Bench Press

I’ve mentioned before that I’m a sucker for the indirect observational techniques that one engages in when doing astronomy/astrophysics. One phenomena that astronomers have yet to be able to observe in any depth is also one of the most fascinating consequences of Einstein’s theory of General Relativity: gravitational waves.

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)

I have always been impressed with the work of astronomers. Unlike biologists and chemists who can, for a wide array of topics, actually touch and feel what they are studying, astronomers have to make conclusions with only careful observations conducted with powerful telescopes and computers informed by understanding the laws of physics (quantum and relativity included) and backed up by complex computational models.

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)

If you’ve never used Google Earth, I’d recommend trying it out, at least once. For those of you not in the know, its an amazing piece of software which lets you access Google’s wealth of geographical and geological information (although with its layers feature, it also gives you access to the oceans, the moon, the sky, historical sites of interest, and Mars).

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)

Having spent a few years working on cell based assays for screening small molecules I became aware of how limited traditional in vitro cell culture can be in modeling biological systems. Traditional tissue culture while fairly easy to do and manipulate for experiments, often produces two-dimensional growth with gene expression, signaling, and morphology that can be dramatically different from those found in vivo. This can make in vitro studies clinically irrelevant. In vivo work while a more accurate model has it’s own drawbacks such as cost and ease of manipulation. Therefore, it would be ideal to develop methods which can make in vitro tissue culture produce in vivo results.

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)

Despite all the cool and meaningful innovations we’ve discussed on this blog, few come as close in terms of impact on a scientific field as the Hubble Space Telescope. And this weekend, you can help celebrate it’s birthday!

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)

If you’re an astronomy buff, February 14 means a lot more than just Valentines Day. It also marks the fateful day (HT: NASA Jet Propulsion Laboratory), in 1990, when the Voyager I spaceprobe took a “family portrait” of all the planets of our solar system that it could see as one last parting gift before it shut down its camera and continued its journey towards “interstellar space”:

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)

It is unfortunate that much of what we need to do to the human body to treat it requires that we cut it open, as this creates a whole set of risks and complications for science and medicine. Thankfully, science and technology march on in the quest to reduce our dependence on invasive surgeries. An interesting Economist article takes a look into some of the more unconventional tools that are being explored as potential non-invasive replacements.

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)

With smartphones becoming more sophisticated and more popular, its only natural that there are a growing number of attempts to use them as a platform for scientific inquiry (pocket ultrasound, microscopy, and astronomy for example). This is especially useful in developing countries, where a relative lack of high-end computers and fixed broadband access make smartphones a very suitable alternative to the more expensive, bulkier solutions that are used in the developed world.

It should come as little surprise, then, that doctors in India are helping to pioneer a new “telemedicine” tool using the camera and processing capabilities of Apple’s popular iPhone to do remote diagnosis of Retinopathy of Prematurity (RoP), a condition which is more likely to afflict infants born underweight. While curable, RoP needs to be treated within days of detecting it as to prevent permanent damage to a child’s eyes, something which the iPhone’s camera, mobile broadband, and robustness of software and security platform allows pediatric eye surgeons to diagnose from remote locations, hundreds or even thousands of miles away.

But, the potential of smartphones to function as a tool for tele-medicine can probably go far beyond this. At least, that’s what i2i TeleSolutions, an Indian-based startup, is betting on. They provided part of the software solution for the RoP diagnosis tool, and are aiming to provide software and services to enable further telemedicine technology – mainly:

• Security – It is important that sensitive medical information is transmitted securely in a way such that only the appropriate medical professionals see the information.
• Data compression – As fast as 3G and the new LTE networks are (and will be), network coverage and data transfer rates will continue to be a limiting factor on the adoption of telemedicine. As such, a true telemedicine solution will require lossless compression techniques.
• IT support – Medical organizations are not especially well-suited for building sophisticated IT capabilities, nor do medical professionals necessarily have the time to learn an arcane user interface. For that reason, telemedicine solutions should aim to provide web-based access methods (in addition to any non-web based methods they may choose to push) to access and react to data.

i2i provides further details on the scope of their platform on their web page, but I think it represents a strong start for a solution. Going forward, I’d like to see them (and any competitors that emerge) provide support for:

• Additional types of data – i2i’s focus seems to be primarily on images, but the full range of capabilities on smartphones is massive – GPS, accelerometer, magnetometer, and even microscopy and other medical attachments – and I would hate to think that tele-medicine would be limited only to its imaging capability
• Deployment on more phones – The iPhone is unique in the maturity of the platform, but it would be nice to see similar applications on other operating systems like Android, Symbian, and Windows Mobile.
• Interactivity – The i2i platform appears to be very unidirectional: (1) take a picture, (2) send it to a remote surgeon. I think the true promise of telemedicine is something which allows for a greater level of flexibility and interactivity on both ends (to refine the view, or make a suggestion on some other place to scan, etc).
• Ability to tack on analytics – There is a significant amount of medical data that needs to be analyzed/processed before it can be acted upon. Building some sort of open protocol or extendability (a la Firefox or Salesforce or LinkedIn/Facebook model) would do a great deal towards enhancing the potential of a telemedicine platform

Anyone else have any other ideas?

