Main

April 09, 2012

How I came to study science in college and my experience doing so.

By Red Sox Steve

Right around the time I was a high school sophomore, I started to understand that it would be a good idea to think about my future. What did I want to do with my life? What did I want to study? What was I good at, and how could I apply my skills, knowledge and talents in a practical way? Suffice it to say that my sixteen year old brain did not spend as much time on these issues as more pressing matters like girls, cars and sports. My regrettable approach to my life (but, justifiable at the time) meant that others could easily sway me - I come from a multi-generational, Italian, working-class upbringing that lives in a tight-knit, small community and I'm the first-born son in my own nuclear family. As soon as I started to read well and bring home good grades, many told me I should become a doctor. And I believed them.

To me, the idea sounded great - for all I knew, doctors worked cushy hours, drove fancy cars, and relished in the type of prominence and esteem that mean so much to so many, especially in a small community. Little means more to many local parents than the ability to tell someone, "my son/daughter is a doctor." So, as I prepared for college, my chosen path was medicine - my parents encouraged me, therefore, to study science. After all, their poor, sometimes unpredictable, blue-collar upbringing required them to always pursue practical goals - they saw ability in me, and we all looked at each other and said, "a doctor. Why not?"

In high school, I got a decent education, what many would call "average" for America. As a result, I entered college a little more well-prepared than some, and not as well-prepared as others. My competitive instincts drove me early and often - my grades were good, my chances of getting into medical school were high and, above all, the continuous positive outcomes confirmed that I - with the financial support of a frugal mom and dad - was on the right track. Over 10 years ago.

There is no MD in my by-line, so you know the story doesn't end there. In fact, that's where it really begins. College was going well at the end of my sophomore year. I was learning a lot, building up a pretty decent medical school application, and the average high school graduate I was had morphed into someone on track to graduate with Latin honors. However, a plan I had at the time was thwarted - my university had options for those who wanted to apply for early acceptance to medical school (my parents and I said, "why wait?"), so I applied, and found out mid-summer of 1998 that I didn't get in. I wanted to continue to move forward, so in spite of this, I threw myself completely into the effort. That summer ended up being pretty good - It was my first in Boston: I had two jobs, studied, and enjoyed myself in the first big city I'd ever seen, visited, or lived in.

When I started my junior year in the fall, I saw no reason to slow down - I was halfway through, and wanted to make the most of my remaining time. So, I took on an undergraduate research project with the hopes of developing my resume and skills. I wanted to remain a competitive applicant for medical school, with the dream my parents and I had still weighing heavily on all my decisions. I concluded, mostly because of what my peers were doing, that getting more practical experience in chemistry (my chosen major) was probably a good idea.

To begin research as an undergraduate at my school, you have to first choose a professor who will lead you. With good grades on my transcript and myopic, but considerable, ambition fueling my desires, I sought out the most prominent organic chemistry professor at my university. This turned out to be an eye-opening experience. Prior to spending my time in an academic research lab, I was a student who sat in class my whole life - I passively absorbed data and regurgitated it for exams and lab sessions, lasting an hour or two at the most. This was different - there were graduate students in the lab, and they had been there for years working towards their Ph.D.s. The professor was responsible for allocating lab resources, guiding his students towards their dissertations, and - most important of all - continuing to bring prestige and funding to the chemistry department and university. Before I became a small part of a large lab, my goals were always front and center - my parents and teachers enabled my dreams unconditionally and supported me through ups and downs. The lab, however, was different, unfamiliar even; and like a sailor in uncharted waters, I didn't realize how unsettling it was until things got choppy.

The problems began within a few weeks - I learned how unhappy the graduate students were and realized that listening to them was unsatisfying; there were romantic affairs among lab members, adding another level of general unease to my time there, and, above all, I felt like these matters were too burdensome for me to continue. Work seemed to be secondary to the soap-opera like undercurrents that flowed through the lab. My first semester was, therefore, my last - I couldn't stomach the nonsense of it all. I saw no benefit to committing the rest of my undergraduate career to working around people like this! I resigned, made an official complaint to the department head about rumors I had heard (but couldn't substantiate), and felt like my hopes and dreams had come crashing down. My plan was a failure and so was I.

I felt like the rest of my time in college was spent fighting an 'uphill battle' - every decision now weighed a ton and it seemed that absolutely nothing was going in my favor. I had another year until graduation, though, and continued to push forward. I worked hard, but the gratification and positive third-party confirmation I previously associated with my efforts was gone. My parents grew anxious, further eroding my confidence, but any honest discussion of it all was swept under the rug - maybe if we acted like nothing was wrong, nothing would actually BE wrong. For the first time in my life, it seemed like the working-class pragmatism that had propelled me upward was starting to drag me down.

In the months that followed, I continued to work hard, but the future seemed more opaque than ever before. Graduation was looming, I had trouble focusing, and - again, for the first time - doubt replaced certainty when I thought of my future. I graduated on time in May 2000, but was tired, burned out, and doubted myself and my abilities - again, something that happened for the very first time. Within a matter of months, my desire to go to medical school had all but vanished, as gone as my undergraduate days, and I had no idea what to do. I found work, but had no understanding of how to leverage the experience - college was easy, but I found my post-college life much more challenging. Anxiety, depression, and a lousy diet led to weight gain, and I was in therapy - you guessed it - for the first time.

I stumbled into my science degree, with all the gusto of a drunk circus clown. I thought it was a means to an end, and that ultimately, all the sacrifice would be "worth it" when I became a doctor. The conversations I had with my parents leading up to my college graduation had been premised on the fact that I would go on to medical school, but, with that option off the table, I concluded that my knowledge and undergraduate degree left me with no appealing choices. Shortly thereafter, I stepped away from science, and worked as a Peace Corps Volunteer, living outside America... for the very first time. The demands I had to meet as a science major left me with no opportunity to satisfy my other curiosities. Two years living and working in a South American jungle were only the start of an experience that helped inform my perspective; what I learned while living there has since shaded every decision I've made. Stay tuned, because that story isn't too far away.






April 06, 2010

In Love With Hubble

By Amba
Blogger’s note: Admittedly, there are way too many links in this post. But with the possible exception of the one to the Hubble-galaxy beer stein—unless of course you happen to want one—they are ALL worth following if you love Hubble. Take your time.

If you searched, you could certainly find coverage of space shuttle Atlantis' successful last mission to service the Hubble Space Telescope—on the official Hubble Site, on NASA TV, on the Facebook page Last Mission to Hubble, even on Twitter, where @IamHubble speaks for itself in a rather bland, not to say HAL-like voice (“They continue to check out my instruments and it is going well”), and @Astro_Mike Massimino has a lot more to say:

Eating chocolates in space, floating them in front of me then floating and eating them like I am a fish

My spacewalk was amazing, we had some tough problems, but through them all, the view of our precious planet was beautiful

Getting re-adjusted to gravity, let go of a small bag of groceries and must have expected it to float, luckily no damage

But if you were just watching cable news, each new twist up there was given about half a minute, if you didn’t have to wait for it in the crawl. Never mind that the decision to keep Hubble alive had been a reprieve won by popular demand. Earth business looms large these days—the economy, our ongoing political civil war, Major League Baseball. The daredevil refurbishing of humanity’s eye on the cosmos seemed relegated to a feelgood sideshow, as if people needed to assume it would go off without a glitch (which, thankfully, it almost did). Perhaps many people were too anxious about basic stuff to enjoy the advanced anxiety of high adventure, much less the overpowering perspective that is Hubble’s two-edged gift.

To science fans and space nerds, though, this was the story, and if we’d had our druthers the coverage would’ve been wall-to-wall. (Literally: in my future world, every home will have a wall-size screen with a live feed from a Webcam on the International Space Station or Cassini.) I have been riveted by the Hubble ever since speed-reading a book Larry Marschall reviewed back in our October 2008 issue, The Universe in a Mirror: The Saga of the Hubble Space Telescope and the Visionaries Who Built It. As its subtitle suggests, Robert Zimmerman’s book is a collective biography of the instrument and the mortals who struggled for decades to heave it into the heavens. (That makes a picture in my mind something like the classic on the right. In Hubble’s case, however, much of the action was dreary lobbying for funds.) In the light of the whole story, this fourth and final servicing mission could not help but make me flash back to the first one, in December 1993—the one that turned Hubble from, in Zimmerman’s words, “what might be the greatest catastrophe to hit American astronomy ever” into a triumph and a turning point in human evolution.

When Hubble was launched on April 24, 1990, forty-four years after its conception and two decades into the design process, scientists quickly realized that something was horribly wrong. Despite the crystalline clarity of orbital space, the images the telescope was beaming back to Earth were blurry. Incredibly, Hubble’s main mirror had been ground—perfectly—to the wrong specifications. How could this happen?? During the fine polishing process, which took nine months, repeated warnings had been ignored, in part because the test instruments that were raising the red flags were so much less precise than the newfangled “reflective null corrector” that the engineers simply didn’t believe them. (Why, then, had that exquisitely machined null corrector needed three washers hand-inserted to make its measuring rod the “right” length?!) This shocking oversight had been shielded from discovery by a mess of other factors: chronic budget crises; the urgency of an already long-delayed project that had just lost another four years to the Challenger disaster; high security at the manufacturing facility (which also did military work) that kept NASA observers out; and the human tendency to “look the other way”—a phrase Zimmerman hammers like a funeral drumroll, for it was what had brought Challenger down. The flaw in Hubble’s mirror was eventually traced to some chipped nonreflective paint that had given a critical laser beam a wrong shiny place to bounce off—1.3 millimeters wrong.

