Saturday, May 24, 2008

Brain, Mind & Brain Waves

Under Most Popular, The New York Times publishes a list of the most e-mailed articles on its website. Over the past month, Sara Reistad-Long's article published on May 20, 2008, and entitled "Older Brain Really May Be a Wiser Brain" ranked second. Katie Hafner's article published on May 3, 2008, and entitled "Exercise Your Brain, or Else You’ll ... Uh ..." ranked sixteenth. Keeping your brain and mind intact is on the forefront of the Baby Boomers' mind. Wii games are advertised to entice the rusty to exercise. Numerous companies are springing up selling computer games for mental exercise. Most intriguing are games with biofeedback provided by electrical brain waves recorded from button electrodes attached to the scalp, i.e. electroencephalography or EEG for short.

I once examined the power of brain waves with EEG recordings in people reading Braille with their fingertips. In that study, waves at about 10 Hz increased most in power while the participants were reading. The greatest increase occurred in the parietal lobe opposite the reading hand. Waves at this frequency are known as alpha waves.

The findings of this study are described in more detail in chapter 6 of "Blindness and Brain Plasticity in Navigation and Object Perception." Button electrodes were attached to various locations on the head according to the 10-20 System and fed the recorded electrical signal via cigarette box-size pre-amplifiers to an analyzer. The power of the signals was measured for select frequency bands and was displayed real time in dynamic bar graphs and power-versus-time plots on a monitor. These displays can be used as feedback to the person executing the task. J & J Engineering of Poulsbo, WA, who manufactured the equipment and software sought to apply the technology mainly in biofeedback applications. I recall one application with immediate practical implications that trains patients in controlling incontinence and another that helps assembly line workers to avoid postures causing chronic pain. There are others that address the mind.

An impressive demonstration of the power of alpha waves used in a game can be found in our local Adventure Science Museum. In Mind Ball, the contenders drive a small ball along a runway electromagnetically using alpha waves recorded from their frontal lobes. The winner drives the ball all the way to the opposite end. Games involving biofeedback through EEG may prove particularly useful to keep your brain in good working order and your mind sharp.


  • Watch this great demonstration of the potential applications for brain waves that CNN aired today (02/04/10):
  • Jim Drury reports in this Reuters video on recent efforts to utilize brain waves recorded from the scalp to remotely control household appliances (10/12/10):

Thursday, May 22, 2008

Build Your Own PC: Episode I

I grew up in an era in which kids learned basic car maintenance so that they knew how to fix problems on the road. I have worked with computers daily for decades, and I found it more and more vexing that I did not have the slightest idea of what was going on inside them. I could not even point out the vital parts of the creature, once the abdomen was uncovered. One day four years ago, I decided that the best way to find out was to construct one from parts. Below, I summarize this experience.

The process was actually fun. The computer cost about $1,500.- including the extras. These days, a turn-key PC sells for as low as $200.-. Of course, that version does not come close to the performance of the computer I built and a bare-bones PC with a comparable performance would cost at least $500.-. I can only speculate whether that system would be equipped with the same quality parts. The consideration is similar to buying a home in a new development. The base price for the home may be economic, but the quality of the piping, the fixtures, the flooring, you name it, will be poor. You may look at early and costly repairs. Of course, you are offered pricey upgrades. I opted for quality parts. To keep the running costs low, I chose a 350 W power supply. Assuming that the computer is consuming half that wattage on average, the monthly expense for electricity is about $11.- in our utility district. We have got three computers in our household that essentially run 24/7. The expenses add up accordingly.

It may seem dated to describe my first experience with computer assembly four years after the fact. Earlier this year, I build my second computer incorporating the lessons I learned from the first. Hence, I sum up the earlier experience in a first installment and will post important aspects of the most recent experience in a second installment.

I wanted a machine that could process great amounts of imaging data fast. I chose an MSI K8T MASTER2-FAR motherboard that accommodated two 64-bit AMD Opteron 242 central processing units (CPUs). I opted for this architecture at the time because it is compatible with Sun Microsystem's Solaris 10 operating system and I needed to run an application that was specifically compiled for Solaris. The latter is doubtlessly an advanced operating system geared toward servers supporting large networks and by far exceeds my small purpose. I found it more appropriate eventually to run the machine with Ubuntu's Linux-based operating system (currently version 8.04). The latter provides up-to-date Gnome and KDE desktops and the recent upgrades have proved flawless in execution and very stable.

