Apparently, a number of groups have decided to try out the Kinect as a “poor man’s” LIDAR (a tool that can be used to see and measure where things are in three dimensions)/complicated 3D camera setups which are expensive and require sophisticated calibration/post-processing analysis.

Of course, the Kinect is not a panacea: it has much more limited range, requires researchers to build their own analytical software, and the Kinect can’t do high-speed video (yet). But, because of its much lower price, its size, and the availability of drivers because of the active Kinect hacking/DIY community (and the support that even Microsoft is providing for people using Kinect beyond gaming), a number of researchers have decided to embrace the Kinect as a scientific tool.

The article profiles two potential use cases which only begin to scratch the surface of what this technology could be capable of: mapping meltwater lakes that form on top of glaciers (see images below) and studying small body impacts in space.

But, potentially the most valuable use of Kinect? As the Wired article puts it:

The Kinect’s best asset may be that it inspires students, Tedesco said. Rather than a daunting black box with convoluted cables and arcane software, the Kinect is something that many students are already familiar with.

“This creates a different mindset in students,” he said. “They’re not so scared about using the Kinect, and they can really get involved in learning and basic research.”

“I’m actually on my way to buy two of them right now,” he added.

(Image credit – Kinect) (Image credit – Kinect glacier map)

• Use human intuition to help solve complicated three-dimensional protein folding challenges which is oftentimes as effective but significantly faster & cheaper than computational algorithms
• Pool together lots of human volunteers
• Turn the whole experience into a game to get more volunteers to spend more time

The result was a nifty little game which contributed findings which have made it, to date, into a number of peer-reviewed publications (see PNAS paper here and Nature Structure & Molecular Biology paper here)!

Well some researchers at McGill University in Canada want to take a page out of this playbook with a game they built called Phylo (HT: MedGadget) to help deal with another challenging issue in bioinformatics: multiple sequence alignment. In a nutshell, to better understand DNA and how it impacts life, we need to see how stretches of DNA line up with one another. Now, computers are extremely good at taking care of this problem for short stretches of DNA and for “roughly” aligning longer stretches of DNA – but its fairly difficult and costly to do it accurately for long stretches using computer algorithms.

People, however, are curiously intuitive about patterns and shapes. So, the researchers turned the multiple sequence alignment problem into a puzzle game they’ve called Phylo (see image below) where the goal is to line up multiple colored blocks. Players tackle the individual puzzles (in a browser or even on their mobile phone) and the researchers aggregate all of this into improved sequence alignments which help them better understand the underlying genetics of disease.

And how has it been doing? According to the McGill University press release:

So far, it has been working very well. Since the game was launched in November 2010, the researchers have received more than 350,000 solutions to alignment sequence problems. “Phylo has contributed to improving our understanding of the regulation of 521 genes involved in a variety of diseases. It also confirms that difficult computational problems can be embedded in a casual game that can easily be played by people without any scientific training,” Waldispuhl said. “What we’re doing here is different from classical citizen science approaches. We aren’t substituting humans for computers or asking them to compete with the machines. They are working together. It’s a synergy of humans and machines that helps to solve one of the most fundamental biological problems.”

With the new games and platforms, the researchers are hoping to encourage even more gamers to join the fun and contribute to a better understanding of genetically-based diseases at the same time.

Try it out – I have to admit I’m not especially good with puzzle games, so I haven’t been doing particularly well, but the researchers have done a pretty good job with the design of the game (esp. relative to many other academic-inspired gaming programs that I’ve seen) – and who knows, you might be a key contributor to the next big drug treatment!

It is also one of the boldest when it comes to instituting policies and reforms: they were the first to implement a congestion tax to help manage traffic. Unlike most countries, Singapore is open to competition and investment from foreigners in strategic areas like telecommunications, power generation, and financial services. Singapore has also been extremely active in attempting to build up its capabilities as a center for life sciences excellence.

So it shouldn’t surprise me that they are among the first countries to actively utilize social media applications like Facebook and Twitter to help deal with a public health risk like Dengue Fever (from The Jakarta Globe):

The city-state’s National Environment Agency (NEA) plans to roll out … providing information on the latest dengue clusters or areas that have been earmarked as high-risk – on these new media platforms within the next three months … Through Facebook and Twitter, the public will also be able to post feedback or provide tip-offs. For example, if Singaporeans notice an increase in the number of mosquitoes in your neighbourhood or find potential breeding sites, they can alert NEA officers by posting on the agency’s Facebook page or tweeting the NEA account. “We need to put more information out in the public space, so more people can be informed and take action,” said Derek Ho, director of the environmental health department at NEA. “Leveraging on new media channels such as Facebook and Twitter is a good way to do that.”