The myopic Hubble became the butt of late-night talk-show jokes and cartoons, such as one showing Mr. Magoo as its designer. It was a low point as low as any in NASA’s history; the very survival of the agency was in doubt. Administrators seriously considered cutting their losses on the $2.5-billion-and-counting project. “[T]he urge to kill Hubble at NASA headquarters was strong,” Zimmerman writes. But the telescope had been designed to be serviced by astronauts in orbit, and diehard astronomers and engineers were already brainstorming a fix. After months of discouraging dead ends, a key design element fell into place at a strategy meeting in Germany when Jim Crocker of the Space Telescope Science Institute went back to his hotel to take a shower. As he folded out the sliding, pivoting European showerhead to the desired angle, Crocker suddenly saw how a suite of small corrective mirrors could be swung precisely into place between Hubble’s misshapen mirror and the instruments it carried. Three years later, in December 1993, a crew of seven astronauts aboard the space shuttle Endeavor put Hubble’s “glasses” on and made several other improvements in “a record five back-to-back space walks totaling 35 hours and 28 minutes.” The prescription was perfect. And the stunning, data-drenched images that have exploded our conception of the cosmos started flooding in. (The “showerhead” device, COSTAR, the Corrective Optics Space Telescope Axial Replacement, was removed on this last mission, since all Hubble's newer instruments have the optical correction built in.)



 Hubble Heroes: Lyman S. Spitzer, Jr., John N. Bahcall, and Sandra M. Faber

Zimmerman’s Hubble narrative is a sort of modern Pilgrim’s Progress. It shows instructively how we humans accomplish great things: in spite of ourselves. Vision, skill, and above all, perseverance must fight their way through the Slough of Bureaucracy, the resistance of error, inertia, politics, and money. The Hubble heroes, hardly household names—Lyman Spitzer, John Bahcall, C. Robert O’Dell, Sandra Faber, and Riccardo Giacconi, among others—come across as very human in every way but one: their almost superhuman refusal to give up.

The result has been “the biggest revolution in astronomy this side of Galileo,” as Miles O’Brien writes in a marvelous summing-up of Hubble’s legacy. And, like Galileo’s, the Hubble’s scientific revolution has proved culturally seismic. Only scientists with supercomputers can decode Hubble’s raw data, but from the start they’ve turned its bits and bytes back into visual images, both as tools of analysis and to share the telescope’s discoveries with the general public. The Hubble has taken more than half a million of them. And those incredible images of the universe, made available for free on HubbleSite (well, not counting your tax dollars), have percolated into every corner of popular culture.

“The Hubble Space Telescope has shown us Einstein’s universe. And when I say ‘us’ I don’t mean just the scientists,” wrote one of them, Mario Livio (PDF), whose book Is God a Mathematician? was on our March Bookshelf.

Hubble has literally brought the wonders of the cosmos into homes worldwide. You now find Hubble images not only in astronomy textbooks, but also on the covers, variously, of a book of music for the trumpet, a German art magazine, a book that teaches English to Japanese children, and an album of a rock group.



HubbleSite itself invites you to download high-resolution images for wall murals, art prints, and computer wallpaper, and of course there are gorgeous coffee-table books, calendars, and even note cards and stickers. But you can also have a distant galaxy or supernova on your beer stein, coffee mug, journal, or custom wristwatch (I confess to breaking down and ordering those last two, as well as this Father’s Day gift for my 91-year-old dad). There’s hardly anyone on the planet who hasn’t absorbed at least a few of the Hubble images into his or her consciousness.




NASA-JPL Hubble slide show

The effect is to make disorientation intimate—to bring the big bang to the breakfast table. On the one hand—thanks a lot, Hubble!—our notion of the universe and our place in it has suffered another wrenching, dizzying dislocation. We’ve known for four centuries that we weren’t exactly the focus of a cozy little cosmos, but it turns out we had no clue. To glimpse the actual, unimaginable scale of things is as crushing as it is exhilarating. “Sometimes people ask me if I don’t feel depressed by the apparently diminishing role of humans in the universe,” Livio writes. As a scientist, he says he doesn’t, because that incredible-shrinking-man feeling is the paradoxical measure of our growth:

[N]otice that the apparent decrease in our physical presence is only a consequence of the tremendous increase of our knowledge. And Hubble played a crucial role in that expansion of our horizons of understanding.

But it’s telling that the question does come up. Maybe better than anyone, Paul Simon captured the feeling in his prescient 1986 song “The Boy in the Bubble”: “These are the days of miracle and wonder/ so don’t cry, baby, don’t cry don’t cry.”

You can’t unsee those images, and they pose a challenge that, while not “humanity’s final exam,” is at least its GRE. Even when we’re not consciously thinking about it, which is most of the time, the Hubble’s-eye view is now the deep background of everything we do. I think we’ve barely begun to process what that implies for our lives and purposes.

On the other hand, having these images, and having them be ours—to put on our coffee mugs and mouse pads if we want—is helping us do just that. It’s so grand out there, and so gorgeous, and somehow, as negligible as we are—just a mite on a mote—we’re entitled. The atoms of our bodies were made in furnaces like those; we’re looking at a show of the forces that formed us. The eyes and brain to see it all are among its most improbable creations. It’s hard not to conclude that the Hubble is serving a re-ligious function—in the original meaning of the word, “to reconnect” to one’s source—for humanity’s next phase, for people who aren’t religious as well as for those who are. “Now the Hubble vistas are our stained-glass windows,” writes my friend Marc Ian Barasch, no churchgoer. Also our Sistine Chapel ceiling, I might add.

Sure, there’s every difference between reconnecting with grand but blind forces of nature and with a deity held to be conscious, caring, and supernatural. But there’s also a similarity: the magnitude of the awe the Hubble views command (“Once... just once... I'd like to be able to look at photos or read an article of NASA’s missions and not [bawl] like a baby”), and the requirement to recalibrate our scale of thinking. If you believe there’s a God, you’ve got to admit we underrated Him: the Almighty of the Book of Job, thundering “Where wast thou when I laid the foundations of the earth?”, is a piker. As a ’30s movie reporter might say, “Get me rewrite!” (But keep the poetry.) If you don’t believe there’s a God, you could still be forgiven for gasping “Omigod!”—or “Holy #@*&!”—at those sights.

The scientists who first conceived the Hubble seem to have had an inkling of this. According to Zimmerman, at a 1965 NASA study conference in Woods Hole, Massachusetts,

the astronomers were in such agreement . . . about building a big space telescope that at one point things devolved into a lighthearted discussion on what to name it. Fred Whipple suggested that they name it the “Great Orbiting Device,” or GOD.

Some of the language surrounding the operation of the Hubble, too, has a poetry that’s almost scriptural: “first motion,” “almost always a big event in the world of space exploration,” and “first light,” the technical term for the first look through any new telescope, which acquires even more of a Genesis resonance now that we may “literally be looking at the first light of the universe,” in the words of USAF Colonel Michael Good, a spacewalker on the just-returned mission. Wondering about the stars is almost certainly an impulse even older than wondering about a God; it could have marked the dividing line we crossed to become human.

So while physically the Hubble may bear an uncanny resemblance to the Stanley Cup, as one wag of my acquaintance pointed out, metaphysically it’s more like that black slab in Stanley Kubrick’s 2001: touch it, and be forever changed. And touch it we do: that the Hubble and its orbit were designed for maintenance by human hands is part of what has made it just the right intermediary and “transitional object” to deliver what could have been a more traumatic initiatory blow. (The other thing that makes it so perfect, after all, is its comeback from imperfection and disgrace. We can relate. Change one letter and it would be the Humble.) Anyone who believes that robotic space exploration, with its lower risk and longer reach, is the only way to go should read this journal entry by astronaut F. Story Musgrave, written just after the return of that December 1993 Hubble-saving mission he captained. It’s a visceral and kinesthetic firsthand account of what Miles O’Brien (repeat link) calls “those high-tech, high-drama ballets in the void. Man meeting machine in the harshest environment of all.” Knowledge isn’t quite real or ours unless we lay our hands and stake our lives on it.

Hubble’s successor, the James Webb Space Telescope, to be launched about five years from now, won’t inspire the same affection: it’s described as “a tennis court-sized telescope” operating in a “distant, isolated orbit,” “far beyond Earth’s moon”—nearly a million miles away to Hubble’s neighborly 360. “It isn’t designed to be serviced,” writes astronaut Steven A. Hawley (repeat link), who was Hubble’s midwife:

[The Webb’s] intended orbit 932,000 miles from Earth will likely put it out of reach of astronauts, at least in the near-term. But, perhaps heeding the lessons of Hubble, NASA has contemplated installing a device that would allow it to be captured by a robot or piloted spacecraft in the future.

Cold comfort. Astronaut John Grunsfeld on the final mission called himself “literally a Hubble hugger;” no one will be hugging the Webb anytime soon. Fortunately, Galaxy Zoo—the subject of Charles Liu’s new “Out There” (Natural History, June 2009), and of my next post here—has invented a new way to get up close and personal with extreme features of the universe, and usefully so. Zoo regulars even get to write their names in galaxies.

So here’s to Hubble—I hoist my galaxy beer stein—“an instrument that conceptually cannot only give us great science, but also give us a sense of what is our place in the universe,” as Story Musgrave told Ted Koppel. We wake in our tiny cradle, an infant that for the first time focuses its eyes and smiles at its mother.

BONUS MATERIAL
  • Slideshow: all about how a Hubble image—perhaps the most famous one of all, the “Pillars of Creation”—gets made from raw data.
  • More on how choices are made in the creation of Hubble images.
  • Some of those choices are frankly artistic. As Joshua M. Greenberg wrote in Public Understanding of Science [subscription only]:
    The picture [“Pillars of Creation”] had been shot at an angle to make the gaseous pillars appear perfectly vertical, while their true orientation from Earth’s perspective is about 60° clockwise (which would have made a markedly less “inspirational” image).

    In the words of Hubble Heritage image processor Zolt Levay (PDF), “perhaps the person most responsible for shaping the public perception of Hubble imagery”—his colleagues call him “the Ansel Adams of space”:

    I hope [to] convey some of the technical things we’re looking at in the image but also, in a more emotional way, convey the grandeur of what we’re looking at and the awe that I feel when I look at these images. . . . The subjective choices are informed by what’s inherently in the data. . . . but also informed by. . . principles from the art world on how to convey images in the strongest way possible.