Image depicting ant movements. Credit: University of Granada.

Its impressive how much humans can learn from biomimicry. Soldiers, for example, may soon owe their lives to the same pesky ants living in your own backyard. Researchers from the University of Grenada(UGR), under Antonio Miguel Mora García, Professor Juan Julián Merelo Guervós, and Professor Pedro Ángel Castillo Valdivieso, have taken inspiration from how ants find trajectories from their colonies to their food sources in order to develop a simulator that can devise the “safest” trajectory in a battlefield between any two points, given the necessary parameters.

Dubbed the “ant colony optimization (ACO),” this algorithm has already allowed Antonio to employ it to the videogame, Panzer General, with promising results. Currently, the University of Grenada has received participation from the Ministry of Defense to devise new strategies for them if its success continues.

The scientists of the UGR have developed a mini-simulator in order to define the settings (battlefields), locate the unit and their enemies, execute the algorithms and see the results. In addition, the software designed by them offers a few tools useful to analyze both the initial map and the results.

To prepare this system, Mora García started from the battlefields present in the videogame Panzer General, defining later the necessary properties and restrictions to make them faithful to reality.

While the ACO has immediate benefits to saving the lives of our soldiers, I’m also excited for its applications outside of the military. By extrapolating its uses, we could potentially use the ACO to optimize shipping orders, create shortest routes, plan airplane seating, etc, all by harnessing the creativity and intelligence of Mother Nature. So the next time you see an army of ants devouring your picnic basket, take some time to marvel at the beautiful tapestry of Nature before squashing all of them with your feet.

(Image Credit)

Dust can be a pain if you’re an astronomer. In the same way that clouds obscure a view of the night-sky, interstellar dust can distort an astronomer’s view (even if through the Hubble telescope) of interesting astronomical phenomena. This problem is compounded when you consider that stars and planets tend to form in dense interstellar dust clouds.

The distortions caused by spacedust are caused by radiative transfer – a process of light absorption and scattering which also explains why the sky is blue and why sunsets/sunrises look red. Astronomers have built highly sophisticated models to understand radiative transfer across a wide range of different dust backgrounds. These models have enabled researchers to build very cool simulations, such as this one of two galaxies colliding:

Interestingly, greater sophistication in our understanding of spacedust and a greater desire for precision and resolution in the modeling has meant that more and more of the computational processing of these radiative transfer models has been spent on calculating dust grain temperatures rather than the math behind the actual radiation transfer (a product of the fact that you need to calculate across many points in the “dust cloud”, across many types/sizes of dust particles, and because you need to iterate many times to find an equilibrium) – something on the order of 10¹¹-10¹² exponentials per simulation!

That traditional processors are not well suited for calculating exponentials and that there were simply so many calculations which needed to be done in parallel convinced researchers to turn to NVIDIA’s CUDA as a potential solution. As we’ve noted before with using raytracing as a means to accelerate radiotherapy dosage calculations, NVIDIA’s CUDA is a standard programming toolset which lets programmers more easily use the power of (NVIDIA) graphics cards for calculations. Because the calculations needed to do high-performance graphics for a game of Modern Warfare 2 are similar to the calculations that supercomputers crunch through, NVIDIA’s CUDA has been demonstrated to be able to accelerate calculation speed by orders of magnitude!

In the case of dust grain temperature calculation, the results were equally impressive. Not only were the researchers able to accelerate dust grain calculation using a NVIDIA Tesla C1060 (with 4 GB of memory) over an 8-core Intel Xeon E5420 processor (with 32 GB of RAM) alone by a factor of 55, they were able to do this despite:

• the fact that 17% of processing time on the GPU solution was dedicated to data transfer (something the CPU-only solution has to worry about less)
• the maximum theoretical capacity of the GPU was only 6 times greater than that of the CPU, highlighting a big difference between the CUDA philosophy (crank up performance) and the CPU compiler philosophy (abstract but flexible)

Amazingly, the researchers found that even if the CPU were to run an interpolation scheme (requires less processing power, but introduces a little more error and makes it harder to do more sophisticated calculations vs. the equilibrium calculations done here), the GPU solution is still faster by a factor of 16 times!

So: spacedust – 0. GPU – 1. Now let’s see if they can tackle the flexible dust temperature problem…

Paper: “Accelerating Dust Temperature Calculations with Graphics Processing Units”, submitted to New Astronomy; ArXiV link