Free Thought
sporte | January 8, 2010These days, DNA sequencing happens in one of three ways.
In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this.
Then, in the 90's, genome centers came along. Genome centers are like giant factories that manufacture sequence data. They have buildings, dedicated staff, and professional bioinformaticians who write programs and work with other factory members to get the data entered, analyzed, and shipped out to the databases. (You can learn more about this and go on a virtual tour in this…
pontiff | January 3, 2010Late notice, but I'm giving the theory seminar at UBC tomorrow, January 4, 2010 at noon:
Title: Adiabatic Cluster State Quantum Computing
Location: Hennings 318
Abstract:
Models of quantum computation are important because they change the physical requirements for achieving universal quantum computation. For example, one-way quantum computing requires the preparation of an entangled state followed by adaptive measurement on this state, a set of requirements which is different from the standard quantum circuit model. Here we introduce a model based on one-way quantum computing but without…
revere | January 1, 2010I doubt many of our regular readers will be surprised to hear that at least one of The Reveres was sort of geeky while young (now, of course, he's just sort of geeky while old). I thought about this objectively (geeks don't think we are really geeky; we just think the things we do that others call geeky are "interesting") when I ran across (via Slashdot: warning sign #1) a link to The Technologizer (warning sign #2) picking the Ten Most Tarnished Brands in Tech. This isn't about scandals. It's about once proud brandnames that nobody cares about any more, like Netscape or Commodore. And on the…
dsalo | December 28, 2009As I watch the environment around me for signs of data curation inside institutions, particularly in libraries, I seem to see two general classes of approach to the problem. One starts institution-wide, generally with a grand planning process. Another starts at the level of the individual researcher, lab, department or (at most) school; it may try to scale up from there, or it may remain happy as its own self-contained fief.
As with anything, there are costs and benefits to both approaches.
Some of the challenges of data-driven research carry costs and infrastructure that only make sense on…
drorzel | December 19, 2009
The Mighty Power of Blogosaurus? | The Loom | Discover Magazine
"I've heard this sort of story many times before, and this is where it usually ends. Blogosaurus slinks back to his office and sulks.
But today the story has another ending. Wedel now reports that someone from the Discovery Channel called him up and is going to make things right. I can only guess that blogs do actually make a difference some of the time. Or maybe just this once."
(tags: media science dinosaurs journalism blogs television)
Bad Year for Weird Fiziks § Unqualified Offerings
"So, a bad year for people hoping to…
drorzel | December 18, 2009
Creating Citizen Scientists § SEEDMAGAZINE.COM
"A few days ago, sitting in my office, I contributed to peer-reviewed scientific research in biology, astronomy, and psychology. Even though I don't hold degrees in any of these fields, my contributions will help advance science: I was doing real investigative work, not the prosaic replications of classic experiments that are typically taught in introductory lab courses. I was taking part in a blossoming "citizen science" movement occurring across a wide swath of scientific fields."
(tags: science seed computing astronomy biology psychology…
pontiff | December 17, 2009The Optimizer has gotten tired of everyone asking him about D-wave and gone and written a tirade about the subject. Like all of the optimizer's stuff it's a fun read. But, and of course I'm about to get tomatoes thrown on me for saying this, I have to say that I disagree with Scott's assessment of the situation. (**Ducks** Mmm, tomato goo.) Further while I agree that people should stop bothering Scott about D-wave (I mean the dudes an assistant professor at an institution known for devouring these beasts for breakfast), I personally think the question of whether or not D-wave will…
pontiff | December 14, 2009A paper dance today! Yes, indeed, it's another slow dance (scirate, arXiv:0912.2098):
Adiabatic Cluster State Quantum Computing
Authors: Dave Bacon, Steven T. Flammia
Abstract: Models of quantum computation are important because they change the physical requirements for achieving universal quantum computation (QC). For example, one-way QC requires the preparation of an entangled "cluster" state followed by adaptive measurement on this state, a set of requirements which is different from the standard quantum circuit model. Here we introduce a model based on one-way QC but without measurements…
goodmath | December 14, 2009 An alert reader pointed me at
href="http://www.uncommondescent.com/philosophy/what-is-intelligence/"
rel="nofollow">a recent post over at Uncommon Descent by a guy who calls
himself "niwrad", which argues (among other things) that life is
non-computable. In fact, it basically tries to use computability
as the basis of Yet Another Sloppy ID Argument (TM).
As you might expect, it's garbage. But it's garbage that's right
up my alley!
It's not an easy post to summarize, because frankly, it's
pretty incoherent. As you'll see when we starting looking
at the sections, niwrad contradicts…
drorzel | December 14, 2009
Blog U.: 'With Their Whole Lives Ahead of Them' - Mama PhD - Inside Higher Ed
"According to the report, the US has now slipped to tenth place in international college completion rates. I don't think it's coincidental that we are one of the few developed countries in which subsidized day care is not a given."