    In this cool slideshow, “Art and the Universe: An Intersection of Understanding and Beauty” (PDF), he illustrates the point with examples from the Hubble, Monet, van Gogh, great landscape photography, and the comic strip “Opus.”

  • Cultural historian Elizabeth Kessler sees the influence of 19th-century American Romantic landscape painting—from another era of discovery—on the Hubble images. Her dissertation was titled “Spacescapes: Romantic Aesthetics and the Hubble Space Telescope Images.”
  • Americans’ annual pizza bill exceeds NASA’s budget.
  • “Oh, baby, look at that.” Mission accomplished, the Atlantis shuttle crew releases Hubble.

Amba has been a freelance critic, writer and author since 1969, has written for nearly every major women's magazine, The New York Times Book Review, Village Voice and The Nation.
Ambivablog






September 23, 2009

Supramolecular Self-Assembly at the Nanometer Scale

By Red Sox Steve

Nanotechnology isn't new, it's a different scale at which scientists can observe phenomena, and take advantage of new information and theories in the process. Same goes for a field called "Supramolecular Chemistry". "Supra", the latin word for "above" is a prefix adopted by scientists centuries later. The idea behind Supramolecular Chemistry is that atoms and molecules can interact with each other in a reversible and noncovalent way. Recall from previous discussions that "covalent" bonds between atoms are bonds where electrons are shared. Supramolecular interactions allow for greater flexibility in the interactions between molecules, and further, don't alter the structure of participating molecules.

Self-assembly is another concept that has gone hand-in-hand with nanoscale interactions in much of the writing I've done here. When molecules self-assemble at the layer of individual crystals or atoms, they are self-sorting in a way that is energetically favorable; molecules are "swimming" around in solution in order to find out where they will be most comfortable (i.e. use the least amount of energy for a given configuration) - wherever they get comfortable, they settle. Self-assembly of single layers of molecules is a "bottom up" approach; in the case of our study cited below, a molecular foundation is laid down, and other molecules are superimposed. A porous layer has been created from the weak molecular interaction between two molecules. If the pores remain structurally stable, additional molecules, with a tendency to self-assemble, can be introduced and find their way into the pores. This will result in a functional self-assembled monolayer that can impact the tiny tiny world of nanotechnology.

First, let's examine the structure of a porous network; then we will look at the molecules that coordinate their way into the pores. In the study cited below, there were two molecules used which were able to bond with each other via (weak) hydrogen bonding. One is called "melamine" (a/k/a 1,3,5-triazine-2,4,6-triamine... can you see why scientists use "melamine" instead? :)) and the other is called "PTCDI" (short for perylene-3,4,9,10-tetracarboxylic di-imide).

Melamine and PTCDI were dissolved in a solvent called Dimethyl Formamide (DMF, for short) and adsorbed (scientific term for attached) onto a gold surface, forming the honeycombed structure you see in (d) above. Scanning Tunneling Microscopy tells us that, aside from a few imperfections, the structure in (d) above is layered on top of the substrate.

So, we've put a porous layer on our substrate, but what about the self-assembling portion?

In order to adsorb molecules into the nano-sized pores, a functional group is needed that can adsorb onto the gold substrate, form hydrogen bonds with its surroundings and be able to attach different functional groups for further examination. Enter thiols! The "thiol" group is a sulphur-hydrogen bond attached to one end of a molecule. Calling a molecule a "thiol" only indicates that it has a S-H group at one end of its structure. In this case, sulphur can adsorb onto gold, while not disrupting the matrix adsorption in the process.

Notice that ASH is a very rigid, cubic structure, different from BP3SH which has more of an "aliphatic" structure ("aliphatic" meaning that it has benzene rings which share electrons amongst themselves) and both are different from C12SH which is a long hydrocarbon chain. All 3 molecules were able to permeate the porous network, and after adsorption, the hexagonal structure of the melamine-PTCDI was maintained, proving that a variety of thiols can be stably introduced into this system.

The specific results and differences amongst the 3 thiols used tell us that there are additional factors to consider when trying to self-assemble thiols onto a porous molecular network. For example, adamantane thiol fills the porous network very quickly, and maintains its structure so rigidly that individual ASH molecules can be spotted during microscopic analysis. On the other hand, both BP3SH and C12SH will break up the pores if exposed to the structure for a prolonged period. Although in the case of the latter two the porous network starts to deform, it is possible to control the rate of the reaction in order to achieve adsorption of the thiol molecules to the gold surface and within the constraints of the porous structure.

Once it was determined that thiols dispersed among a porous network could form a stable structure, additional tests were done to determine the characteristics of the structure. One problem that scientists had previously encountered was that uniform self-assembly structures were unable to act as barriers to contain additional molecules. This concept was tested on the melamine-PTCDI network with electrochemically deposited copper ions. The entire thiol/porous matrix was deposited in a copper solution, and scientists noticed that copper ions inserted themselves in the monolayer between the thiol molecules and the Au substrate; however no copper ions were able to permeate the melamine-PTCDI/Au layer. This proved that the melamine-PTCDI honeycombed structure can serve as a selectively impermeable barrier for ions. Electrochemically depositing ions into the honeycombed network can be controlled by using melamine-PTCDI as the diffusion barrier.

At the nano-scale, the melamine-PTCDI structure created here can control the self-assembly of thiol molecules and act as an impermeable barrier to other ions. Scientists can take advantage of the fact that self-assembling molecules will organize around an already existing structure and can manipulate molecules with nano-level precision. Further, the melamine-PTCDI network not only can direct molecules into its structure, it can also serve as a blocking mechanism to prevent the adsorption of certain molecules to the substrate layer. Scientists can build structures to specifically control the behavior of molecules at the nano-level. The idea that introducing physical parameters into a system to control molecular tendency to self-assemble means that specific structures can be built with nano-level precision.

Citation:

Functionalizing hydrogen-bonded surface networks with self-assembled monolayers
Rafael Madueno, Minna T. Ra, Christophe Silien & Manfred Buck
Vol 454
31 July 2008





July 06, 2009

Explorers



In the meantime, there is a plethora of excellent knowledge to be had on where we are heading and what's gaining importance in the near future in our archives to the right. Peruse away!




May 25, 2009

Pons

By Red Sox Steve

Last time, we discussed one of the parts of the hindbrain which also controls our nervous system, the medulla oblongata. The medulla connects our brain to our spinal cord, and contains white and gray matter which transmit and process electrical signals within our body. The nerve cells in our body are connected to nerve terminals via insulated axons - the electrical signal travels from the cell to the terminal via the axon, which is how our brain receives its messages.

There is another part of the hindbrain, which sits right above the medulla and below the fourth ventricle's cavity. It connects the cerebellum in the midbrain to medulla. Yep, I'm talking about the pons. The pons functions as both a center that receives information from the nervous system as well as a "way station" that connects nerve fibers traveling between the cerebral cortex (forebrain) and the cerebellum (hindbrain).

The pons, like the medulla, is connected to the nervous system. The pons works with some of the nerves that make up the peripheral nervous system (PNS). The PNS works on the periphery of our functioning network of nerve fibers, and connects limbs and organs to our central nervous system (CNS), the brain and spinal column. More specifically, one of the pons' key functions is to serve as the beginning or end for four of the PNS' 12 cranial nerves - these four cranial nerves transfer information between the facial region and brain. Note that the cranial nerves connect directly to the brain, and perform various functions as outlined in the photo below.

Each nerve is also referred to by its roman numeral as they are a part of the cranial nerve system. For example, the trigeminal nerve is also called the "fifth cranial nerve".

The trigeminal nerve controls sensation and motor functions in the face. It is the largest of the cranial nerves, and branches into three separate nerves for sensory function:

1) the ophthalmic nerve - senses information coming from the scalp, forehead, upper eyelid, cornea, nose and sinuses
2) the maxillary nerve - senses information from the lower eyelid, cheek, upper lip, upper teeth, gums and palate
3) the mandibular nerve - senses information from the lower lip, lower teeth, chin, jaw and external ear as well as the meninges (membranes of the central nervous system)

The mandibular nerve controls motor function as well. There are a series of muscles at the end of the mandibular nerve which control various regions of the mouth, and in addition a single region of the ear. Scientists have concluded that an injury to a peripheral nerve can paralyze the muscles on one side of the jaw, causing the jaw to shift to the weaker side when open.

The abducens nerve innervates an eye muscle called the "lateral rectus muscle". It runs through a layer of the skull and then pierces the skull before entering the sinus and then the carotid artery. Because it travels from the base of the brain, through the skull and then the carotid artery before reaching the eye, it is vulnerable to damage in a number of locations. Both injuries to the temporal bone (side of the skull) and brain lesions that put pressure on the brainstem can damage the nerve.

The facial nerve connects to the muscles of the inner ear and face, neck and scalp as well as playing a role in facial expression. The facial nerve goes from the pons, through a canal in the temporal lobe called the "internal auditory meatus" (or "internal acoustic meatus") and spreads out across each side of the face. The facial muscles can be paralyzed due to nerve damage at the brainstem, and can also cause a loss of taste sensation.

The eighth cranial nerve known as the vestibulocochlear nerve starts at the juncture of the pons and medulla oblongata and ends at various points in the ear. For this reason, it is also referred to as either the "auditory nerve" or the "acoustic nerve". There are two main components to the vestibulocochlear nerve: the cochlear nerve which wends its way to the hearing part of the ear, and the vestibular nerve, which works with the equilibrating pieces of the ear. The cochlear nerve ends in a part of the inner ear called the "Organ of Corti" which contains the auditory cells the ear uses to hear. The sensory endings for the vestibular nerve also end in the inner ear, however, they are attached to structures related to equilibrium, not hearing.

Now, lets discuss the pons as a "crossroads" between the cortex and the cerebellum. There are nerve fibers which start with neurons in the cerebral cortex and terminate at the pons. Subsequent to this journey, the crossed fibers serve as a bridge that connect each cerebral hemisphere to the opposite half of the cerebellum. These nerve fibers are called "crus cerebri", and are found in what is called the "cerebellar peduncle" (nerve bunches in the cerebellum).

