Free Thought
goodmath | October 24, 2007 One of the problems with many of the interesting graph algorithms is that they're complex. As graphs get large, computations over them can become extremely slow. For example, graph coloring is NP-complete - so the time to run a true optimal graph coloring algorithm on an arbitrary graph grows exponentially in the size of the graph!
So, quite naturally, we look for ways to make it faster. We've already talked about using
heuristics to get fast approximations. But what if we really need the true optimum? The other approach to making it faster, when you really want the true optimum, is…
sporte | October 23, 2007It's hard to teach bioinformatics when schools work so hard to keep us from using computers.
Anecdotes from the past
Back in my days as a full-time instructor, I fought many battles with our IT department. Like many colleges, we had a few centralized computer labs, tightly controlled by IT (aka the IT nazis), where students were supposed to go to do their computing. Instructors also had a centralized computer lab, but over the years, we gained the right to have computers in our offices. Our major battle was whether or not we'd be allowed to use Macs.
There are certainly advantages in…
goodmath | October 22, 2007 The bulk of this part of the review is looking at the total train-wreck that is chapter 4, which contains Bittinger's version of dreadful probabilistic arguments for
why Christianity must be true. But before I do that, I need to take care of one loose
end from part 1. I should have included chapter three in part one of the review, since it's really just a continuation of the paradox rubbish, but I didn't.
The basic idea behind chapter three is that Jesus is the most fundamental
resolution of paradox. All of the most important of the (Bittinger) paradoxes that we
encounter in our lives are…
drorzel | October 20, 2007
...My heart's in Accra » Pop!Tech 2007
More interesting conference blogging posts than I can link individually
(tags: gadgets society science computing economics education)
The Prize That Even Some Laureates Question - New York Times
Nobody likes the Bank of Sweden Prize in Economic Sciences in Memory of Alfred Nobel
(tags: economics Nobel)
clock | October 17, 2007Nobel Prizes are not the only awards given in Stockholm these day. Karolinska Institute also gives an annual Lennart Nilsson Award for photography. This year's prize has just been announced and I am happy to report that the recepient is a friend of mine (and Scifoo camper), Felice Frankel for her amazing science photography. From the Press Release:
Felice Frankel, a scientific imagist and researcher at Harvard University's Initiative in Innovative Computing, has been named the recipient of the 2007 Lennart Nilsson Award. Frankel was sited for creating images that are exquisite works of art…
drorzel | October 4, 2007
Stopping atoms
A "coil-gun" method for slowing atomic beams without lasers, from the Raizen group at Texas
(tags: physics low-temperature science atoms)
Confessions of a Community College Dean: An Open Letter to Mayor Richard M. Daley
The Dean Dad is less polite to Hizzoner than I was
(tags: academia stupid education)
Finance Blog - Market Movers by Felix Salmon: Blogonomics: RSS Feeds - Portfolio.com
The economic case for full-text RSS feeds. Cory Doctorow has been pushing this for years.
(tags: blogs economics RSS)
Next steps for physics graduates - Physics World - physicsworld.com…
goodmath | October 1, 2007 Among many of the fascinating things that we computer scientists do with graphs
is use them as a visual representation of computing devices. There are many subtle problems that can come up in all sorts of contexts where being able to see what's going on can make a huge difference. Graphs are, generally, the preferred metaphor for most computing tasks. For example, think of finite state machines, flowcharts, UML diagrams, etc.
One of the most interesting cases of this for one of the biggest programming problems today is visual representations of concurrency. Concurrent program is incredibly…
neurophilosophy | September 23, 2007
(Gene Genie logo created by by Ricardo Vidal)
Welcome to the 16th edition of Gene Genie, the carnival of genes and genetic diseases.
In this edition, genetics gets personal. The recent publication of Craig Venter's genome (and, before that, James Watson's) was big news. It ushered in the new era of personal genomics, to which a special section of this edition of Gene Genie is devoted.
So, without further ado, let's take a look at the entries for this edition.
Genes & genetic diseases
First off, we have several posts about cancer genes. BRCA1 is a tumour suppressor gene that…
revere | September 18, 2007When you use as part of your daily work a unit of measure that Wired magazine lists as among the Best Obscure Units, you know you are in trouble. Thus I found pack-year, one of an epidemiologist's favorite smoking exposure measures listed there along with a couple of other units I knew about. Pack-years is a cumulative measure calculated by multiplying the number of packs of cigarettes a person smoked per day by the number of years they smoked them. Thus a 25 pack-year smoking history can be accrued by smoking a pack a day for 25 years, or, heaven forbid, 25 packs a day for one year.…
jrosenhouse | September 6, 2007D. James Kennedy died earlier this week.
Shortly after I moved to Kansas I discovered the local Evangelical radio station. This was my introduction to precisely what Christianity means to very large segments of the South and Midwest. Preacher after preacher blared forth from my speakers, each one doing his darnedest to out-stupid his predecsessor.
