Tuesday, November 29, 2005

TiVo + iPod = Networks + Lawsuits = Stupidity

Just the mention that TiVo was planning to make it easier for owners to transfer video from their boxes to iPods was apparently enough to freak out some TV networks (see the link to a iLounge article, from title). Right now, people can transfer programs to their PCs and watch them there or burn them to DVD. Or, someone with a VCR can tape a TV show. What exactly are the networks trying to prevent? As one of the commenters to the iLounge article says:

Look, I WANT to watch yoru [sic] shows. STOP TRYING TO STOP ME.

Sunday, November 27, 2005

Calculator math

I guess I can laugh while reading the post at Tall, Dark, and Mysterious, linked from the title above, because my wife and I plan to live in our daughters' high school classrooms. Seriously. Right now, our younger daughter is in a K-6 program that requires at least 80 hours of parent participation each year. We expect to continue this, resorting to bribery if necessary. And can anyone explain the appeal of a graphing calculator, anyway? If you really have a problem that requires an electronic aid to make graphs, it seems to me the a calculator will not be much help; you'll need something more like MATLAB.

I also plan to subject any boy who comes within 10 feet of either of my daughters to a polygraph and urinalysis. There will be time enough for dating in their 30's...

NSF Grant proposal: Draft Complete

It's amazing what you can do when you single-mindedly neglect your other responsibilities (translation: I've got a lot of grading to catch up on). In this case, what I have is a first draft of the grant proposal. The project description is 22 pages of 12-point type (as opposed to the NSF limit of 15 pages of 10-point type), double spaced. It will eventually get edited down to the right size, hopefully without me having to reduce the point size (after all, it's all about making things clear and easy to understand). The final organization even came out pretty much the same as I anticipated. Since I started out writing this by outlining the plan of what I wanted to do, the budget is worked out, and it can now be circulated within the campus, at least, for comments and approvals. Locally, the most important things are what I commit the university to support (things like course releases, or teaching specific courses in specific time frames) and what my budget looks like (since the university assumes fiscal responsibility).

The feedback I get, including two or three letters of support, will figure into the editing of the project description. Then, there will be the final "compression" down to 15 pages.

Topics: , .

Wednesday, November 23, 2005

Thanksgiving cooking

It's the day before Thanksgiving, and I'm ready for some serious cooking. I like to slow roast the turkey; I think it comes out much juicier and more tender (falling of the bone). As usual, we went to the supermarket, bought $25 worth of groceries to get the discounted price on the turkey, and then asked for the biggest they had: 24 pounds. At 300° F, this bird would take six to eight hours or so to cook. Instead, I want to cook it overnight at about 190° F: the desired internal temperature when it's done (to ensure all bacteria are killed). The rule of thumb I have from Let's Cook It Right is three hours at reduced temperate for each hour it would have cooked at the higher, conventional temperature. So, assuming I'll roast the turkey for an hour at the start and two hours at the end at high temperature, and using eight hours as the cooking time, I get a total cook time of 18 hours. I'll start it around 10PM tonight. What fun!

If you're going to the trouble of cooking turkey for Thanksgiving, you simply must make your own gravy. There's simply no comparison between home-made gravy and store bought; it's worth the trouble. Here's a recipe modified somewhat from the November 2002 issue of Sunset:

Giblets, neck, and liver from turkey
2 onions, peeled and quarters
2 carrots, peeled and cut into 1-inch chunks
3/4 cup celery
approx. 2 quarts broth
1/2 cup corn or potato starch
Salt and pepper to taste

Chill liver to add later. Put giblets, neck, onion, carrots, celery, and 1 cup water in 6 qt. pot. Bring to boil; reduce heat and simmer 15 minutes. Uncover and stir over high heat until liquid evaporates and contents are browned and begin to stick (15-20 minutes).

Add 1 qt. broth and pepper; stir to free brown bits. cover, reduce heat, and simmer, stirring occasionally, until gizzard is tender (1 to 1.5 hours). Add liver; cook 10 minutes longer.