Fibres originating from neurons in the cerebral cortex terminate at the pontine nuclei (cell nuclei in the pons), which in turn project to the opposite hemisphere of the cerebellum. These fibres, called crus cerebri, form the middle cerebellar peduncle and serve as the bridge that connects each cerebral hemisphere with the opposite half of the cerebellum. The fibres originating from the cerebral cortex constitute what is called the "corticopontine tract" (a stretch of nerves that extends from the brain's motor function center to cranial nerves found in the pons).

The pons also controls respiration via two nerve domains: 1) the apneustic center in the lower pons, and 2) the pneumotaxic center in the upper pons. The apneustic center sits right atop the medulla and promotes inspiration by stimulating nerves in the medulla. The pneumotaxic center in the pons, also known as the pontine respiratory group (PRG), works to inhibit the stimulation provided by the apneustic center. By doing this, it is able to regulate the volume of air that enters the lungs and the overall rate of respiration.

Although the pons is small it is critical to life. It sits at the top of the medulla oblongata and is linked to parts of the cranial nerve network. Similar to its neighbor, part of the pons is automatic - no active thought is required telling us we need to breathe. In addition, scientists know that injury to cranial nerves connected to the pons, or temporal lobe damage, may manifest themselves in the face and jaw due to cranial nerve structure. We've now explored two parts of the hindbrain - the medulla oblongata and the pons, knowing that they have each evolved over hundreds of millions of years to provide critical operation to the body by being part of its most important organ, the brain.





May 23, 2009

Why You Don't Have to Think to Beat Your Heart - the Medulla Oblongata

By Red Sox Steve

If you click your mouse a couple of times, you'll find a great article under Life in the Aerie which discusses the various manifestations of a human's decision making process. All the choices we make, all the thoughts we form, all the voluntary and involuntary actions we take have a common source: our brain. What is in the brain? What do we know about the brain? Is it really true that humans use a very small percentage of their brain matter in everyday life? What kinds of electronic, chemical, and biological interactions take place in the brain?

Scientists have theorized that the first vertebrate (a "protovertebrate") was small and soft-bodied; as a result, many believe that a protovertebrate fossil will never be found. Scientists have found, however, evidence of vertebrate existence going back to what is called the Cambrian era, approximately 500 million years ago. It is thought that all vertebrates in existence today have evolved from "cephalocordates" which are considered to be one group sharing various anatomical characteristics - vertebrates are included within this grouping.

In vertebrates, the brain exhibits three regions: the hindbrain, the midbrain, and the forebrain. It is the brain's job to "take up" sensory information and produce a motor response, and in higher vertebrates (such as humans) the brain is the center for all learning. Although the brains of both lower and higher vertebrates exhibit these regions, the brain undergoes even greater development in higher vertebrates during embryonic development - thought to be the first 8 weeks after fertilization.

The medulla oblongata ("medulla") is part of the hindbrain and sits on what is known as the brainstem, below ("inferior to") the pons, and above ("superior to") the spinal cord. The medulla transmits signals between the spinal cord and the higher parts of the brain and also controls the autonomic nervous system (ANS). Our autonomic nervous system can also be called our "automatic" nervous system based on the actions it controls: heart rate, digestion, respiration, salivation, perspiration, and pupil dilation among many other things.

The medulla contains two types of nerve fibers which it uses to send messages between the brain and the spinal cord. White matter, or white nerve fibers surround gray matter or gray nerve fibers. What's a nerve fiber and what's the difference?

First, a nerve fiber is also known as an axon, and it conducts electrical impulses away from the cell body to what is known as the axon terminal. When individual nerve fibers are bundled together as they are in the human body, they make up nerves. Nerve fibers are extremely thin (on the scale of a micrometer), but can extend throughout the body. The longest individual nerve fiber in the body makes up the "sciatic nerve" and extends from the end of the big toe to the base of the spine. One other thing to know about a nerve fiber is that the axon which connects the cell to the axon terminal is "myelinated". What this means is that myelin sheaths surround the axon and insulate it. Myelin is made up of a number of proteins, and furthermore, it helps "push" the electrical signal along the axon because it prevents the signal from falling away from the axon.

Now, what about white and gray matter? When the brain is cut open, white tissue appears as a result of the presence of myelin surrounding axons. Myelin is pinkish white because it contains mostly lipid (carbon-based molecules) and a small amount of capillaries (blood vessels). Gray matter, on the other hand, is made up of the cell bodies of neurons and other types of neural cells. Although both contain myelinated axons, the major difference in appearance between white and gray matter is that white matter is almost all myelinated axons, whereas gray matter is composed of a variety of other neural cells. In terms of function, therefore, because the white matter is entirely myelinated axons, its job is to transmit the electrical signals. Because gray matter has a much more complex composition of cell bodies, its job is to process the signals it receives.

Let's talk about one more key component of the medulla, which helps the brain "float" within the skull. There is a series of ventricles within the brain which contain cerebrospinal fluid (CSF). CSF is a clear liquid that surrounds the brain and spinal cord. It provides a mechanical and immunological cushion around the brain, and also lubricates the interaction between bones and the spinal column. CSF is formed in the brain's ventricles and makes its way around the skull and down the spinal column.

The medulla's function in all this is that it contains what is known as the "fourth ventricle" - the fourth ventricle (the other three are known as the left and right lateral ventricles, and the third ventricle) extends from the cerebrum and runs as a central canal in the spinal cord, through the medulla. The fourth ventricle is shaped like a diamond when viewed in a cross-section, and can traverse either the pons or the upper medulla before reaching the spinal column. The CSF that surrounds the brain does so in a cavity called the "subarachnoid space". The subarachnoid space that surrounds the brain is one of the membrane layers that allows the brain to remain in a stable and protected environment.

When considered in its entirety and importance, the brain is the most complex and critical organ in the human body. The brain must be broken down into its component pieces so we can grasp how the function of each contributes to the whole. The medulla oblongata can be considered one of the parts we don't miss until it's gone - it controls all the functions most of us take for granted - breathing, heartbeat, pupil dilation, etc. Although the medulla clearly has a part to play, we aren't necessarily aware of it when it works properly. Understanding the medulla gives us more insight into this complex and intriguing organ that has been in existence in vertebrates for over half a billion years.

Sources: Wikipedia, Encyclopedia Brittanica





May 17, 2009

Surface Composition of the Sun

By Red Sox Steve

Last time, we discussed the incredible power of the earth's most important star, our sun. It is massive and dense and produces much more heat and light than all the planets in our galaxy can absorb. The source of all this energy is the nuclear fusion reaction which forces protons together that repel in many other natural environments. At the core of the sun, atomic fusion creates the subatomic particles that form the heat and light we experience every day of our lives.

So, we got down the fundamentals, but if we take out a telescope and study what is visible, what are we looking at, and what role does it play in the sun's environment? What are the chemical components of our sun?

At the sun's core, nuclear fusion takes place producing both (^4)He and neutrinos in the process. Energy is generated from the kinetic energy of the (^4)He and (^1)H products as well as the gamma rays and neutrinos. One of the theories that scientists are examining is based on what is known as the sun's "convection zone". The sun radiates heat generated from its core out to its surface via the heat transfer process of convection. What this means is that heated substances (in this case all our reaction products) move radially away from the relatively hot core to the cooler surface. In the process of getting there, they exchange heat with their surroundings until the temperature of both the particle and its surroundings reaches equilibrium. There is a random component to convection as well - these particles move in a number of directions, however until they are able to lose their heat to their surroundings they have enough energy to remain in motion. Therefore, only particles that move radially away from the sun's core transfer heat away from the 15,000,000 K (K=Kelvin, a unit of temperature measurement) environment they came from.

Heated gases (in the form of plasma, an ionized gas) make their way towards the sun's surface, known as the photosphere. If the plasma is able to cool significantly before it gets there, it travels no further. If, however, it makes it all the way to the photosphere, it is because it is still significantly hot enough to do so.

What is it that determines how far from the sun's core the plasma will travel?

In any star in the galaxy, the core is always hotter than the surface - the core is the densest part of the star, and, separate from its less dense gaseous exterior, rotates around a central axis as a complete body. The photosphere, therefore, is the gaseous surface that is the coolest part of the stellar body. The difference in temperature between the core and the surface is measured by the "temperature gradient". The temperature gradient is the star's temperature as a function of the radial distance away from its center. If the temperature gradient is steep (meaning that it gets COOLER QUICKLY as the DISTANCE from the radius INCREASES, or that it gets HOT QUICKLY as the DISTANCE from the radius DECREASES), then hot plasma will quickly rise to the photosphere, and cool plasma will quickly descend.

How do we know this takes place? Scientists have been able to determine that there are both light and dark regions appearing on the photosphere. In a solar phenomena known as "limb darkening", the sun's observers can see that there is a decrease in brightness going from the center of the observable disk to its outer edge or limb. Astrophysicists have observed that the darkening effect is greatest for blue light and attribute the entire darkening phenomena to the presence of the temperature gradient - a decrease in solar temperature as distance from the sun's core increases.

Another phenomena that is seen on the sun's surface is granulation, which is the formation of cells containing the convective heat and energy that have made their way to the sun's surface. Granules can exist for about 25 minutes, and the hot gases rise off the sun's surface at about 300 meters/second. The granules dissipate either by fading or expanding outward into neighboring granules. Beyond the pattern of solar granulation resulting from convection, there are discussions of mesogranulation and supergranulation, which are designations of different scales of granules. Mesogranulation, a phenomena whose existence is still in dispute, is thought to occur when granules collect to form a pattern from 5-10 thousand kilometers in diameter; supergranulation, a granulation pattern having a diameter beyond 20,000 km, is a photospheric occurrence that is not disputed by scientists.



You Tube Link

What we are seeing in this video is the convective heat pockets that have made it to the surface of the sun to form granules. New granules continuously arrive at the sun's surface, releasing hot gases and then dissipating or aggregating with granules in their proximity. Dark and light areas are in constant flux due to the changing presence of cool and warm gases at the sun's surface.


