David Kirkpatrick

August 19, 2010

Graphene and DNA sequencing

News on potential applications of graphene is always interesting, but I’ll have to admit I’d like see more actual market-ready solutions. This news is both intriguing and promising, but the nut graf contains those dreaded words, “could help (insert the gist of any story here).” It’ll be a pretty exciting day when I blog about something that will help, instead of could help with graphene as the key helping element.

From the second link:

Layers of graphene that are only as thick as an atom could help make human DNA sequencing faster and cheaper. Harvard University and MIT researchers have shown that sheets of graphene could be a big improvement over membranes that are currently used for nanopore sequencing–a technique that promises to speed up and simplify the sequencing of long strands of DNA.


The researchers create their membrane by placing a graphene flake over a 200-nanometer-wide opening in the middle of a silicon-nitride surface. Then they drill a few pores, just nanometers wide, in the graphene with an electron beam. The membrane is finally immersed in a salt solution that’s in contact with silver electrodes. The researchers observed dips in the current when a DNA strand passed through the pore, showing that the method could eventually be used to identify DNA bases.

January 8, 2010

Get a free online education with Khan Academy

Filed under: Arts, Business, Media, Science, Technology — Tags: , , , , , , , — David Kirkpatrick @ 11:00 pm

I came across this post at Metamodern discussing a very interesting, and utile, online resource — Khan Academy. If you’re looking for short, to-the-point online lessons (more than 1000) on mathematics ranging from basic arithmetic and algebra to differential equations, physics, chemistry, biology and finance, this is a great resource.

From the first link:

I got a pointer to a free, online educational resource today.

It deserves more attention.

The eyeballs of a few million students might be a good start. Students in elementary school, grad school, rural Africa… places like that.

It consists of 1000+ brief lectures on YouTube.

It centers on math, but goes beyond.

November 5, 2009

Genome 10K Project

Filed under: Science, Technology — Tags: , , , , — David Kirkpatrick @ 2:59 pm

Via KurzweilAI.net — Interesting. And it is just amazing to think DNA sequencing costs are expected to go down by an order of magnitude or more over “the next couple of years.”

Genome 10K: A new ark
Science News, Nov. 4, 2009

The Genome 10K Project aims to collect tissues or cells from at least 10,000 vertebrate species, enough to catalog DNA sequences from about every vertebrate genus.

Its designers have decided to wait for sequencing costs to drop by a factor of 10 or more — probably in the next couple years — before launching their analytical program.


Read Original Article>>

February 21, 2009

News from the American Naturalist

A fun group of article summaries from the American Naturalist:

Honest crabs, power to the hungry, nice mice and clever meerkats: News from the American Naturalist


An article by Princeton Biologist Mark Laidre suggests that when an animal signals an intent to attack, chances are it’s not bluffing. Using hermit crabs as subjects, Laidre tested previous mathematical models that predict animals have a significant incentive to give dishonest signals about their intentions. Some models suggest that animals may lie about their intentions up to 40 percent of the time. Laidre used dummy hermit crabs to invade the personal space of live crabs. Contrary to the models, the crabs nearly always backed up their threats with an attack. Those that didn’t signal a threat nearly always fled. The findings, Lairde says, suggest that animals don’t lie about their actions nearly as much as theorists once predicted.

Mark E. Laidre, “How Often Do Animals Lie About Their Intentions? An Experimental Test,” 173:March.


Flocks of birds, swarms of insects and herds of ungulates don’t need to take a vote to choose their leaders. According to research led by Larissa Conradt (University of Sussex), leaders in large animal groups can emerge automatically. Conradt and her colleagues created a theoretical model that simulates the movements of a large group in which members have conflicting plans about where they’d like to go. The simulation showed that individuals who valued their preferred destination over group cohesion often led the group—even if they were in the minority. Those who were less concerned about the destination went along for ride just to stay with the group. “As a consequence,” Conradt says, “large groups are often automatically led by those members that are most desperate to reach a particular destination, or are most indifferent as to whether or not the group breaks up.” There’s some empirical evidence to back up the model. Studies have shown that food deprived fish move to the front of shoals, presumably to steer the group toward food.

L. Conrad, J. Krause, I. D. Couzin, and T. J. Roper, “‘Leading According to Need’ in Self-Organizing Groups,” 173:March


Sometimes the nice guy gets the girls. At least that’s how it is for striped mice. A research team led by Carsten Schradin (University of Zurich and University of the Witwatersrand) studied the breeding strategies of striped mice in South Africa. They found that dominant males who controlled breeding groups had lower testosterone levels than subdominant males. “What is unusual about this society is that the dominant males are in fact the most sociable, often grooming other group members,” Schradin says. “It is the smaller and solitary living males, which roam from one group to another, that have the highest testosterone levels.” The roaming males try to coerce females to mate, which, as one might imagine, is less successful than establishing a breeding group.

Carsten Schradin, Michael Scantlebury, Neville Pillay, and Barbara König, “Testosterone levels in dominant sociable males are lower than in solitary roamers: physiological differences between three male reproductive tactics in a sociably flexible mammal,” 173:March


Meerkats’ cooperative social structure may have led them to evolve a specialized system of alarm calls, according to an article by Roman Furrer and Marta Manser from the University of Zurich. Meerkats have the ability to vary their alarm calls depending on what type of predator threatens them. In other words, they use one call when threatened from the air by an eagle, and a different call when threatened from the ground by a snake. But Cape ground squirrels, that live side-by-side in the same habitat as meerkats, have not evolved this type of alarm call. So why would such calls evolve on one species and not the other when both live in the same area? Furrer and Manser suggest it has to do with social structure. Meerkats are highly social creatures. They coordinate their foraging activities as well as their escape plans. So knowing what predator is approaching helps in coordination. The ground squirrels, on the other hand, act largely independent of each other and may have less need for specified alarm calls.

Roman D. Furrer and Marta B. Manser, “The evolution of urgency-based and functionally referential alarm calls in ground-dwelling species,” 173:March.