A refreshing understanding of the uses of social media by a government agency – more interesting than that, though, is the work Singapore’s NEA is doing to build image recognition capabilities into smartphone apps like the NEA’s iPhone app to help field workers (and potentially the public) track and identify mosquitos and mosquito larvae!

The NEA is also in the process of developing a mosquito-recognition program that can identify the species of mosquito from a photograph of its pupae or larvae. With such software, and with the help of a mini microscope that attaches to the camera on a personal digital assistant or cellphone, NEA officers will be able to take photographs of larvae or pupae found in mosquito-breeding sites and instantly find out if they belong to the Aedes species, which spreads dengue … When it is ready, the agency hopes to be able to integrate it with the NEA iPhone application, so that the public or grassroots members conducting checks around the neighbourhood can use the technology as well.
Early identification will allow the NEA to act more swiftly to curb the spread of dengue in potential high-risk zones.

Very cool demonstration of the power of smartphones and of a government that is motivated to try out new technologies to tackle serious problems.

A rigorous understanding of gravitational waves is far beyond the scope of this post (and also far far far far far far beyond my limited comprehension), but the basic concept comes from Einstein’s idea that gravity as we know it is actually a “bending” in spacetime that happens wherever there is mass. This curvature is what causes most of the effects of gravity that we can observe (i.e. you feel a pull towards the center of the Earth because the Earth’s mass bends the neighboring spacetime that you are in). As the Earth moves around the Sun (and as the Sun moves around the Milky Way galaxy and as the Milky Way moves…), the curvature in spacetime also moves with it. In certain types of motion (i.e. when an object is part of a binary orbiting system), this movement in spacetime curvature actually results in “waves” of spacetime curvature emanating outwards, kind of like ripples in a pond. These “waves” are called gravitational waves and, because they carry energy, are also called gravitational radiation. Because of the nature of these waves, they have three unique properties which make them interesting tools in the study of astronomy:

• they move at the speed of light
• unlike light, these waves don’t get significantly scattered/blocked
• they don’t require the existence of matter (so they can be used to study black holes)

The problem? They are extremely difficult to detect, because their effects are remarkably small. In fact, the first indirect observation of gravitational waves, found in the change in orbits of the Hulse-Taylor binary system (pictured above-right) won the researchers the 1993 Nobel Prize in Physics.

So, what to do? While there have been many attempts to do this, they are plagued by the difficulty of detecting such weak waves in the presence of as much noise on Earth. Potential solution? The use of a multinational space-borne laser interferometry setup called LISA (Laser Interferometer Space Antenna). With the use of laser light and interferometry (which allows you to measure small changes in distance by observing interference between a beam of light and a reflection), three identical solar-powered spacecraft will be set up in an equilateral triangle orbiting the sun at an angle relative to where the plane of the orbit of the other planets in the solar system (see below).

What’s especially remarkable is the precautions NASA is taking with the LISA spacecraft to correct for error and insure greater accuracy and precision in their measurements:

• Use of microthrusters to maintain drag-free flight by constantly monitoring the position of the test-weights the LISA spacecraft is flying around (and maintaining position of the instruments relative to the test-weights of ~10nm)
• Use of a transponder (which calculates the phase of an incoming beam of laser light and electronically setting the phase of the outgoing beams) instead of a mirror for interferometry to avoid diffraction (light scattering) from a traditional reflection approach
• Use of time-delay interferometry and continuous frequency monitoring/stabilization to correct for the effects of frequency noise

Given the technology and the theory involved, LISA’s potential to change astronomy could potentially rival the Hubble telescope’s, opening up new ways to study distant astronomical phenomena and potentially some of the more exotic topics in physics like string theory and strong-field gravity. There’s a lot more information on the potential topics of scientific inquiry which LISA could be used to study on NASA’s LISA science page.

Let’s cross our fingers that it will stay on schedule for launch in the 2018-2020 range and deliver not only concrete observations of gravitational waves but a whole wealth of information on the universe we live in.