Strain mixture into a bowl. Remove the meat from the neck and chop the meat, giblets, and liver. Discard the bones and vegetables. Measure stock and add broth to make 1 quart. Combine everything into unwashed pot.

When turkey is done, remove rack and bird; skim fat from drippings. Add 2 cups broth to roasting pan and stir over low heat, scraping brown bits free. Strain mixture into pot with stock and bring to a boil.

In small bowl, blend starch and 1/2 cup water. Add to stock and mix until boiling, 3-5 minutes.

Topics: , .

Creek Running North: Another career-limiting post

Chris Clarke writes one of the most literate and eclectic blogs out there, and the post linked from the title above is hilarious! I was also impressed by his pruning poetry, though I think December is a bit early to prune fruit trees, isn't it?

Sunday, November 20, 2005

NSF grant proposal: Organization

In this entry, I will summarize how I'm organizing my proposal. The primary reason for me writing this is to help me think out the proposal; I'd appreciate any comments you might have. If you find this useful in some way (even as a negative example), good for you. The purpose of a grant proposal is to convey to the reviewers a clear and precise understanding of what you want to do, how you will do it, how it extends the state-of-the-art or the state of our underderstanding of the natural world, and what additional benefits the work will have (what the NSF calls "broader impact"). Call me naive, but I don't view this as a sales job, but rather as an exercise in clarity. The starting point for this is the set of instructions for writing grant proposals; for the NSF, this is the Grant Proposal Guide (GPG), NSF 04-23 as of this writing.

If someone writing a proposal can't even follow explicit preparation instructions, how can you trust him or her with money to do work that is merely promised? This is the question that has run through my mine when I've been reviewing proposals. The NSF GPG contains explicit instructions on the organization and content of a grant proposal. If the NSF program you're applying to says to prepare the proposal according to the GPG, then read the GPG and do what it says. Think of it this way: you are not awarded points for organizational creativity. This is an exercise in efficiently transmitting information to a group of people who may be in fields only tangentially related your own and who will be reading a couple dozen proposals. Have your proposal stand out because it gave the reviewers what they wanted without extra effort on their part. Not everyone does this.

The full proposal should present the (1) objectives and scientific, engineering, or educational significance of the proposed work; (2) suitability of the methods to be employed; (3) qualifications of the investigator and the grantee organization; (4) effect of the activity on the infrastructure of science, engineering and education; and (5) amount of funding required.
    -- NSF GPG
There are some basic requirements regarding formatting. In my case, I use LATEX, and so all of the basic formatting (margins, etc.) is taken care of for me and I can concentrate on content, in this case of the Project Description (everything else is either simple stuff, like a brief bio, or derived from the Project Description).

The Project Description is limited to 15 pages, not including references (which are a separate section). So, I'm not going to present an exhaustive review of the relevant literature, which is a relief, since that would be a very large book in my case, covering neuroscience, information theory, and nonlinear dynamics. As it is, I will need to be brief to cover the basics and still have room for a complete description of my research plan, methods, and broader impact. These are the key parts: what are my objectives for the proposed work, how these fit in with my longer-term objectives, how these fit in with the field in general, specifically what do I propose to do, and how will I do it. I need to address the matter of broader impact "as an integral part of the narrative"; in other words, not as an afterthought tacked on because it's required. In my case, and after some thought and reorganization, the sections will be:

  1. Motivation and Background
    1. Biological Significance and Motivation
      1. Effects of Noise and Jitter on Neural Responses
    2. Nonlinear Dynamical Significance and Motivation
    3. Biocomputing Awareness
  2. Goals and Objectives
  3. Detailed Project Plan
    1. Physiological Neuron Model
    2. Simulation and Analsysis
    3. Training and Outreach
    4. Project Schedule
Note that the goals will appear twice: once at the beginning as an introduction to the entire proposal and again, in detail, after I've covered enough background and motivated the work. In this case, the background is biological, mathematical, and pedagogical. I need to justify that this is an important biological problem and that the mathematics to be used (models and techniques) are appropriate and interesting. I also need to show that introducing students at my school and in local community colleges and high schools to biological applications of computers will benefit them and CS by showing that it's not all hacking away at a computer by yourself: that computers have an impact in a range of interesting and exciting fields.