Granulation on the photosphere is not only related to the convective behavior of heated gases, but also the formation of a magnetic field bounded by the supergranulation pattern. The edges of these magnetic fields which exist just above the sun's surface appear bright, while the center of the magnetic field appears dark. The presence of dark areas on the sun's surface, when observed at different wavelengths of emitted light, indicate what substances exist on the sun's surface.

When scientists observe the dark areas within a granular magnetic field, what they are seeing is the absorbtion of photons by the elements that exist there. Photons emitted by atomic fusion reactions at the sun's core are sent to the surface and collide with certain elements there. The elements either absorb photons they collide with or emit them depending on ionization energies and electron affinities of the particular element. Dark areas within a magnetic field indicate that photons traveling at given wavelengths are being absorbed; knowing the wavelength of the absorbed photon as well as the particular characteristics of the element, scientists can determine which elements exist on the sun's surface. They've discovered, based on this type of examination which is known as "solar spectral analysis", that the photosphere is made of Oxygen, Carbon, Iron, Sulfur, Neon, Nitrogen, Silicon, and Magnesium, in addition to Hydrogen and Helium.

Although most of the sun's power is generated by the nuclear fusion chain reaction we discussed last time, there is a dynamic and influential photosphere that is where much activity takes place. Scientists have been able to understand what goes on within the inner layers of the sun by observing the granulation patterns that take place on the photosphere, and by analyzing the light emitted at the photospheric layer. Although the sun is critical to life on earth, it is also a star among many others in the solar system. In this way, the sun is able to tell us about itself and other stars so we can continue to expand our knowledge of the known universe.



You Tube Link

Here are some of NASA's images of the sun. Enjoy!








May 15, 2009

The Science of the Sun

By Red Sox Steve

Last time, we discussed the science behind the construction of man-made proteins - by understanding DNA and its role in the formation of proteins, scientists can start to elucidate a role for man-made proteins that mimic naturally occurring proteins and can also self-generate.

We're going to move away from the cellular world and discuss the largest amalgamation of matter in our known galaxy; the thing that makes up over 99% of all the matter in our solar system: the sun.

Anyone who has ever left a cold drink out on a hot summer day, has gone to a ski slope or a beach, or done any one of millions of activities where natural light is a factor understands only a fraction of the sun's power: scientists have calculated that the amount of energy ALL planets together absorb from the sun is 1 part in 120 million. In other words, the sun emits 120 million times the energy used by all the planets. By some estimates, the sun has been burning for over 4 billion years and its radius is 109 times that of earth's. The sun is over 90 million miles from us and it's mass is 330,000 times that of earth's.

I could go on and on about the sun, and I will (from Encyclopedia Brittanica):

1) The temperature at the core of the sun is 15,000,000 Kelvin (take Kelvin to be sufficiently similar to Celsius for our purposes).
2) The sun's surface temperature is anywhere from 4,000 - 8,000 Kelvin.
3) The pressure at the core of the sun is 10,000 times that at earth's core.
4) Because of the high temperatures at the sun's surface, it is difficult for solid matter to exist - the surface is mostly gaseous.
5) By some calculations, the sun becomes 10% brighter every billion years.
6) When we see the sun from Earth, we are looking at its surface, known as the photosphere. This is the layer that creates most of the radiation that reaches earth.

Let's flesh out some important concepts now, to build on our understanding of the most important star in our galaxy.

What materials are used to generate solar energy?

The sun is composed of nearly 90% hydrogen atoms. Each hydrogen atom has a mass of 1.0078 amu ("atomic mass units"). Hydrogen is the simplest element known to man - it has one electron and one proton. Furthermore, it is highly likely that hydrogen nuclei will come into contact with one another because of the amount of heat and pressure at the sun's core. It is the fusion of one hydrogen nucleus to another that triggers the entire process I am about to describe. The sun is a self-perpetuating chain of nuclear fusion reactions with a number of intermediate steps. This process creates the energy generated by the sun, and because of the amount of hydrogen in the sun's core, this can continue for billions of years.

How is the fusion of hydrogen atoms converted to energy?

There is something called "electrostatic repulsion" which governs interactions between atoms. It's a phenomenon that is easily understood when you put two refrigerator magnets together - they repel each other because they have a similar charge. The nucleus in an atom works the same way because it is positively charged, causing Hydrogen atoms to repel each other. In the case of the sun, however, both heat and pressure are so strong that hydrogen is able to overcome its tendency to repel other hydrogen atoms. The hydrogen atoms are literally squeezed together, triggering a number of reactions. This takes place at the core of the sun where energy is generated in the form of what is known as a neutrino.

Neutrinos are the result of 2 Hydrogen atoms colliding with one another, generating what is known as a "deuteron" (a/k/a deuterium). The difference between a deuteron and a hydrogen is a single neutron. Hydrogen has a proton and no neutron, deuteron has a proton AND a neutron. Both have a single electron. Dueteron, therefore, is able to retain its neutral charge, and is slightly heavier than hydrogen, but because it only has one electron, it is lighter than the next element on the periodic table, helium.

How does deuteron form if hydrogen has no neutrons?

Because there is an abundance of hydrogen, and so much pressure at the core of the sun, once every few billion years (seriously) one hydrogen is close enough to another to undergo a process called "beta-decay". When there are too many protons in an atom's nucleus (in this case as a result of the heat and pressure forcing hydrogen atoms together), and too many surrounding electrons, it becomes impossible for a proton to emit a positive charge (called a positron). When this happens, one proton's positive charge beta decays, becoming a neutron.

Electrons and protons are referred to as "beta particles". Beta decay is a process where a beta particle is emitted by a radioactive atom. In other words, it is when a proton or electron is transformed through subatomic particle release by an atom. Losing an electron or proton is referred to as "beta decay". In the sun's case, a proton is converted to a neutron, an electron is captured by the atom, and the resulting substance emits both positron (positive charge emitted by a proton) and neutrino (particles that lack a charge) which are released with energy. Although neutrinos are low energy particles relative to the generation of energy by the sun, their presence gives scientists great insight into the process I describe above. Scientists have been able to determine that in every square centimeter of the earth at every second, approximately 80 billion neutrino particles hit the earth!

Beyond neutrino production, the energy made by the sun takes other forms, heating the earth, and producing light visible to the naked eye. Neutrinos are produced when two hydrogen atoms form a deuteron atom. After neutrino formation, deuteron can fuse with another hydrogen atom, producing a radioactive form of Helium, known as "Helium 3" or "tritium". Helium in its stable monatomic (1 helium atom by itself) form has an atomic number of 2 meaning it has a proton and a neutron along with 2 electrons. Tritium, denoted (^3)He in scientific literature, has an atomic number of 3 - it has 2 protons and one neutron in its nucleus. The next energy emitting reaction that takes place is the fusion of two tritium atoms, producing (^4)He and 2 Hydrogen atoms. If 2 atoms of tritium collide, we are talking about the fusion of 4 protons and 2 neutrons - the result is a (^4)He atom with 2 protons and 2 neutrons plus 2 Hydrogen atoms which each have only 1 proton.

Helium has an atomic mass of 4.0026 amu. In other words, approximately four hydrogen atoms give us a helium atom. Approximately. Here's the math:

4 hydrogens put together = 4*1.0078 or 4.0312 amu
1 helium is 4.0026 amu

The amount of excess mass (in the form of positrons, neutrinos, gamma rays) created from this fusion?
4.0132-4.0026 = .0106 amu

From the fusion of 4 hydrogen atoms, you get a helium atom and energy, created from the excess mass. Helium is stable with a given number of electrons, protons and neutrons. Any excess BEYOND what is required to form helium becomes energy in the form of particles (gamma rays, photons, neutrinos). In this case, the excess energy exists in the form of the subatomic particles lost in the proton-proton chain reaction.

Einstein's equation E=mc^2 (read as "E equals mc squared") gives us nearly 7 million electron volts of energy created from the excess mass generated by this series of reactions. Taking into account all the hydrogen within the sun involved in this process and the time it takes for a single reaction to take place, some scientists believe the sun can shine for 10 billion years.

One thing to keep in mind is that at the core of the sun, the atoms are completely ionized due to heat and pressure in the surrounding environment. This is one of the reasons that hydrogen atoms in the fusion reaction above can also be called protons. When photons (in the form of gamma rays) are released by the proton-proton chain reactions they too collide with ionized hydrogen atoms (a/k/a protons). Because the core of the sun is so dense, it is difficult for a photon to reach the sun's surface and be emitted from the sun as light without colliding with a proton and then being re-released... by some calculations, this takes place 5x10^19 times. Nearly as soon as a photon is released by the reaction above, it immediately collides with another hydrogen atom. At an atomic level, the photon is taking what is known in chemistry and physics as a "random walk" to reach the surface of the sun. Scientists have concluded that because of the amount of collisions that occur, it takes a photon 10 million years to reach the surface of the sun once released by atomic fusion. This is a big difference from the time it takes a photon to travel from the sun's surface to the earth, which is only eight minutes.

Our sun is among the most massive stars in our galaxy and is, along with a number of other stars, the most powerful collection of matter in the known universe. The extent to which the sun is able to continuously regenerate the substances it needs to provide light and heat are awesome in scale. Nuclear fusion takes place billions of times every second, and the power that is generated by the sun is far in excess of planetary needs. Scientists have been able to discover much about the principles that govern the atomic world by understanding the reactions that take place in and on the sun. Furthermore, understanding the magnitude of the physical properties of the sun's core and surface give us much to imagine about the circumstances surrounding the formation of our galaxy, and the possibility of life in other star systems that currently exist beyond the limits of our understanding.






May 12, 2009

Amino Acids, Proteins, and Bionanotechnology Pt. 2

By Red Sox Steve

Last time, we got a sense of some of the basics of protein construction - cellular DNA contains the instructions, amino acids are available in the extracellular environment, and a cell's ribosome does the work, producing a given protein. By examining this process, scientists are attempting to alter DNA to construct certain proteins.