(Image credit: NASA) (Image credit: NASA)

One phenomena which astronomers can use to better explore deep space is an effect predicted by Einstein’s theory of general relativity called gravitational lensing. General relativity predicts that the path of light can be bent by gravitational fields; the most dramatic example of this would be a black hole, where gravity is so strong that light “falls” back into it. The same effect, on a less dramatic scale, could result in the path of light being bent on its way to Earth by the gravity of another object. The term “gravitational lens” refers to the fact that this bending is similar to the bending of light by a telescope lens.

Now, for the layperson, the fact that light can bend is probably just a cool effect which has no practical importance. But, to a well-trained astronomer, the knowledge of how gravity works lets them use the phenomena of gravitational lensing to understand both the objects that are emitting light (because the lensing effect allows us to see objects which are so far away that they are blocked by another object) and the “lens” itself (understanding the mass, structure, and position of what is bending the light).

Take a look at the pictures (HT: Wikipedia) below of Einstein rings. These occur when the line of sight to a bright, faraway object is being blocked by another object. However, because of the gravitational lens effect, the light from that faraway object can bend around the closer object, resulting in a ring which gives scientists a chance to study not only the faraway object but also understand the structure of the intervening space.

There are countless other examples of the application of gravitational lensing in the study of astronomy, but one of the most clever that I heard about recently was the study of dark matter. The theory in a nutshell: the universe is believed to be mostly dark matter – matter which does not reflect or emit any light whatsoever. Because it doesn’t seem to emit or reflect electromagnetic radiation, there has been no direct observational way to study it. However, dark matter does have mass. This means it has gravity and can thus bend light as a gravitational lens!

Researchers were able to took astronomical survey data from around the world and, using sophisticated computer algorithms and programs, compile a picture of gravitational lensing due to dark matter. From that, they were then able to digitally put together a picture of the structure of the dark matter in (at least part of) the universe and get a sense for how it’s evolved over time (the further from Earth you look, the further back in time):

And with this they made a striking conclusion – we all have dark matter to thank for the existence of the stars and the galaxies:

Our results are consistent with predictions of gravitationally induced structure formation, in which the initial, smooth distribution of dark matter collapses into filaments then into clusters, forming a gravitational scaffold into which gas can accumulate, and stars can be built.

Awesome.

(Image credit) (Image credit)

The magic of new, cheap and powerful technologies and information sources like Google Earth is that they can also be used to push additional experiments and discoveries. Widely available mathematical analysis tools like Mathematica let a professor figure out what instruments made up the mysterious “twang” at the beginning of the Beatles classic “It’s Been a Hard Day’s Night.” Advances in gaming and graphics technology make it possible for gaming consoles and personal computers to do sophisticated number-crunching. And, Google Earth helped make it possible for a team of students to take pictures from near-space for only $150.

More recently, Google Earth helped a team of researchers led by the University of the Witwatersrand’s Professor Lee Berger to find and unearth new fossil remains, including those of the newly discovered Australopithecus sediba (pictured right) in the Cradle of Humankind World Heritage Site in South Africa.

Berger and his associates used Google Earth to learn how to identify cave sites from satellite imagery and to help supplement on-foot exploration to map out ~500 previously unknown caves and, subsequently, 25 new fossil sites!

This discovery has been especially exciting as some have argued it could potentially be “the point from which the genus Homo [the genus we humans are a part of] arises” and “a good candidate for being the transitional species between the southern African ape-man Australopithecus africanus (like the Taung Child and Mrs. Ples) and either Homo habilis or even a director ancestor of Homo erectus (like Turkana Boy, Java man, or Peking man).”

Check out the University’s web coverage of the discovery as well as the Google blog’s coverage of the event as well as the video celebrating Professor Berger’s find (below):

(Image credit – University of the Witwatersrand website)

Science papers by Berger’s group: (1) and (2)

That aim is what makes this paper by Souza et al. in Nature Nanotechnology so impressive to me. In this paper they describe a method for culturing cells three-dimensionally by magnetically levitating cells grown in the presence of a hydrogel consisting of gold, magnetic iron oxide nanoparticles, and filamentous bacteriophage. 