Unfortunately, my CPUs are not yet the type that is enabled for virtualization. Thus, running virtual machines is not as efficient as with more recent AMD CPUs (look for "-V" in the name). Despite this shortcoming, I am running Microsoft's Windows XP on QEMU with satisfactory results.

I bought most parts from internet vendors. At the time, I did not feel confident enough to mount the CPUs myself and had that done for a small fee by Spartan Technologies from whom I purchased the motherboard, the processors and coolers. Everything else I put together. The assembly did not require a great level of experience and was straight forward. Following the instructions provided in MSI's motherboard manual was a safe route to success. An important rule to obey is ensuring that you are not statically charged by electrically grounding yourself before you touch any parts. That is, tape the exposed end of a copper cable to the skin of your arm with medical tape and wrap the other exposed end tightly around a water faucet in your kitchen or bathroom. Waterlines provide the best connection with the ground. At first, I was confused by the great variety of power supply connectors and the many different adapters. Closely studying the drawings and photographs in the MSI manual straightened out the misunderstandings. My choice of hard drives, the memory, the CD/DVD writer and the graphics card was guided by the list on the motherboard retailer's website of items that other customers bought with the motherboard. In the meantime, I have developed a few own preferences:

  • I prefer Kingston Technology memory. I purchased HyperX DDR400 PC3200R memory (KRX3200AK2/1G) for this machine. Before you order the memory modules, validate the specifications with the recommendations on the manufacturer's site.
  • I prefer hard drives manufactured by Seagate Technology. They really served me well over the years. One is 15 years old and still works without fail. I decided to use two SATA drives mirrored in a RAID for user data. Both drives could be connected directly to the motherboard. An additional ATA drive stores the operating system.
  • I chose Pioneer's DVD/CD writer DVR-108, perhaps because my first hifi headset was made by Pioneer.
  • Unfortunately, the motherboard does not provide on-board firewire connectors. If firewire connectivity is desired, a PCI card needs to be installed, taking up one slot.
  • I prefer the more expensive flexible rounded cables to connect the ATA hard drive and the DVD/CD writer to the motherboard over the conventional flat cables. The rounded cables come in lengths that match the distances in the case and are more flexible and thus easier to bend. A rounded ATA cable came with the motherboard. However, it was too long and stiff. I bought extra sets from In general, SATA cable connectors are flimsy. While moving the computer to another room, they shook lose on the motherboard side, resulting in BIOS errors at boot time. I felt tempted to glue them in place with Silicon glue, but refrained.
  • The MSI motherboard has four slots for PCI cards and one for an AGP graphics card. I chose a ATI Radeon 9600 Pro card. This card provides excellent support for a 19" LCD at 1024 x 768. I recommend to use a more upscale card for larger screens and higher resolutions. Moreover, I strongly recommend to ensure that the card of choice fits in the case before it is ordered. The Radeon 9600 card is comparably short. Upscale graphic cards can be quite long and the available space in the case must be shared with the thick cables connecting the hard drives and other peripherals to the motherboard. Room may run out even in a standard case for ATX-size motherboards.
  • The heat sink on the Radeon 9600 graphics card processor and the fan are small. I decided to replace them with a copper heat sink and a larger fan I found at CompUSA (VGA Cooling Kit SKU 336044). The heat sink slightly egged on a capacitor on the card. I ground an indentation into the sink large enough for the components not to touch. Though rough, the solution improved cooling remarkably. Before mounting the heat sink on the processor, it is important to apply a thin layer of the thermal grease provided with the kit evenly on the chips surface. The kit came with a number of additional small heat sinks that can be glued on various integrated circuits on the board. I mounted them all, thinking that every little bit helps. The kit cost less than $20.- and visibly stabilized the cards performance. The screen does not flicker anymore when its hot. Finally, leaving the PCI slot next to the graphics card open considerably boosts heat dissipation.
  • Running a wireless internet adapter PCI card on Linux is problematic. Before you order, ascertain that the manufacturer supports your operating system or, at least, that the drivers are available for the card of your choice. I have had satisfactory experience with D-Link's DWL-G520. Instructions for the installation and the configuration of the driver can be found here. By contrast, NETGEAR does not provide any support for Linux. An opensource project develops Linux drivers for ACX-111 chipset-based cards (e.g. NETGEAR's WG311). However, compiling and inserting kernel modules is needed, potentially interfering with your next kernel upgrade. You may be facing a new install instead of an upgrade.
  • Finally, I can give some advice on fans. My computer houses seven fans, two in the case's front, one in the rear, one in the power supply, one on each CPU and one on the graphics card. As a result the machine vacuums up air-borne dust with remarkable efficiency. Once we had construction in the house several rooms away. An old wall was broken down. I forgot to turn off the computer on that day. The fine, invisible dust from the construction ruined the bearings of the spinners on the CPUs and the graphics card as well as the large fan in the case's rear. The fans did not stop spinning, but could not maintain the required speeds to cool the CPUs effectively. Temperatures reach more than 100° F (38° C) outside for several weeks over the summer where we live. It does not cool down much during the night and attempting to save on the electric bill exposed the CPUs to the risk of overheating. In this situation, the Cooler Master's Aerogate II fan and temperature control unit I had installed in one of the external bays in the case's front warned me of the impending disaster and saved the CPUs.
  • I installed magnetic levitation fans and one of Y.S. Tech's tip magnetic driving (TMD) fans as replacements. I used teflon screws to mount the TMD fan. It is fabulous. A good demonstration of these fans can be found here.

