small science (let's say 2 departments such as CS and History working together) can leverage large science. NASA, Historical Archives and a variety of organizations make large amounts of data publicly available; these data can be used and added to at the local level. Perceptions of both fields can be changed and information made available that otherwise might gather dust. Here is a great example: check out this project, which one of the meeting participants is working on: Digital Durham, a fascinating integration of computing and history.

Arg. I'm out of space (assuming the general protocol of not making a post tooooo long). To be continued...

Monday, May 2, 2011

Interdisciplinary Computing Meeting Number 2: Day 1, Part 2

In our afternoon discussion of faculty motivation for interdisciplinary computing (IC) I learned several interesting things. First the small but amusing: we had been flinging acronyms around quite a bit, and at one point someone used UTA right in the middle of a sentence. No one asked what this meant so I was brave. UTA: Undefined Three Letter Acronym. Cute.

Some food for thought items came out of the motivation conversation that addressed the questions (what is motivating about IC, how to support it) in a memorable way. I'll start with those.

 - "The transaction between 2 people in different domains is what makes each one better informed and knowledgeable." This might be taken as a a given, but it is interesting to consider it under the realm of "motivation". The affective side our reactions is often as or more motivating than the cognitive side of our reactions. If a synergy develops between two people discussing, brainstorming, and creating, then yes, this can be exciting (an affective response) - hence motivating.

- "It's data; it's representation. The domain doesn't matter". There were some interesting examples of this, such as all the ways to represent data in a form other than rows and columns or bar graphs. We saw a magnificent and beautiful simulation of what happens when people get into an elevator. Apparently this has been studied quite a bit. There are definable patterns of behavior that have a very mathematical predictability. The more data (people) you add, the more interesting the scenario gets. The collaboration was between CS and Art. We watched a colorful square show how people realign themselves as more people enter the elevator. For example, at first one or two or three (ish) people arrange themselves equidistant to one another. Then as more people enter, people spread out towards the walls, leaving a central open space. As more people enter, there is a shuffling around until everyone has almost exactly the same amount of space between them and are fully distributed through the elevator.

Now here is the even cooler part. If you REALLY want to make someone uncomfortable,  move over next to them - we watched this on the simulation as the little colored dots shifted around. If you do this, the other person will immediately try to reposition to regain their equidistant space. This can set off a domino effect of the entire elevator realigning itself.

Later on, a friend and I got in the elevator and watched people's behavior and yes, all of this was absolutely true. It all seemed to happen without anyone consciously thinking about it. We had a little conversation about whether or not we should test out the last part of the theory by engaging in conversation while casually moving closer and closer to someone. But we didn't carry through on that.

The elevator simulation was just one engaging example resulting from close collaboration and the synergy it produced.  It could not have been developed without the art and cs faculty in close communication.

Originality: One of the meeting participants gave us a short demo about teaching algebra using a rope. Someone suggested obtaining a video of the performance and posting it on YouTube. I sure hope that happens; I'll link to it. Hard to describe but the basic idea is that knot tying can demonstrate algebraic concepts e.g. "single instruction, multiple data = sheep shank". The premise is that math can be mapped onto many different systems; in this case the system was a rope. I'm telling you, the math concepts stuck in my head better than I ever remember from dragging my way through theoretical descriptions and chunking through example after example of plugging in numbers. We, the group, were transfixed and the presenter was clearly enjoying himself - very motivated.

We focused much of our conversation about Action Items (to support motivation for IC) in breakout groups. There are far far more than I can list here; some of them made it into my previous post. Many of the ideas related to putting in place support mechanisms to ease logistical hurdles (geographic, fiscal, advancement/promotion, departmental assessment/accreditation mechanisms, etc). The list was long. The ideas varied from top down to bottom up. Just to give you a flavor, here is one top-down item: Because they have clout, organizations, leaders, funders should voice public support for IC;  people who otherwise might not listen, will often listen if the message comes from someone in a position of respect and authority. One bottom-up item: hold a mashup of people who come together to discuss and address an issue: get them all in the same room to attack a given problem. (Sort of like what all of us were doing)
To try to sum up (a difficult task): An overarching action item: Develop a Framework of how to solve IC problems.