(tags: academia education society culture social-science kid-stuff gender blogs inside-higher-ed)
Conversation Hackers
"Two important men are having a careful conversation on military training. What do you call the guy who, having no particular competence or interest in the matter at…
neurophilosophy | December 13, 2009
IN February of this year, Jacopo Annese (above), a neuroanatomist and radiologist at the University of California, San Diego travelled to Boston to take delivery of a brain. For Annese, collecting brains is not unusual - he is, after all, director of UCSD's Brain Observatory, which will eventually become a comprehensive library of brains donated by people who had neurological conditions such as Alzheimer's Disease, as well as by healthy people of all ages. This time though, the brain he collected was very special: it belonged to the amnesic patient Henry Molaison, who for more than 50 years…
jdupuis | December 12, 2009The latest issue of IT Professional (v11i6) has some interesting articles on strategic planning for IT organizations.
Information Technology Strategic Planning by Hong, Edward K
IT Innovations: Evaluate, Strategize, and Invest by Sahoo, Manas
Professional and Interpersonal Skills for ICT Specialists by Llorens-Garcia, Ariadna; Llinas-Audet, Xavier; Sabate, Ferran
IT and Business Alignment: The Effect on Productivity and Profitability by Nash, Elby M.
Finding Your True IT Transformation by Kraynak, Peter
Copyright Infringement and Protection in the Internet Age by Berti, John
Virtual Teams…
razib | December 5, 2009About six months ago I had a post up on the Cape Coloureds of South Africa. As a reminder, the Cape Coloureds are a mixed-race population who are the plural majority in the southwestern Cape region of South Africa. Like the white Boers they are a mostly Afrikaans speaking population who are adherents of Reformed Christianity. After the collapse of white racial supremacy many white Afrikaners have argued that it is natural and logical to form a cultural alliance with the Cape Coloureds because of the affinity of language and faith (Afrikaans speaking Coloureds outnumber Afrikaans speaking…
drorzel | December 1, 2009
A Good Author Is Hard to Find - Books - The Stranger, Seattle's Only Newspaper
"Mention the word "slush" to anyone who's worked in publishing for longer than five minutes, and you're likely to get an expression of sheer horror. Slush pile is a term used to refer to the collective mass of unsolicited manuscripts and query letters--novel or nonfiction synopses with a few sample pages attached--that daily deluges the offices of agents and editors throughout the industry. Occasional hits emerge from the morass: Twilight began as an unsolicited query. But far, far more often, the slush pile's…
pontiff | November 30, 2009Stuff to read while you wait around for finals and the Christmas holidays:
Via alea one of the odder invocations of NP-completeness: Rowing and the Same-Sum Problem Have Their Moments
An update on the status of US science funding for the next budget year at Computing Research Policy Blog
An interesting paper is out on < a href="http://arxiv.org/abs/0911.3635">Quantum Metropolis Sampling. The key insight (slaps head) in getting a Metropolis like algorithm to work is not to make a full energy measurement but to only reveal a small bit of the information relevant for whether to accept or…
drorzel | November 28, 2009
Colliding Galaxies For Fun and For Science! : Starts With A Bang
"Galaxy Zoo has developed an outstanding game where you can help astronomers by doing something that humans easily defeat computers at: visually matching galaxies to simulations!"
(tags: science astronomy computing internet blogs starts-with-bang)
Should You Get a Ph.D.? : Mike the Mad Biologist
"My very short answer: no."
(tags: academia science jobs biology education blogs mad-biologist)
December 2009: James Wolcott on Reality Television | vanityfair.com
"The influence of Reality TV has been insidious, pervasive. It has…
pontiff | November 27, 2009The list of talks accepted at QIP 2010 is now online. As a member of the PC I can tell you that there were way more good papers than available speaking slots and made some of the final decisions hard to make.
One talk that I think will be a highlight is the invited talk by the optimizer: "Efficient simulation of quantum mechanics collapses the polynomial hierarchy." Quantum computing skeptics of the "BQP=BPP" kind may just found their island significantly smaller and lonelier. The QIP=PSPACE will also be given a talk slot. Quite a year for quantum complexity theory, I think.
clock | November 27, 2009Quantification of Circadian Rhythms in Single Cells:
Earth's 24-h-rotation around its axis is mirrored in the circadian clock that resides within each of our cells, controlling expression of ~10% of all genes. The circadian clock is constructed as a negative feedback loop, in which clock proteins inhibit their own synthesis. During the last decade, a picture has emerged in which each cell is a self-sustained circadian oscillator that runs even without synchronizing cues. Here, we investigated state-of-the-art single-cell bioluminescence recordings of clock gene expression. It turns out that…
agelman | November 26, 2009Julien Emile-Geay writes about a postdoc opportunity for a postdoc in climate
dynamics, applied statistics, or applied mathematics:
"Beyond the Hockey Stick: new approaches to paleoclimate reconstruction"
In 1998, a seminal study by Mann, Bradley and Hughes took advantage of climate signals embedded in an array of high-resolution paleoclimate proxy data to conclude that "Northern Hemisphere mean annual temperatures for three of the past eight years are warmer than any other year since (at least) AD 1400." The so-called "hockey stick" reconstruction showed relatively stable temperatures for…
drorzel | November 26, 2009
The Mid-Majority : Assistant Coach for a Night
"[Northwestern State Coach] McConathy did things a little differently than most coaches -- he subbed his players five-in, five-out, ran an offense that was almost as old as the NCAA Tournament itself. He often allowed coaching friends and local children into the locker room at halftime, even for big games. He let national journalists give pregame pep talks. And for the middle part of this decade, his unconventional ways were paying off. The Demons had a long string of 20-win seasons, and made four consecutive Southland title games.
But now, the…