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Deepak's recommendations

Cancer and Statistical IllusionToday

Shared by mndoci
Haven't read the article, but IMO one of the central ideas of future medicine is early detection and prevention

The cover of this month's Wired promises "The Truth About Cancer" but the article inside is a tissue of misleading statistics and faulty logic. The article begins with fancy graphics telling us "If we find cancer early, 90 percent survive" but "If we find cancer late, 10 percent survive." And this:

Find the disease early "and the odds of survival approach 90 percent...This reality would seem to make a plain case for shifting resources toward patients with a 90 percent, rather than a 10 or 20 percent, chance of survival."

Thus, the opening block of text commands, "Scientists should stop trying to cure cancer and start focusing on finding it early. It's the smart way to cheat death."

The fallacy in all of this is painful easy to spot. If we measure survival, which these studies do, with a 5 or 10 year survival rate then obviously people whose cancers are detected early will survival longer than people whose cancers are detected late.

The key question is whether people who are treated early survive longer than people whose cancers are detected early but who are not treated. In Thomas Goetz's long article there is not a single piece of evidence which demonstrates that

Watson's solo discovery of DNAToday

Shared by mndoci
Chris and co, time to hack some changes :)

Well, my memory must be truly failing. No offense to Honest Jim, but I always thought he had a partner in finding the structure of DNA. And didn't some third guy share in the Nobel also? Plus, isn't there some experimentalist that people grouse should have gotten some credit?

But, I stand corrected:

In the last 50 years since Watson first discovered the structure of DNA, many advances have been made to enable researchers to study and dissect this macromolecule.

Now, some might warn that the Internet doesn't always have reliable information, but this is from a .edu site (and not some student's personal page either), so it must be right, right?

Jing Goes Pro: One of Our Favorite Screencasting Tools Just Got BetterToday

Shared by mndoci
h.264 for $15. Hmm ... nice

Jing, one of our favorite free screenshot and screencasting tools, just received a major update. Besides adding a new look and feel, TechSmith, Jing's parent company, also announced a new Pro version of Jing, which, for $14.95 a year, allows users to record their screencasts in HD H.264 video, directly upload them to YouTube, and remove the Jing logos that appear at the beginning and end of videos produced with the free version of Jing.

Sponsor

The free version also got a major face lift. While there aren't too many new features, one new function we definitely like is the ability to customize Jing's buttons according to your own workflow.

High Quality Video and Direct YouTube Uploads

For just about $15 a year, the Pro version is quite a bargain. Thanks to using the H.264/MPEG-4-AVC video codec, Jing now not only makes it easy to capture high-quality vi

Rotamer optimization for protein design through MAP estimation and problem-size reduction.Today

Rotamer optimization for protein design through MAP estimation and problem-size reduction.

J Comput Chem. 2009 Jan 2;

Authors: Hong EJ, Lippow SM, Tidor B, Lozano-Pérez T

The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* search (DEE/A*) has proven useful, but may not be strong enough as we attempt to solve protein design problems where a large number of similar rotamers is eligible and the network of interactions between residues is dense. In this work, we present an exact solution method, named BroMAP (branch-and-bound rotamer optimization using MAP estimation), for such protein design problems. The design goal of BroMAP is to be able to expand smaller search trees than conventional branch-and-bound methods while performing only a moderate amount of computation in each node, thereby reducing the total running time. To achieve that, BroMAP attempts reduction of the problem size within each node through DEE and elimination by lower bounds from approximate maximum-a-posteriori (MAP) estimation. The lower bounds are als

InnocenceYesterday

An overcast morning, the forecast rain. Already you can feel the invisible droplets touching your face, as though the wind were secretly in love with you. You walk into a coffee shop, order a cappuccino. The girl at the next table is listening to La Boheme, you can hear it through her headphones. Si mi chiamano Mimi. You want to tell her it's too early for that, but instead you dig about in your backpack, take out your notebook, find a pen. The waiter comes over and serves your coffee. You add a sachet of sugar, end up spilling some. The powdered sugar on the dark table top looks like dust, like ash. You open your notebook to a new page but cannot bring yourself to write on it. On your way out you leave two creased notes on the table, weighing them down with a single coin. At the door you notice a scattering of white petals in a puddle. You are careful not to step on them.