In the body, different proteins exhibit a variety of characteristics - collagen makes up skin, bones, and tendons; albumin works to regulate fluid pressure; and elastin gives skin its elasticity to respond when poked or pinched. Because the structure of these proteins is controlled by their respective strands of DNA, scientists can explore the possibility of using DNA to build a single protein that combines various natural processes.

Scientists have been examining elastin-like polymers (ELPs), with the desire to create an artificial protein with biological compatibility. Elastin exists in human tissue such as lungs and it stores mechanical energy, so an organ can return to its original shape after being extended. It does this by forming sheets of cross-linked polymers of its precursor, tropoelastin. Tropoelastin is a water soluble protein synthesized by the ribosome. Right after it is synthesized it forms cross linkages (resembling a web) and goes by its new name, elastin. According to the study I've cited below, scientists have found elastin to "show a versatile and ample range of interesting properties that are not easily found together in other materials, going beyond their simple mechanical performance." In other words, elastin is an ideal protein for examination and alteration.

The properties of different ELPs (containing different amino acid sequences) have been examined to determine responsiveness to external stimuli like temperature and acidity. One type of ELP, when placed on a silicon-based substrate (a flat surface that binds to the ELP) in an acidic solution appeared flat. When the same ELP was put on a silicon substrate in a basic solution (not basic as in "simple", we're talking acids and bases here), nano-level pores appeared in the protein. Essentially, this difference is related to the structure of the protein - glutamate, one of the amino acids that appears multiple times in the peptide chain, is our culprit. The pores appear throughout the cross-linked pattern as a result of glutamate preventing certain sections of the protein sheet from fully linking with neighbors in a basic solution. This type of acid/base sensitivity is referred to as "smart" behavior of the ELP.

A cell's extracellular matrix (ECM) attaches to epithelial cells, to provide a cushion and support so the cells can remain in position. Scientists have been able to construct an ELP with four different functional sections (a/k/a "domains") imitating some of the properties of elastin, which is able to interact successfully with the ECM. The first domain (which repeats throughout the protein) allows the ELP and ECM to bind, producing a mechanical response which mimics elastin's behavior. Next, a substitution of the amino acid isoleucine by lysine is made at certain points within this repeating domain, retaining the ELP's ability to cross-link (similar to naturally occurring elastin).

The third functional domain contains an amino acid sequence which allows the protein to connect with endothelial cells (called the "CS5 human fibronectin domain"). Finally, the fourth domain in the ELP contains a domain which acts as the elastase target sequence. Elastase, an enzyme that breaks down proteins, is released by tissue cells when the tissue decides to break down the ELP. After its release, elastase binds to the target sequence on the protein, and begins the process of breaking down the ELP. Successfully constructing an ELP which contains many of the key properties of elastin is a useful starting point for "bottom-up" construction of proteins.

The technology being used here has widespread appeal. Although it is not yet possible to construct genetically modified elastin within the human body, scientists are able to use DNA to build these proteins. Prior to obtaining the ability to modify DNA and amino acid sequences, scientists were confined to building proteins via a field known as polymer chemistry. They would have to think up dozens if not hundreds of chemical reactions to produce a desired protein - a much less efficient and effective process. In this case, they are using naturally occurring proteins, as well as the DNA that shapes them, to modify what is already found in mammals.

Citation:

J. Biomater. Sci. Polymer Edn, Vol. 18, No. 3, pp. 269–286 (2007)
Biofunctional design of elastin-like polymers for advanced applications in nanobiotechnology
J. CARLOS RODRÍGUEZ-CABELLO, SUSANA PRIETO, JAVIER REGUERA, F. JAVIER ARIAS and ARTUR RIBEIRO





May 09, 2009

Amino Acids, Proteins, and Bionanotechnology Pt. 1

By Red Sox Steve

Last time, we talked about how the chirality of a molecule can be used to construct a molecular switch. External stimuli like light and heat can induce changes at the molecular level, effecting a change in a molecule's structure. The flexibility contained in a molecule's stereochemistry allows it to change from one enantiomer to another. Scientists are examining how these changes can be used in various switching mechanisms.

This week, we are going to examine something that the human body, and all cells in all living organisms do billions - if not trillions - of times over the course of a lifetime: construct proteins needed for a number of functions in the body. One of the first things that is taught in biology is that amino acids are the building blocks of proteins. In order to construct a protein, DNA, our genetic messenger, contains step-by-step instructions on how to order amino acids to make a given protein. After the amino acids are linked together in a chain (known as the "primary structure"), their sequence determines how the hydrogen bonds between amino acids connect ("secondary structure"), and ultimately how the protein chain is able to form a 3-D functioning molecule ("tertiary structure"). In other words, the function of a protein is determined solely by the sequence of its amino acids, which is determined by the instructions found in DNA.

What is an amino acid and where do amino acids come from?

The code in DNA provides instructions to make proteins from only 20 amino acids. In other words, the cell uses 20 unique amino acid molecules in a variety of lengths and sequences to make all the proteins in the body. In a theoretical protein consisting of a chain 100 amino acids long, there may be 1.3 x 10^130 different possible sequences of amino acids. The potential to vary the structure and function of protein molecules based on the amino acids available is enormous.

There are two types of amino acids: Essential and Non-essential. ALL amino acids are critical to the function of life. What "essential" means is that the human body is unable to construct the amino acid from ingested proteins, therefore certain types of foods containing the amino acid are required. "Non-essential" amino acids can be constructed from the breakdown of ingested proteins, therefore do not need to be specifically sought out in a diet.

An example of a non-essential amino acid is serine. Although it is an amino acid itself, serine can be synthesized by the message provided in DNA. Recall that we discussed serine on Tuesday - one enantiomer exists predominantly, and scientists have theorized that because of how it is constructed in nature, it may be produced in very cold regions of space. Recall that last time, we discussed the sensitivity of serine to light causing it to change from one enantiomer to another.

One example of an essential amino acid is lysine. The "L" enantiomer of Lysine is a building block for all proteins in the body. L-Lysine is found in foods like soybeans, spinach, and quinoa and it is critical to calcium absorption, building muscle, and recovering from surgery or sports injuries.

I want you to notice some things about the basic structure of each of these amino acids, as illustrated by the picture below:

1) each has an "amine group" (the NH2), and a "carboxyl group" (a/k/a carboxylate or carboxylic acid where the COOH exists). All amino acids have these two groups, as well as a unique side chain.

2) when these amino acids are linked together to form a chain (recall, this is the primary structure of a protein), it is the amine group of one linking to the carboxyl group of the other. The bond formed between the amino acids is called a "peptide" bond, and the reaction is called a "condensation" reaction because water is a byproduct of the reaction.

How do we get from DNA to a protein?

DNA exists in a cell's nucleus as a double helix. This means that two strands of complementary DNA base pairs are bound to each other through hydrogen bonding, and then the resulting ladder-like structure is wound around itself, creating a helix. When it comes time to synthesize a protein based on the sequence of a DNA molecule (as indicated by the presence of certain molecules outside the cell binding to the cell, kick-starting the process), enzymes within the cell are "activated", beginning a process called "transcription". The cellular DNA is "unzipped" by different enzymes into two single strands which are each then converted to a substance called messenger RNA ("(m)RNA" for short), and sent out to another part of the cell called the ribosome. Decoding of mRNA by the ribosome to construct the protein is known as "translation". If we think of the cell as a factory, the nucleus contains the instructions for protein manufacture in the form of DNA. The ribosome receives those instructions in the form of mRNA. The ribosome does all the work - it builds the protein by grabbing amino acids from its cellular surroundings and linking them together.

Now that we understand some of the biology behind the creation of proteins, we will be able to explore ways that scientists are manipulating this process. Scientists are able to investigate the various uses of naturally occurring proteins and understand how they are made in the cell with relative ease. Rather than conduct a number of man-made reactions to produce a desired protein, scientists are changing the instructions found in DNA to achieve this result. By altering the early steps in the process (the DNA sequence), as well as changing the structure of amino acids, scientists can develop specific tailor-made "bottom-up" approaches to protein construction.





April 20, 2009

Delivering Drugs to Cancerous Cells Using Nanotechnology

By Red Sox Steve

We've discussed here the signifigance of Carbon in nanotechnology, how we can use nanomaterials to detect harmful substances, and the wide variety of applications and possibilities of nanotechnology based on the endless discoveries that scientists continue to make. The good news is that because nanotechnology continues to play a larger and larger role in science and scientists keep thinking up new ways to use it, I won't run out of things to write about for at least a few decades! Look, the point in all this is that one way or another this stuff is coming. We've got an entire century of high-tech development that still has to take place, and nanotechnology is one of the ways we are going to get humanity to 2100 and beyond! Through government-funded projects like the National Nanotechnology Initiative, we are going to continue to incorporate nano-related discoveries into all aspects of our lives.

I usually follow up my introduction with something that tells us what nano is, and the fundamental science behind it. If you've read any of my previous writings on nanotechnology, your synapses should already have made the necessary nano-level connections, so I'm going to skip that. For newcomers, check out this, this or this to get an idea of the foundation of nano-science, then scoot right back here and you'll be on the same page as all the rest of us. Damn the web makes life easy... don't it? :)

I hope you don't need me to tell you how dangerous and uncontrollable cancer is. At a cellular level, cancer cells replicate more quickly than healthy cells; at a treatment level, medication levels need to be handled delicately to carry out search and destroy missions against cancerous cells while, at the same time, minimizing the impact on the rest of the body.

Let's talk about drug delivery. How do we get drugs to go ONLY into tumor cells? What are the tools at our disposal to accomplish this? Let's get into a little chemistry and biology first so we know what we are talking about. Cells are the basic building blocks of life. In the normal, every-day course of business, they live, they replicate, they consume energy, they release heat and waste, and when they cannot function, they die. Because cells contain DNA, cellular function is how a human or animal changes over time - everything from hair to teeth, head to feet; humans have over 1 trillion cells in their body at any given time.

How cells absorb materials is a critical part of understanding how we get drugs into cells. First, cells are surrounded by a cell wall, which is made up of what is called a "phospholipid bilayer". Our phospholipid bilayer is made up of chemicals that are simultaneously hydrophobic ("water hating") and hydrophilic ("water loving"), among other things. A phospholipid is a long chain-like molecule, where one end is attracted to water, while the other end is repelled by water (all due to its chemical structure).