And from out of this maelstrom of malarkey came one preacher who towered over all the others. That was D. James Kennedy. With that combination of ignorance and arrogance so typical of his breed, Kennedy would stand before his distressingly…
mikethemadbiologist | September 6, 2007General Petraeus is bringing new meaning to the phrase 'head count':
Intelligence analysts computing aggregate levels of violence against civilians for the NIE puzzled over how the military designated attacks as combat, sectarian or criminal, according to one senior intelligence official in Washington. "If a bullet went through the back of the head, it's sectarian," the official said. "If it went through the front, it's criminal."
Which led to this assessment:
"Depending on which numbers you pick," he said, "you get a different outcome."
Gee, do ya think?
So let's think about this 'metric'…
neurotopia | September 5, 2007Ha ha, fooled you!
The Discovery Institute has just issued this on their blog, the inaccurately named Evolution News and Views:
According to CSC senior fellow and leading ID theorist William Dembski, what follows is:
"[A] big story, perhaps the biggest story yet of academic suppression relating to ID. Robert Marks is a world-class expert in the field of evolutionary computing, and yet the Baylor administration, without any consideration of the actual content of Marks's work at the Evolutionary Informatics Lab, decided to shut it down simply because there were anonymous complaints linking…
jlynch | August 14, 2007Births
1892 - Louis, 7th duc de Broglie, French physicist, Nobel Prize Laureate
1893 - Leslie Comrie, New Zealand astronomer and computing pioneer
1896 - Gerty Cori, Austrian-born biochemist, Nobel Prize Laureate
Deaths
1953 - Ludwig Prandtl, German physicist
1982 - Hugo Theorell, Swedish scientist, Nobel Prize Laureate
2004 - Sune Bergström, Swedish biochemist, Nobel Prize Laureate
vhughes | August 10, 2007
Science is perhaps the academic discipline most dependent on acronyms, from the common NASA (National Aeronautics and Space Administration) and DNA (deoxyribonucleic acid) to the less recognized laser (light amplification by stimulated emission of radiation). In fact, Wiley Publishers' dictionary of "Scientific and Technical Acronyms, Symbols, and Abbreviations" includes more than 200,000 entries!
On Thursday, Mind Hacks pointed out some of the cleverest acronyms used in cognitive science, and asked readers to send in any especially "awkward, contrived or borderline inappropriate acronyms…
sb admin | August 9, 2007It's been a few days. I was out in West Virginia last weekend watching my cousin get married. After driving back Monday, I started the new job with Linden Labs, and that has been occupying most of my focus.
I've spoken at length before (in that and other posts) about why, despite how much I loved the science and the teaching, it was time for me to leave academia. I have asserted, however, that my new job isn't just "rebound" (i.e. me saying, ak! I'm sad! Find me something else!), but actually something that I'm really looking forward to.
Why?
(Before I go further, I should underscore what'…
neurophilosophy | August 7, 2007A few new additions to my feed reader:
Advances in the History of Psychology - whose "primary mission...[is] to notify readers of publications, conferences, and other events of interest to researchers and students of the history of psychology." By Jeremy Trevelyan Burman, Ph.D. student in the history and theory of psychology at York University.
Brain in a Vat - "a neuroscience research digest." By Noam, who "recently graduated from Yale with a double major in Philosophy and Molecular Biochemistry and Biophysics [and is] conducting laboratory research at the University of Pennsylvania…
goodmath | August 6, 2007
So, in my last post, I promised to explain how the chaos game is is an attractor for the Sierpinski triangle. It's actually pretty simple. First, though, we'll introduce the idea of an affine transformation. Affine transformations aren't strictly necessary for understanding the Chaos game, but by understanding the Chaos game in terms of affines, it makes it easier to understand
other attractors.
An affine transformation is a simple set of linear equations which has the effect of doing a simple
scaling of any geometric figure put through it.
So, for a two-dimensional affine…
neurophilosophy | August 4, 2007
IN The Matrix (Andy and Larry Wachowski, 1999) Keanu Reeves plays a computer programmer who leads a double life as a hacker called "Neo". After receiving cryptic messages on his computer monitor, Neo begins to search for the elusive Morpheus (Laurence Fishburn), the leader of a clandestine resistance group, who he believes is responsible for the messages. Eventually, Neo finds Morpheus, and is then told that reality is actually very different from what he, and most other people, perceives it to be.
Morpheus tells Neo that human existence is merely a facade. In reality, humans are being '…
goodmath | August 1, 2007 Moving on from simple graphs, one of the things you can do to make things more interesting
is to associate numeric values with the edges, called the weights of those edges. This variation
of a graph is called a weighted graph.
Weighted graphs are extremely useful buggers: many real-world optimization problems ultimately
reduce to some kind of weighted graph problem. A few examples include:
The traveling salesman problem (TSP): given a set of cities, and information about travel-times
between pairs of cities, find the shortest route that visits all cities. This is actually an
incredibly…
dmunger | July 26, 2007Fox News has a very detailed review of the so-called $100 laptop, officially called the XO. The technology sounds quite impressive:
Even though bright sunshine is beating down upon the laptop screen, you're having no trouble reading the display.
But the sunlight is OK, since it's powering your system through a small, low-cost solar cell. And the XO doesn't need much power since it runs at a fraction of what laptops that are considered "green" run at.
The review only gets more glowing from there:
I expected to be impressed simply by the economic, low-power capabilities and wireless mesh…