Anyway, this has probably gone on long enough. I need to make a pass through the document, get everything in the right place, write introductory and transitional material, and trim down what I already have on methods and preliminary results to the essentials.

Topics: , .

Thursday, November 17, 2005

NSF Grant: Background

In this series of blog postings, I'm going to summarize my process of going from early draft to final product in preparing a grant proposal for the National Science Foundation's Mathematical Biology Program. We'll see if there is any value in doing this after the fact. In this post, I'll go over the background behind the proposal, including both a vague outline of the science (non-technical, so I'll dispense with references) and the basics of my proposal preparation process (such as it is) to date.

It's often said that preparing a grant proposal can take six months to a year of work. I'm sure that some people actually spend that much time focused purely on developing a proposal, but that doesn't seem a very attractive way to spend my time. Instead, I've spent my time (well, yes, more than 6-12 months) actually doing research. At this point, I've got a firm understanding of the biological, dynamical, and computing/theoretical basis for my work, I have preliminary results that demonstrate that I can do the work and that this is at least a feasible line of inquiry, and I enjoyed the process. One of the reasons you go into academia is to do research; why spend maybe 1% of your life merely working on proposing to do research? Of course, if you need a billion dollar spacecraft to do your research, then things (such as your planning time horizon) are a bit different. Computer scientists are, by comparison, cheap dates.

So, what's my research on? I want to understand brains as computing devices. Now, this is a tall order, so I've personally "settled" for trying to understand how very small networks of nerve cells (neurons) do their thing. You may have heard of all sorts of exciting results in the neurosciences, and how researchers are closing in on the secrets of the brain. Couple this with the first, real non-industrial commercial/near-commercial robots, and it really looks like we're close. I'm not so confident of that.

First of all, progress in robotics is misleading, because most of it is in sensors, actuators, and processing power. Little of it derives from any deep understanding of biological information processing. On the other hand, it is certainly true that we have entered a golden age in the neurosciences, with an amazing array of tools that allow us to gather all sorts of information about brain, network, and cell function. You may have seen "pictures of the brain working": functional magnetic resonance imaging (fMRI) that shows how active different areas of the brain are while a person does some task. This is often accompanied (for non-technical consumption) by an article that talks about how much this tells us about how the brain works. OK, I'm contrary by nature, but in my opinion this tells us very little about how the brain works. Yes, it narrows the focus of our inquiry from the entire brain to maybe 10% of it. Yes, it tells us something about which areas are active at the same time, and even sequences of activation in time. But we're still talking about the activity of hundreds of millions, even billions, of neurons. To me, this is just the peeling of the outer skin of the onion.

I don't want it to seem that I'm saying that these investigations aren't worth it or that they don't produce great data; they do. It's just that the brain is so incredibly complex: the most complex object in the known universe. A research data flow of petabytes per year over decades may only scratch the surface of what we need to learn before we understand how the brain works (assuming we're capable of assimilating so great a flux). This complexity may very well extend to the smallest level: while many researchers consider individual neurons to be simple devices (in a computational sense), this is really just an assumption. The fact is that a good simulation of a neuron, including its shape and the interactions of its internal molecular machinery with its external electrical and chemical activity, is a job for a hefty supercomputer. If this structural complexity shows through to a neuron's computational complexity, then we're suddenly dealing a brain as a complex network of billions of supercomputers.

There's so much complexity in nervous systems that entire aspects of them are almost ignored, or at least given second-class status in the search for understanding. Just one example: I've mentioned nerve cells, or neurons, as making up nervous systems and brains. But there's another class of cells that's actually more numerous in our brains: glial cells. They're usually dismissed as serving only structural and physiological functions: scaffolding and waste disposal. But they can produce external electrical and chemical activity. What does it do to our view of neural computation if glial cells play an important role?

