Scientific Seen

News, Commentary, and Tutorials from a Scientific Perspective

A few years ago XVIVO and Harvard University released a video of a scientific visualization entitled, “The Inner Life of the Cell.” I wasn’t a big fan. It was a fairy-tale vision of cellular activities.

If you saw a simulation of traffic flow on the highways and every vehicle in each lane was going the same speed, maintaining proper following distance, signalling and changing lanes only when necessary, merging and exiting with decorum—it might be nice, but it would be so fanciful that it would do more harm than good if you were trying to understand highway traffic in the real world. When you look at real-world traffic, you have difficulty believing anyone can travel the highways safely, but the simulation would make it hard to imagine there could ever be such a thing as a freeway collision.

A scientific visualization should induce a mental model that catalyzes an improved understanding of reality, and the 2006 simulation failed.

Of course, a simulation like this is going to be unrealistic. Molecules aren’t distinguished by hues, atoms don’t remain stationary with respect to their neighbors, and there’s no classical music soundtrack in a real cell. But the 2006 simulation was so far removed from reality that (in my opinion, of course) it served more to confuse than clarify perceptions about molecular activities in a living cell. My biggest peeve: all the molecules were shown in stately glides as if a miniature synchronized swimming team was displaying the results of years of practice. On those scales, the “aqueous” environment behaves more like peanut butter. Kinesin molecules grab onto microtubules and pull because they have to to make it through the thick goop through which they travel, and none of that difficulty was shown.

Protein Packing in the Cell

A lot to admire in the new XVIVO/Harvard scientific visualization of molecular activities within a living cell.

Now the same scientific visualization team has created a new video, “Inner Life of a Cell—Protein Packing.” This one is so much better. It’s a much more crowded world, and the actions of proteins are limited by interference from all their neighbors. None of the small molecules are shown (not a criticism—if water, ions, and sugars were visible you wouldn’t be able to visualize anything through the resulting mess), but many of the proteins are shown. Of course it’s not “accurate”—it’s a visualization!—but this one is much more representative of the kind of confused and crowded environment within living cells. The new simulation makes it much clearer that the normal processes of life are challenged with every motion, and the new video makes it easier to be awed by the mere fact that we are alive. Heartily recommended!


From the day I began working as a science writer (starting as a “hobby” while I was a gainfully employed optical systems research engineer) I’ve covered new breakthroughs — discoveries or inventions that have revealed or used new principles or techniques. The challenge of covering that “beat” is that the mere fact that a discovery or invention has been made says absolutely nothing about the use or application of the advance. So there’s a bit of a disconnect between news of technological or scientific progress and the availability of the fruits of that progress to a wider community. But there is a definite process that these things tend to follow: initial work–>use by a handful of specialized practitioners–>availability of the method to a technically capable general population–>accessibility to all. Of course, not all breakthroughs make it through all these stages, and one of the most fascinating aspects of following science and technology is to predict which ones will hit the big time.
Applying that model to the development of general lighting with LEDs, the first breakthrough was simply crashing through the performance, cost, and reliability (i.e., quality assurance and product validation) barriers to bring solid state lighting to market. Any walk through a big box hardware store will demonstrate that basic LED technology is now in the fourth stage of development.

Controls Adding Value

The subsequent stage is to realize even more value from LED lighting by incorporating it into an overall control system, i.e., Smart Lighting. I’d say that’s at the third stage (perhaps on the cusp of the fourth), where folks who are generally capable around technology can now incorporate advanced controls into their lighting systems. Proving the point are commercially available systems such as the Hue system from Philips bringing those capabilities to the general consumer, and companies like Redwood Systems, that offer integrated controls solutions to commercial and industrial customers.

Image of LED lights controlled by smartphone app.