You may wish to check out this
book, if you need more advice. I own a few in this series and found
them helpful.

Thursday, May 15, 2008

Human Frontiers, Brains & Space

Today, I saw for the first time a person suspended from a set of jet-powered wings in free flight. Reuters provides footage of this stunning performance that took place yesterday near Bex,VD, Switzerland, on May 14, 2008.

The pilot, Yves Rossy, successfully managed to soar at great altitude out from the Alps into the Rhone Valley below, proving to the world once more that something seemingly impossible can be achieved after all.

Alas, observing the audacious aviator looping at break-neck speed high in the sky gave me pause. The breath-taking footage rendered a vivid picture of the fragility of the human body. I was reminded of our modern day frontiers and the yet unknown limitations they may impose upon us.

Multiple nations help maintain a permanently-inhabited space station in orbit around Earth. According to the National Air and Space Agency, the U.S. president is firm in the Federal Government's continued commitment to manned interplanetary space flight. The BBC reports that the Peoples Republic of China aims to establish a human presence on the moon in the next decade. Reuters reports that the Russian and the European Space Agencies may join in the development of a spacecraft capable of transporting personnel to the moon. In the face of such ambitions, it is important to understand that we actually know little about the effects that extended tours in weightlessness may have on our body.

As John Steinbeck aptly described in his book The Log from the Sea of Cortez (chapter 4), all organisms on Earth develop and live under the influence of the planet's gravity and its tidal changes imposed by the lunar pull. I have not found a study yet that sheds a light on the question whether a mammalian brain develops normally in the absence of these forces.

Animal models are available to answer this fundamental question. For example, in layer IV of the mouse's somatic sensory cortex cell aggregates known as barrels topographically represent the whiskers on the face.
The picture on the right (courtesy of H. Van der Loos) shows a micrograph of an 80 micrometer-thick section cut tangentially through the left cerebral hemisphere of a Swiss Webster mouse cortex embedded in celluloidine. The left side is up. The nose is right. The section was stained for cell bodies with a blue dye. The barrels are clearly visible as nerve cell-dense rings surrounding cell-sparse centers. The large barrels are arrayed in five oblique rows representing the five rows of long whiskers on the snout. The whiskers on the face are sensory hairs with thousands of touch receptors embedded in their roots. The nerve cells in a cortical barrel respond most vigorously to deflections of the whisker the barrel represents. The barrels develop during the first week after birth. If a whisker is damaged at birth, the corresponding barrel will not develop, suggesting a strong influence of the sensory periphery on cortical development.

Examining the brains of mice taken to the space station shortly after birth for a week would inform us immediately whether microgravity gravely disrupts brain development.

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In this grasping adventure story for kids, Brian Greene explains in most insightful and easy-to-understand fashion the relationship between gravity, speed and time.