Dr. Souza’s group tested their hydrogel with glioblastoma cells as seen in the figure above. Application of a magnetic field allows the cells to counteract gravity floating in the media and allowing for three-dimensional growth. The field also concentrated cells resulting in cell to cell interactions consistent with previous work on tissue engineering scaffolds designed to provide a cell growth advantage. In addition, the shape of the magnetic field can also be used to shape cell growth.

While the ability to promote three-dimensional growth without biodegradable porous scaffolds or protein matrixes is remarkable, the truly impressive part of this technique is that the cells exhibit differential protein expression that more closely resembles that of in vivo tumor xenografts as seen in the figure below thanks to their new growth conditions.
The ability of these three-dimensional cultures to mimic in vivo samples effectively is remarkable and the simplicity of this technology could provide a less time intensive and cost effective solution to traditional experimental methods. It’d certainly be nice to someday be able to design in vitro assays which produce truly clinically relevant data. Maybe with techniques like this one we’ll be able to accomplish that soon.

(Source – Nature Nanotechnology : Three-dimensional tissue culture based on magnetic cell levitation)

Officially launched on April 24, 1990 (can you believe that was 20 years ago!?), it has provided one of humanity’s best looks into deep space and has, among other things:

• Helped refine the field’s understanding of Hubble’s Law and the Hubble Constant
• Showed that the expansion of the universe was not decelerating, but accelerating, suggesting the existence of dark energy
• Helped to establish the existence of massive black holes at the center of galaxies and their relationships
• Provided sharp images of the impact of comet Shoemaker-Levy 9 into Jupiter
• Collect data on extrasolar planets and protoplanetary discs
• Furthered the study of Wolf-Rayet Stars, suspected to be the precursors of Gamma-ray bursts, the most powerful energy bursts known in the universe
• The mindblowing look 13 billion years into the past known as the Hubble Deep Field

And, potentially, most important of all: the gorgeous pictures of deep space (from Space Telescope Science Institute’s HubbleSite website).

Happy 20th birthday, Hubble!

(Image credits – Hubble Site via Space Telescope Science Institute)

The diagram above shows the 60 frames that Voyager I took. The pictures aren’t high-resolution beauties (as a result of needing to use optical tricks to correct for the amazing brightness of the sun and the light it scatters, and smearing from the long exposure times needed to capture Neptune and Uranus), but it is still amazing to think that this is the only family portrait mosaic of the solar system ever taken. Closeups on the 6 prominently visible planets are below (left to right and top to bottom are Venus, Earth, Jupiter, and Saturn, Uranus, Neptune):

More details are at the NASA JPL page, but I will leave you all with this bit from Carl Sagan:

This was the image that inspired Carl Sagan, the the Voyager imaging team member who had suggested taking this portrait, to call our home planet "a pale blue dot."

As he wrote in a book by that name, "That’s here. That’s home. That’s us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. … There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world."

Happy 20 year anniversary to the grandest family portrait humanity has ever taken, and happy Valentine’s Day to all.

(Image credits – NASA JPL)

Let’s take a classic problem which often has a surgical solution: the removal of a cancerous tumor. How could we solve this without resorting to the use of a scalpel?

• Of course, there’s radiation – which, as we’ve discussed before, is potentially dangerous if the radiation dosage isn’t calculated sufficiently well.
• The use of ultrasound as a means to visualize what’s going on under the skin is commonly known. But a small startup in Washington called Mirabilis Medica came up with a means to use ultrasound not only to see a tumor or blood clot, but also to focus it and generate enough heat to destroy the tumor/blood clot (what they’ve called High-Intensity Focused Ultrasound or HIFU; explanatory diagram below).

• Professor Weihong Tan at the University of Florida published a paper in PNAS in early 2009 a means of using light as a way of non-invasively activating blood clotting. The system is described in the picture below, but relies on a means of inhibiting the activity of Thrombin (a protein that helps control blood clotting) with short stretches of DNA (which they’ve cutely termed “Thrombin-binding Aptamers” or TBA) that have been chemically modified to be able to change shape in the light (cis-trans isomerization under photon stimulation). The vision is to one day be able to inject a patient with these Thrombin-TBA “molecular clasps” and hit the patient with a light source, cutting off the blood flow to the tumor and all without needing invasive surgery!

These only scratch the surface of what new technologies and scientific advances might be capable of. Son et lumiere (sound and light) as surgical tools indeed!

(Image credit) (Image credit – Mirabilis Medica) (Image credit – PNAS publication)