Philips’ Hue system brings LED lighting control within grasp of the tech savvy. (Courtesy of Philips Communications)

Although the market penetration for LED lighting in general is still proportionally very small compared to the overall industry, that’s now a marketing challenge more than a technical one. The next wave in LED lighting is to start to apply the inherent controllability of solid state lighting to use light to define spaces and optimize suitability of illumination for any circumstance. Specifically, LEDs offer an unprecedented degree of control over the distribution, spectrum, and intensity of light in a space — including the ability to vary those parameters over time.
At the Strategies in Light Conference, Hans Nikol, VP for Strategy and Innovation at Philips Lighting, discussed how a significant percentage of the market for the Hue LED lighting system is driven by teenagers — looking to show off the cool lighting at their homespun raves (if anyone uses that word any more). But that’s not the kind of value that’s going to drive widespread adoption of solid state lighting. What’s needed is a way to identify specific benefits of lighting control — aspects of illumination that improve human health, productivity, or perhaps even some more nebulous sense of well-being.

Quantifying the Promise of LED Lighting

Lighting Research Center's Home Lighting Design Tool

Knowledge of the effects of light can help produce illumination designs that influence behavior and health. (Image courtesy of RPI’s Lighting Research Center)

Also at Strategies in Light, Mark Rea, Director of the Lighting Research Center at Rensselaer Polytechnic Institute, spoke about various ways to quantify the value added by the ability to spectrally and temporally tune illumination. He is pushing the industry to help identify quantifiable metrics that can be applied to commercial, industrial, educational, and domestic environments to present a clear story of the value of controlled illumination in those environments. Of course, identifying a metric is different from establishing the connection of that metric to human health and performance. That work is in its early stages, with the exception of a few tantalizing tidbits. But enough work has been done to understand that human well-being, alertness, and productivity are influenced by lighting choices. Although some may quibble, I’d contend that this field is still at the stage where researchers are making their fundamental discoveries, and significant expertise is necessary to investigate and apply these illumination methods. It’s also my contention that herein lies the true value of solid state lighting. Without the ability to control illumination, it didn’t make much sense (and was difficult to do anyway) to investigate the effects of various illumination levels, colors, and timing. Now those investigations are underway, and the results should drive the value of LED lighting well beyond that of simply upgrading incandescent light bulbs.


Solid-state lighting — using light emitting diodes for general illumination — offers a host of advantages over incumbent technologies. For starters, LED lighting is five times (or more) as efficient as incandescent lighting, it has no components requiring hazardous material waste provisions (as do fluorescent lamps), and LEDs instantly respond to electric current, eliminating the delays inherent in high-intensity-discharge at startup and allowing the illumination level to be controlled. And those really are just for starters, as there are many other advantages.

But LED lighting has one big disadvantage: it’s completely different from other lighting technology. For example, LEDs are generally driven with DC current as opposed to the AC that powers just about every other source. Another big difference is that LED packages themselves (the LED chip, encapsulant, and primary optics) shape and direct the light. Contrast that with the tungsten-alloy filament at the heart of an incandescent bulb. When the filament heats up it puts out light (about 5 to 10 percent of its electrical power usage) in every direction.

Manufacturers can make specialty incandescent bulbs that have internal mirrors to direct the light in a certain way, but in general, one light bulb is just like another. You can replace a Sylvania bulb with a General Electric bulb with a Phillips bulb and you can put it in a desk lamp, an outdoor sconce, or a recessed fixture. Incandescent bulbs are commodities because the physics determines how a filament works, and there’s not much any manufacturer can do do distinguish their offering from another company’s. The good part is the interchangeability; the bad part is that the light output of incandescent lamps is cut down by the fixture efficiency (the amount of light that doesn’t get where you want it to go. Because the light from the bulb itself is uncontrolled — spreading out in every direction — you can’t match a bulb to the fixture in which you’d like to put it, so light (and energy) is wasted.

Matching the Light Source to the Task

What if, though, you could buy a different light bulb for every fixture, one tailored to minimize wasted energy for that one particular application? It would be expensive. And every few months or so it would burn out and you’d need to run down to the hardware store and buy a replacement bulb (selecting from the scores your retailer would need to keep in stock). So that’s not really a viable solution for incandescent bulbs. But it is for LEDs.
One of the advantages alluded to above is that LEDs can last a really long time (there are some issues with exactly how long, but that’s for another day). Long lifetime means that it’s reasonable to select an LED lighting solution specific to each application — because you won’t need to change it out for 5, 10, perhaps even 20 years or more. In practice, it’s a little more complicated than that because there’s not just one LED that will go in every desk lamp or cove light. Every luminaire (light fixture) manufacturer selects and arranges LEDs in a different fashion. So if you really want to optimize LED lighting you have to buy an entire fixture. It’s still a money-saving proposition (it’s not uncommon for industrial customers to get payback times of anywhere from a few years to several months), but it creates a dilemma for LED lighting.