The key to the phospholipid bilayer's function is that it is "selectively permeable". In other words, it contains other embedded molecules that allow materials to go in and out of the cell. What is allowed to pass through determines how the cell functions.

There are two key items I want you to take away:

- cells are made up of a hydrophilic and hydrophobic phospholipid bilayer
- the phospholipid bilayer is selectively permeable

The DNA found in the cell's nucleus provides instruction for how the cell should divide and replicate itself. When a cell replicates, it uses enzymes to divide the strand of DNA (remember DNA is a DOUBLE helix, so it can be split in two) into complementary pieces.

Let's talk about some of the basics of DNA: One of the first things to know about DNA (which every living thing has in its cells) is that it is a combination of a 4 different chemical compounds: Adenine, Cytosine, Guanine, Thymine. These compounds are so specific in their chemical structure that ONLY Adenine and Thymine connect on different DNA strands, while ONLY Cytosine and Guanine can connect on different DNA strands. Adenine and Thymine are therefore "complementary" base pairs of DNA, while Cytosine and Guanine are also known as "complementary" base pairs of DNA.

In this manner, what would happen if a strand of DNA were cleaved down the middle? Well, you'd have two single strands that were only able to bind with complementary strands that had the same DNA sequence of the strand that just broke away. This is what happens when cells replicate.

All the genetic information in a person's body is in their chromosomes. The chromosomes are very long strands of DNA, which are found in the nucleus of every cell in our body. Your hair, skin, mouth, and nails all have the same genetic information. For our purposes, when cells divide, the DNA is replicated because complementary base pairs separate and newly created base pairs from within the cell "latch on" to its complementary base pair on the strand. This happens to both separated strands of DNA, creating two new double helices from a single double helix.

Now we know the basics of cellular biology and are ready to explore how scientists use nano-level science to deal with cancer cells.

The drug, which is quite dangerous (isn't that the point?) needs to get where it is going without harming any healthy cells in the body. The anti-cancer drug I have been reading about is a prototype called Doxorubicin ("doxo", trade name: Adriamycin). Since its discovery, scientists have made minor changes to doxo's chemical structure in order to tweak its effectiveness as a drug.

If humans were to take any medication which consisted solely of the active ingredient needed to make us better, it wouldn't work and would do us great harm in the process. The actual pills that we ingest are made of many compounds designed to protect both the active ingredient and our digestive system, so the drug can be properly absorbed into our blood stream.

In the case of delivering doxo, scientists have created an artificial structure called a "liposome", which contains the drug. What is a liposome? Remember the phospholipid bilayer that we discussed earlier? Yep. That's all it is. It is an enclosed structure with a hydrophilic outer and inner wall, and a hydrophobic interior with doxo on the inside. It works very nicely with cells, principally because they have the bilayer in common.

Scientists have created liposomes with specially designed ligands (ligands are proteins that bind to other cells), which increases the chance that the liposome will locate and bind only with the cancerous cells. Receptors (not exactly the most original name... but I digress) are found outside cells attached to the cell wall, and they dictate whether their cell can bind with others and of course what types of material the receptor will actually bind with. In this case, scientists have attached ligands to the liposome which bind with receptors found on cancer cells. Voila! The doxo is safely absorbed into cancer cells, and manages to avoid healthy cells.

How does the doxo do it's thing once it gets into the cell? Here's where our knowledge of DNA replication comes in. In order for DNA to be physically be broken in half and then replicated, a number of enzymes (found in the cell) have to be involved. The enzymes work together during cell replication to target spots on the DNA where they can then cleave the base pairs, allowing the cell to create new base pairs, and even checking for any errors in the process. One of the types of enzymes used is called Topoisomerase II. Topoisomerase II (aka "Topo II") is used to unwind the DNA double helix, and, if Topo II is not allowed to do its job, the cell containing the DNA will die because the DNA cannot be recombined. There are numerous theories as to when during the process of DNA replication doxo enters the picture, but, suffice it to say that when doxo is working DNA strands are unable to replicate and normal cellular function is inhibited, effectively killing cancerous cells.

It is the nano-scale liposomes which scientists are scrutinizing. The liposomes can be anywhere from 100 to 200 nm in diameter, AND scientists have recently figured out how certain types of "targeted" liposomes can successfully bind B Lymphoma Cells (related to B Cell Lymphoma). Certain types of liposomes are also able to simulate white blood cell responses to infections or toxins (harmful chemicals produced by living organisms). If scientists can continue to understand and create liposomes that successfully target and kill cancerous cells, we will have yet another breakthrough in our fight against this deadly disease.

Science continues to push the ball forward, using every available tool to battle deadly diseases more effectively and more humanely. Our understanding of a world based on measurement of things on the order of a billionth of a meter is going to lead discovery and technological advancement into the 21st century, and as it does our lives and our world will continue to reap the benefits.

Source: Anal Bioanal Chem (2006) 384: 620–630; Nathaniel G. Portney . Mihrimah Ozkan
Nano-oncology: drug delivery, imaging, and sensing





April 13, 2009

Carbon Deux!

Last time, we discussed some fundamental aspects of the Carbon atom: how many electrons, protons and neutrons it has, how the electrons are distributed in the atom, and, most importantly, the role that the electrons play in bonding.

We've got to elevate our understanding even further. For instance, graphite and diamonds are both 100% carbon. If that's the case, why do they look different? Why do they have different properties?

So, we know that Carbon has orbitals which contain electrons - closest to the nucleus, there is an "S" orbital which holds its maximum of 2 electrons. The next layer has an "S" orbital which holds 2 electrons and a "P" orbital which holds 2 electrons. That gives us a total of 6 electrons, which makes sense when we consider that carbon has 6 protons (remember, atomic number of 12) that are positively charged, and 6 neutrons, which have no charge. If Carbon were to bond with another atom, an electron moves from its 2S orbital into its 2P orbital, so that both the 2S orbital and 2P orbital are half full:

Now, we are ready to rock and roll! When Carbon creates a bond, it is simultaneously lending its own electron, and borrowing an electron from another atom. In this case, this is called a "single" bond - because Carbon has 4 valence electrons, it is able to form 4 single bonds, in a tetrahedral structure. There are a number of other bonding possibilities as well, but let's stick with this example to discuss something key to what a Carbon atom is all about: hybridization!

Here's the thing: we know that Carbon can bond with 4 separate atoms, and CH4 (methane) is a very useful teaching example. BUT, if we stuck with the fact that both the 1s and 2s orbitals were completely full, that would only leave us with 2 electrons in the 2P orbital - not enough to create 4 bonds... we'd only have 2 electrons to share, so we could only create a CH2 molecule (NOT stable enough to exist unless in solution with other molecules). Orbital theory holds: it's not stable because the 2P orbital would only be holding 4 electrons, when it needs 6 to be full.

How Carbon gets together with 4 other atoms is based on hybridization. In other words, when Carbon's valence electrons are configured so there is one in the 2S and 3 in the 2P, this is called "SP3 hybridization". It's called SP3 because one S orbital is being used, and 3 P orbitals are being used. The electrons are distributed throughout the Carbon atom so that when 4 molecules approach the Carbon and are willing to share, they are bonding with each of the SP3 orbitals. In the case of CH4 (methane) the Hydrogen atoms form bonds - 4 "single" and "covalent" bonds are formed between the atoms.

So far, here's what I want you to know:

- when Carbon bonds with 4 other atoms or molecules, it shares 1 electron in each bond
- the orbital on Carbon that this shared electron is hanging out in is called the SP3 orbital
- each of the four SP3 orbitals forms a tetrahedral structure surrounding the Carbon atom
- this link gives additional background on what we are talking about

Alright, so we went all the way from Carbon's position on the periodic table and its subatomic particles to hybridization and chemical bonding. With SP3 hybridization, Carbon can bond with 4 other atoms to create a chemical compound. What if Carbon forms a bond stronger than a single bond, like a double bond? What does the hybridization look like?

In the case of ethene (CH2CH2), there is a carbon-carbon double bond. Carbon still has 4 valence electrons, but is sharing 2 with another carbon, and one each with 2 other hydrogens. In this case, the hybridization is sp2, because only 2 of the 3 "p" orbitals are used in hybridization. There is an unused electron in a "p" orbital, but don't worry, we'll discuss it later.

We've moved pretty far, and I don't want to discuss further theory here. I want to point out, however, that it is possible for the electrons in Carbon's 2nd layer to form bonds based on sp3 hybridization with 4 other atoms, AND it is possible for the electrons to form bonds based on sp2 hybridization with 3 other atoms.

Now, let's talk about the strength of these bonds, and what the electron distribution looks like. In the case of CH4, there are 4 single bonds holding the Carbon to the Hydrogens. Because the Hydrogen only has a 1s1 electron configuration (recall its atomic number is 1, its group is 1 and its period is 1), it can only form bonds with other atoms called sigma bonds. These are the strongest type of chemical bond because the electronic distribution overlaps evenly among the 2 atoms. Furthermore, based on scientific evidence, it is equally easy for ANY of the Hydrogen atoms to be removed from a CH4 structure, which means all the C-H bonds are of equal length, and equal strength. They are all sigma bonds (recall that "S" orbitals form sigma bonds).

Remember our example of ethene? CH2-CH2? Here's the story - sigma bonds are formed there too, but remember, there is an unused electron in the Carbon that needs a mate (another electron). That's perfect, because there is an unused electron in the other Carbon atom that also needs a mate (neither of the hydrogens have an unused electron, they are already sharing theirs). Experimentally, it's been proven that these unused electrons form a bond, however the bond is slightly weaker than a sigma bond. It is called a Pi bond because it involves the interaction of the unhybridized P orbital on each of the Carbon atoms. Yes, the Pi bond is weaker than the sigma bond and orbital theory is consistent with this, HOWEVER, the C-C DOUBLE bond (combination of sp2 hybridized orbitals bonding with each other AND the "p" orbitals bonding with each other) is shorter and stronger than the C-C single bond, which has been proven experimentally.