Anyway, my research focus for this grant proposal is on error correction coding: looking at how characteristics of the output of one neuron could be used to allow other neurons to recover faster if an error occurs. Think of it as the neural equivalent of a CD still being playable despite the fact that it's scratched. This is small enough scale for me to be able to wrap my mind around it. Whether this is reflective of the true complexity of the subject matter, or merely the complexity of my mind, is another story.

So, back to the grant proposal. I know what I want to do, I can explain why I think it's important, I can relate it to biology and mathematics, and I have a lot of material I've already written about the subject (four conference papers and a journal paper). Writing should be a piece of cake, right? I give myself three months to do it, working part-time, of course (I still have teaching and a journal paper to finish writing while I'm doing this). More on this to come...

Topics: , .

Wednesday, November 16, 2005

In defense of academic blogs

Rebecca Goetz, a history graduate student with an "academic" blog, has an article in The Chronicle of Higher Education (linked from title) rebutting the two articles written there pseudonymously by "Ivan Tribble". And what she says makes perfect sense to anyone in academia with an actively maintained web presence: blogs (and the like) are fun, they are an outlet for thoughts that are either not ready for formal (reviewed) publication or not intended for that kind of venue, and they allow us to network with colleagues who we are unlikely to have met in any other way. I have some additional thoughts about academic blogging, and why it shouldn't be controversial:
  • I guess it never occurred to me that some people would look askance at blogging because computer scientists have had on-line presences for such a long time. Go to any CS department's web site, and you'll almost certainly find links to faculty sites with personal sides (photos of family, discussions of recreational activities, semi-academic hobbies, etc). Even before the web, academics (grad students and faculty) participated widely in both academic and non-academic oriented USENET newsgroups.
  • Blogging is enjoyable, and it's enjoyable writing. Anything that increases the amount of writing we do seems worthwhile to me. The fact that the audience is not as specialized as one's academic peers (to whom one writes in refereed publications) is even better, as it demands a level of clarity and transparency of explanation that might even improve one's "serious" publications.
  • One academic fantasy that many of us have involves something like a little cafe filled with relaxed colleagues with whom we can discuss research or other interesting topics: a society of the mind -- like "Cheers", but with stimulants. There may even be actual physical places like that. But a blog, by virtue of being a bidirectional communication medium, can serve this function, too. Yes, it's not the same thing, but the coffee's cheaper and you can contribute your part of the conversation at midnight while wearing pajamas.

I must confess to a case of blog envy: I wish my own blog had more academic content. Now, I don't blog about my teaching and professional experiences (except as abstractions) because I'm not doing this anonymously -- it would be unprofessional to comment on students and colleagues thus. But what about research? My excuse has been, "You can't handle my research." Seriously, I'm not sure that anyone beyond a circle of a few dozen people or so care about my research (if that many).

On the other hand, I keep feeling that a blog can be useful in helping "real" work. Now, at the time of this writing, you would note on the left hand column of this site a set of 43 things entries that include "Finish research proposal draft" and "Finish journal paper". By making part of my to-do list public, I have this hope that I'll meet these deadlines. But I think this blog can be an even greater help, so I'm going to try to experiment with blogging my grant proposal preparation. After all, once it's funded (note I didn't say "if"), it becomes public information. And it's a continuation of research I've already published: I want to disseminate these ideas. So, I'll give it a try: blogging my grant proposal preparation for a more general audience (more general than the folks who would be reviewing it or reading my publications, that is). Now I've said it, and now I'll either do it (and, by way of prerequisite, actually finish the proposal) or face the embarrassment of the ten people or so who read this blog knowing I'm all hat and no cowboy.

Topics: , , .

Friday, November 11, 2005

LibraryThing: I'm in the top ten

If you haven't found LibraryThing, and you're into books, or you're just anal like me (I started using 3x5 cards to catalog my books when I was about 10 years old), you simply must check it out. The title above links to the "science fiction" tag in LibraryThing. I'm in the top 10 of quantity of science fiction books. We'll have to see how long that lasts.