LED lighting can be forced into an Edison-Screw bulb.  Image from U.S. Department of Energy.

LED lighting can be forced into a traditional incandescent bulb shape — but should it be?
Image from U.S. Department of Energy.

Retrofit or Redesign?

LED lighting manufacturers have two choices: they can make fixtures that optimize the distribution of light to fully take advantage of the new capabilities offered by solid-state lighting, or they can design retrofit bulbs that can be put into place as one-for-one replacements of existing incandescent or fluorescent fixtures. At last week’s LED Show the dilemma was (quite literally) on display. The purists argue that forcing LEDs to mimic (crappy) incandescent or fluorescent sources will set the industry back because customers will see energy savings, but not much more of the advantages of LED lighting. The retrofit folks argue that the replacement bulb solution lowers the barriers to entry, giving LEDs an absolutely necessary foothold into the general illumination market. At times, there’s some visible contempt expressed on one side or the other.

The logical path (one that’s already being played out) seems to be that retrofit solutions get LEDs in the door, where they then get to display some of their other advantages. Those bonus advantages then create showcase solutions that become selling points for designs that fully embrace the LED lighting solution.


It’s interesting to watch the evolution of a technology.  I attended my first LED lighting conference in 1998 and I’ve attended at least one in every intervening year.  In those first years, Las Vegas was the primary customer.  Nowhere else was lighting such a significant expense — and such an essential part of marketing.  Higher efficiency and lower maintenance represented a huge savings for casino operators on The Strip.  But the ability of LEDs to manage the distribution of light (direct it to the consumer instead of spraying it into space) and the flexible control of LED lighting (to easily reconfigure displays) added to the energy savings to make LED lighting worth the investment.

But there’s a big difference between convincing casino operators to upgrade their high-value, high-maintenance displays and getting consumers to shell out big bucks to replace their 25-cent incandescent bulbs.  The fundamental problem is that LEDs are significantly different than their incandescent predecessors, but it’s difficult to take advantage of their new capabilities within the current infrastructure.  So people pushing for LED adoption have to limit their argument to two factors: it will save energy and it will reduce maintenance costs.  It’s kind of like arguing for replacement of horsedrawn buggies with gas-powered automobiles, but having your arguments for change limited to discussions of lower hay costs and reduced need for street cleaning.

LED lighting squeezed into a familiar incandescent bulb form factor.

LED lighting can be made to look like an incandescent bulb, but that’s like requiring a buggy whip on a Ferrari.

Even with that limited evaluation, LEDs are now well past the point where they are economically viable (after some intense political, economic, and technological growing pains), so just about any lighting project today needs to at least consider LEDs as an option, and for many developers they are the option of choice.  But now that LED general illumination is in place, system operators are realizing some other benefits.

Networked Capabilities of LED Lighting

At the LED Show (starting yesterday in — fittingly enough — Las Vegas) Kelly Cunningham of the California Lighting Technology Center (CLTC) at the University of California-Davis described a networked implementation of LED lighting control on the university’s campus.  Outdoor LED lighting at the campus is triggered by passive infrared sensors that provide little more than a simple present-or-not signal.  Even with that limited input, the control system anticipates pedestrian and cyclist movement, bringing lighting up to full brightness levels before the traffic reaches the lit area.  The ability to remotely control and instantaneously modify the illumination level of LEDs is central to the operation of this kind of system, and the immediate benefits are impressive.

For example, 100 wall packs (those curious rectangular fixtures affixed to the outside of buildings and washing the walls with light) detected only a 28 percent occupancy rate, leading to an 85 percent reduction in energy costs — over and above the reduction simply due to LED efficiency alone.  The CLTC implemented the same kind of system on a stretch of urban roadway.  Although the final report has not been released, Cunningham said the results are similar.

