Friday, July 6, 2012

Friday Links: DNA + dark matter, E.O. Wilson, skeleton racing

More Friday Links! 

A really cool research venture: using DNA to detect dark matter. Deep sequencing technologies require you to compactly array DNA molecules (all of different sequences) on a solid surface, and biologists have standard techniques (PCR + sequencing) to uniquely identify a DNA molecule from any given spot in the array. Guess what? That's a great setup for detecting dark matter. The hypothesis is that the Earth should be plowing through dark matter as it revolves and/or rotates, assuming that dark matter is diffusely distributed.

Essentially, here's how the DNA dark matter detector works:
1) Earth rotates, brushing through dark matter in a predictable rhythm that varies directionally throughout the day
2) DNA molecules are arrayed on a gold sheet. Dark matter can knock gold nuclei out of the sheet and into the array of DNA molecules.
3) The gold nucleus cuts a swath through the forest of DNA molecules, severing them
4) severed DNA molecules fall from the array and are collected, then amplified by PCR and sequenced so the biologists can figure out exactly which DNA molecules were severed
5) since they know where each DNA molecule was anchored, they can put together the path that the gold nucleus took
6) Match the path with the direction from which you'd expect the dark matter to be coming from at the given time of day.

One word: awesome.

E.O. Wilson, the famed evolutionary biologist who studies eusocial organisms, advocates the kind of cross-pollination exemplified by the above DNA-dark matter example. His message to scientists-in-training: learn broadly and collaborate broadly. Too many PhDs spend all their time doing experiments in a narrow field and never venture into other areas. But they are missing out: new discoveries are found in non-intuitive connections between different fields.

One idea I had relevant to MD/PhDs was inspired by E.O. Wilson's two strategies for doing good science:
1) Medicine shows the problems. Seek to learn all the problems (literally, ALL) then look for scientific phenomena that can explain the problems and provide a means to intervene
2) Science observes phenomena without necessarily knowing if they have consequences relevant to human well-being. Seek to learn all (literally, ALL) the phenomena then look for problems that might be linked to the phenomena and apply your knowledge to the problem

Every sport is a unique combination of agents (players + equipment) and rules that those agents follow (official rules + rules of physics). Fortunately, that's all you need to create a model of something, with the purpose of identifying the most important factors, and to predict and explain emergent properties.

Here, Freakonomics spotlights the Australian team in the skeleton, an Olympic sledding sport. They don't have career skeleton athletes (except one) and they don't have a chance to practice because, well, they're in Australia. You might think that the skill and practice time of the athlete are the two most important factors. In fact, that might be true in most sports. But if you carefully examine the rules of the game, you'll realize that there are two components to a race: the actual sledding, and the 30-meter sprint beforehand to get the sled going. Guess what? Australia has plenty of good sprinters. And as it turns out, using a little bit of modeling, you can show that the actual sledding is of minimal importance in terms of time. Skill might prevent you from wiping out, but as long as you stay on course you're not going to shave much time off with good sledding. So instead, they focused their efforts on finding really good sprinters and training them.

The result? An Australian qualified for the Olympics within 18 months, getting in about 1/10 as much practice time as a "career skeleton athlete." Very often, working smarter is 10x than working harder. Science knows best, and conventional wisdom fails miserably.

Haha all of San Deigo's July 4 fireworks goes off all at once:

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About Me

MD/PhD student trying to garner attention to myself and feel important by writing a blog.

Pet peeves: conventional wisdom, blindly following intuition, confusing correlation for causation, and arguing against the converse

Challenges
2013: 52 books in 52 weeks. Complete
2014: TBA. Hint.

Reading Challenge 2013

2013 Reading Challenge

2013 Reading Challenge
Albert has read 5 books toward his goal of 52 books.
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Goodreads

Albert's bookshelf: read

Zen Habits - Handbook for Life
5 of 5 stars true
Great, quick guide. I got a ton of work done these past two weeks implementing just two of the habits described in this book.
The Hunger Games
5 of 5 stars true
I was expecting to be disappointed. I wasn't.

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