Wednesday, November 09, 2005

Ernie's 3D Pancakes: We're doomed

The title above links to a great quote at Ernie's 3D Pancakes that points out that CS departments are in danger of becoming irrelevant to science and math as those latter departments teach their own computing courses. Why? The quote implies that we computer scientists spend too much time navel-gazing and too little time talking about how CS can impact life (and science and math). In my opinion (expressed as a comment to the linked post), part of the problem is the short shrift given to non-majors courses in CS departments. If we want other departments to look to CS departments for educating their students about computing, then we need to deliver something compelling and non-trivial. That will take hard work.

Monday, November 07, 2005

Of toaster ovens and clock radios

Sometimes, accomplishing even the simplest things can can be a great task. One of these chores can be finding an "ordinary" appliance, the fashion these days being to drive every product towards either the low or high end of the spectrum. A case in point is our recent searches for a replacement toaster oven and a new clock radio.

Previously, we had purchased Black and Decker toaster ovens, because they were reasonably priced and had the features we wanted, primarily being the ability to toast bread (with the occasional cheese or other topping), heat small servings (those too small to justify the use of a regular oven), and clean up fairly easy (primarily a slide out tray and a door that dumps any crumbs on it into the tray rather than onto the counter). But Black and Decker's products seem to have sped their way to the cheapest end of the appliance heap. (I wonder if there's a connection between licensing the company name rather than doing the manufacturing and this?) The most recent toaster oven of their's that we owned had metal parts that fatigued, presumably due to heat cycling, and their current products seemed even cheaper, so we did some more extensive shopping around.

We quickly found that there are almost no "simple" toaster ovens around anymore. If it's primary feature isn't rock-bottom cheapness, then it's an array of dubious features that we'd use once in a blue moon. I suppose if you cook a lot of frozen pizza, then you might want one of the very large ovens that abound that can hold an entire pizza, but that's not a selling point for us. We probably searched for a month before we found a Hitachi toaster oven at Fry's at an acceptable price (more than we originally wanted to pay, but we could live with it, given the unit's quality). We still have to wipe the crumbs off the counter after using the oven; it seems that none of them have the door hinged any more so that the crumbs are dumped into the oven.

More recently, we went on a search for a new clock radio. Our old radio hasn't been receiving radio so well lately: I believe that this is a result of its aging analog tuner. It was about 13 years old, so there was no reason to be upset. I've got some homework for you: try to find a clock radio with a digital tuner. Despite the fact that they come with CDs and a thousand other features, clock radios still by and large come with analog tuners. You'd think that, given the word "radio" in their name, clock radios' tuners would be the subject of major refinement. Why then the analog tuners? And God help you if you don't want a CD player. Often, clock radios being electronics, the products have raced to both the feature laden and cheap ends of the spectrum simultaneously, and so you end up with clock radio CD players that cost $25 and yet have the look and feel of something that should cost $5. Eventually, we found a Sony clock radio on Amazon.com with a digital tuner that was, again, of acceptable price.

I tell you, it's enough to make me not want to go shopping anymore. Oh, wait, I don't like shopping anyway. Well, another reason, then.

Topics: , , .

Thursday, November 03, 2005

When will the first direct-to-iTunes TV series happen?

I've been thinking about the failed bid by fans of Enterprise to raise money to essentially buy an additional season of the show after its cancellation was announced. Now that I've seen the movie Serenity and all the episodes of Firefly I've missed on the Sci-Fi Channel, I'm wondering what the economics of a direct-to-iTunes TV series might be. At $2 a pop, how many of each episode does one need to sell to pay for a series like Firefly? If George Lucas could go it alone to make Star Wars, how about a TV series?

Garden photo of the week

Originally uploaded by stiber.
We were away from our house for a year while I was on sabbatical at the University of Florida, and in that time, our golden hops plant (Humulus lupulus 'Aureus') took over a section of the garden. Luckily, there's not much to worry about there, as it dies back to the ground each year.