That’s encouraging news for the industry, because those are the kind of integrated lighting systems that insiders have been claiming would lead to additional levels of savings (and other capabilities, but that’s another story), and this provides another fairly significant example of the promise coming to fruition.  It also demonstrates another general truth: if you don’t have a capability, then you don’t have any idea what you’ll do with it; but when you develop the capability you will apply the capability in clever ways.  That’s true for networked lighting now.  In the near future, the precise control LEDs offer over color, intensity, and distribution of light will be used to modify illumination in our work and home environments to enhance our comfort and productivity in ways we can only glimpse today.


Remember the hullabaloo a few years ago about camcorders capable of infrared photography — folks modifying their camcorders to see through clothing? One of the more annoying elements of the press coverage was the label “x-ray” for that kind of image. Sure, it’s a quick way of saying the modified cameras can see through clothing that appears opaque to the eye, but the infrared wavelengths are about a thousand times less energetic than x-rays.

And speaking of wavelength, there’s a lot of confusion about infrared cameras in general. The confusion stems from the fact that the infrared region of the spectrum is about 200 times as wide as the visible light spectrum. That is, if you reflect a beam of deep blue light off a mirror, it will act (just about) exactly like a beam of red light — so the two ends of the visible light spectrum act almost exactly the same way.

The Infrared Spectrum

Not so for the infrared. The infrared is roughly and loosely divided into three (or more) regions: the near-infrared (NIR), the midwave-infrared (MWIR), and the longwave- (or far-) infrared (LWIR). Those regions act completely different from each other. A material that absorbs energy in the NIR can be transparent in the MWIR and reflective in the LWIR.

Those regions of the infrared spectrum are generated in different ways as well. Every object in the universe emits radiation, at wavelengths that correspond to the object’s temperature. The human body, for example, emits light in the LWIR region. An army tank or an airplane emits in the MWIR. A hot stove emits in the NIR — and when it gets even hotter it emits in the visible…leading to our familiar experience of something being “red hot.” There are dozens of different types of infrared cameras, imaging different parts of the infrared spectrum.

The modified camcorders that do the “x-ray” infrared photography work in the near-infrared spectrum, so they aren’t creating pictures from the infrared energy originating in the human body. They create images from reflected NIR. At night, when there is not much visible light around, these cameras would shine a NIR “flashlight” and capture the infrared wavelengths reflected off the object. Even though the scene would be dark, the camera would capture a perceptible scene.

Near-infrared photography creates subtly different effects.  Image courtesy of Wikimedia Commons
Near-infrared photography creates subtly different — almost eerie — effects.

The sun and artificial light sources emit near-infrared radiation, but they also emit visible light. The detector in the camcorder could sense the NIR, but it’s usually not the image you want during the daytime, so an infrared blocking filter is put in front of the detector. To take the night-time photos, the infrared blocking filter is flipped up, out of the optical path. If the filter is flipped up during the day, the detector senses the NIR, but there’s so much visible light around that the infrared image would be swamped by the visible light. To get around that, some users put a visible light blocking filter in front of the camera. Then, during the daytime, the camera senses the NIR without all the extra visible light. That NIR image captures NIR reflected from the scene, in the same way that visible light images capture light reflected from the scene.

Seeing Through Clothes

So how did that “see through the clothes” thing work? Well, there are some materials that are transparent in the NIR and opaque in the visible. Some (usually thinner cotton) fabrics do not reflect near-infrared. Meanwhile, the undergarments, fabricated from different materials, do reflect NIR. The effect is almost as if the outer garment isn’t there.

It’s really not too common a situation, where the external clothes are transparent in the NIR, but the uproar over the situation was enough to cause camcorder manufacturers to make it much more difficult to use the cameras to image NIR under daylight conditions. It’s a shame, because there are some really interesting effects possible with daytime infrared photography. Still, since there are some scumballs who do things like take “naked” photos of the Chinese diving team with their modified cameras, one can see why the manufacturers have tried to eliminate the infrared imaging capabilities of their cameras.

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