So, let's bring it all the way back to our original question: diamonds and graphite are both made of Carbon, so why are they so different? The answer lies in orbital theory. Diamonds are made entirely of Carbons that bond with each other through SP3 hybridization. Throughout the structure of a diamond, its strength and conductivity (recall that "electricity" is the movement of "electrons") are consistent, no matter the orientation of the carbon atom, or its bonds. We are dealing with a 3-D world and in the case of a diamond that is 100% pure, all bonds between atoms are exactly the same! Also, if you've ever seen a jeweler examine a diamond, what he or she is looking for are "impurities"... they may or may not know this, but not only are they looking for any non-Carbon materials in the stone, they are also using light to determine whether there are any C-C bonds that are not SP3 hybridized, which would refract light differently than the rest of the stone!

Graphite, on the other hand, is 100% SP2 hybridized - remember, this involves sigma bonds and pi bonds. In Graphite's case, the sigma bonds create electronic movement between the Carbon atoms, however the pi bonds are much weaker, and do not transfer electrons. In our 3-D world where Graphite molecules are layered on top of one another as well as side to side, the pi bonds prove to be much weaker at holding the entire structure together. As we know it today, graphite is a soft material. If you've ever had to replace the brakes on your car or sharpen a No. 2 pencil, you know what I'm talking about.

The catch in all this is that between diamonds and graphite, there are variations (buckminster fullerene and carbon black, for example) of carbonaceous materials used by man today. Understanding how each is different from diamond and graphite and from each other is critical to understanding the role that carbon will play in our nano-based world. We're going to talk more next time about nanotechnology, however, I felt that it was important for me to revisit my training as a chemist AND reacquaint myself with some (long lost?) principles that are still relevant to the scientific investigation taking place today. Further, I want to point out that our examination of Carbon here also gives us great insight into other elements on the periodic table. Orbital structure and chemical bonding is merely the beginning of man's investigations into the subatomic world, so we have to be somewhat conversant with the world of electrons, protons and neutrons and how they build the universe surrounding humankind, as well as humankind itself.





April 10, 2009

What About Carbon Makes It So Important to Nanotechnology Anyway?

Carbon is a critical element to plant and animal life, while simultaneously found in many non-biological compounds as well. If we are thinking about the future, and thinking about the cutting-edge science being done today that will change our lives forever, we have to understand the role that carbon will play, as well as some of its fundamental characteristics. In short, we've got to talk "carbon"!

Taking a look at a Periodic Table, we can see that carbon is in Period (row) 2, and Group 14. Carbon also has an atomic number of 6, as well as an atomic weight of 12.01 amu (atomic mass units). Our take away from that is as follows: because Carbon has an atomic number of 6, we know that it has 6 protons (6 positively charged subatomic particles), and if Carbon is in its neutral state, having a charge of 0 (a/k/a having no charge), it has 6 electrons (6 negatively charged subatomic particles) as well. Its atomic mass of 12.01 amu is the sum of the masses of all the protons, electrons and neutrons (subatomic particles with no charge) in a single Carbon atom.

Now, lets talk about bonding. A chemical bond (H 2 O, CH2O - formaldehyde, and C6H12O6, glucose) is created when two atoms decide to share electrons with each other. In other words, in water, Oxygen shares one electron with one Hydrogen and another electron with another Hydrogen, creating H2O. The electrons they are sharing are called valence electrons. Valence electrons are electrons that exist in the outer shell of atoms, as those are the only electrons that can be shared. There is much more to say on the electronic structure of a given atom, but for our purposes, let's stick with the concept of one valence electron of one atom bonding with one valence electron of another atom to create a bond.

All the elements in Group 14 have four electrons in their outermost layer, available for sharing with other atoms. Carbon - as I've demonstrated, only has 6 TOTAL electrons. Looking just beneath Carbon, Silicon has 14 TOTAL electrons, Germanium 32 TOTAL electrons. Counting across for Silicon, it has the same number of valence electrons as Carbon, 4. Carbon has 4 electrons to share with other molecules - there are 2 in Carbon's inner layer, and 4 (for sharing) in Carbon's outer layer, for a total of 6 (recall Carbon has an atomic number of 6). Silicon can share 4 electrons when it bonds, as can Carbon. Germanium actually shares 14 electrons - 4 from its outer shell, and 10 from its next outermost shell, in a slightly more complex arrangement.

What we next need to examine is how electrons from one atom are able to be distributed between two atoms, when a bond is formed. Orbital theory gives us the answers we are looking for. The understanding scientists have on orbital theory is well developed, however it is HIGHLY theoretical. Many years ago, quantum physicists like Neils Bohr and Wolfgang Pauli developed the theory of orbital and electronic structure of atoms - where the electrons in an atom are located is related to the atom's orbital structure. Later, this grew into theories on chemical bonds - electrons in certain orbitals of one atom can only bond with electrons in similar orbitals of other atoms, for example.

If you've gotten this far, here's what I want you to know:

- Carbon has 6 electrons, but can only share 4 of them with other atoms
- Carbon can bond with 2-4 other atoms at any one time

We've got to go deeper on orbitals, and this is going to be a tricky, but critical journey if we are going to understand Carbon's role in nanotechnology. There are different types of orbitals: "S" orbitals, "P" orbitals, and even "D" orbitals. S orbitals hold 2 electrons, P orbitals hold 6 electrons, and D orbitals hold 10 electrons. Further, they exist in different shells (a rudimentary way of describing an electron's distance from the nucleus) - the 1st shell is closest, then 2nd then 3rd, and so on. Now, let's look again at the periodic table - the Period (row) where an atom lies tells us how many shells it has. Hydrogen and Helium have only 1 shell. Lithium, Carbon, have 2 shells; Sodium, Sulfur, 3 shells. Can you figure out how many shells Selenium has? How about Tin? If you answered 4 for Selenium, and 5 for Tin, you are on your way to understanding chemical bonds!

Back to Carbon - scientists discovered that, in accordance with the orbital theory I've discussed above, it actually has this electron configuration:

1s2 2s2 2p2

What does this mean? In its 1st shell, there are two electrons, and it is full. In its 2nd shell, there are 4 electrons - a full "S" orbital, and a partially full "P" orbital (recall, P orbitals can hold 6 electrons). In this case, Carbon is in its "ground" state, which means it is unwilling to bond (share electrons) with other atoms.

Now, when Carbon is in its "excited" state (and ready to share with another atom), here is what happens:

1s2... just like always
2s1... we lost an electron... where did it go?
2p3... right here!

In the "excited" state, one electron from the 2s orbital leaves to fill the 2p orbital. When fully bonded, all electrons are paired, producing a stable molecule, which is unable to accept or donate any more electrons. Did you also notice that, when in the excited state, both the "S" and "P" orbitals are half-full, ready to combine their electrons with the electrons of an incoming atom to form a chemical bond?

Carbon, in order to fill its "S" and "P" orbitals, can accept 4 electrons from two or more atoms (remember a full "S" orbital holds 2 electrons while a full "P" orbital holds 6). Carbon can bond with 4 atoms, each sharing one electron, so orbital theory holds! Why are Carbon and Silicon so far to the right? Because Carbon and Silicon and all the atoms around Groups 13-18 have "P" orbitals in their outermost shell. In other words, the first 2 Periods that are in Groups 13-18, have ONLY "S" and "P" orbitals, while the remaining Periods in those same Groups have "S", "P", and "D" orbitals. There are a number of other reasons for their location on the Periodic Table in addition to orbital theory.

I want to go no further at this point - we are developing our understanding of the scientific concepts that underpin man's knowledge of chemistry, biology and physics. Over the past few months, I've written about the critical role that carbon is playing in the nano-based world we are building. We need to continue to work on understanding the fundamentals of how electrons, bonding, nuclei, and ultimately, atoms and molecules, function to gain a deeper understanding and appreciation of the technology that will build our future.










April 04, 2009

Searching For My Lost Shaker of Salt!

By Red Sox Steve

Part of the problem in discussing the world's lack of water is that there is so much to say. The list of evidence that we have a real problem as it relates to water is long and undeniable: environmental evidence, epidemiological evidence, demographic evidence, economic evidence... you get the picture. What we need to find is an example of a problem we have solved. We need a workable solution we can implement to address our immediate need for water.


Over 90% of our water comes from groundwater (located in aquifers, mother nature's underground storage) and surface water - lakes and rivers catch and collect pure water from rain storms and the melting snow and ice on mountaintops... we collect it, clean it, and pipe it where it's needed. In addition to that, only 1-2% of the water on earth can actually be used by people.

There are only two viable solutions - we either desalinate seawater and brackish (look it up...) water, or we treat the wastewater we create. Because there are already at least 1 billion people in the world who do not have access to drinkable water and the world's population will continue to grow, this is a problem that will not abate. Our best scientists and engineers need to innovate a way out of this problem, so that demand and supply find an equilibrium that is appropriate for life in the 21st century. In short, billions living without clean water is no solution, in fact it's the problem.

Fortunately, there are examples where solutions are being implemented, and some are right here in the United States. San Diego county is the largest population center in the southwestern US. A glance at a map of that part of the country quickly tells us a few things. First, the population centers are widely disbursed, with vast distances between them. Second, there are a lot of deserts - dry and hot 12 months a year, with very little sustainable water sources to be found. It's what is found to the WEST of San Diego, however, that is beginning to be used to meet water demand. Yes, the ocean!

Carlsbad, California sits right up the I-5 from downtown San Diego. There, they are implementing the Carlsbad Desalination Project to meet the region's needs. 90% of the water currently consumed by the regions' homes, farms and industries is imported from sources like the Colorado River, and 50% of the population of San Diego county live within 10 miles of the coastline. San Diego is also home to world-leading biomed companies, engineering companies, defense companies, and naval construction companies. In short, San Diego has EXACTLY the types of companies that will lead the United States out of this economic crisis, it will continue to attract the best and brightest scientists and engineers from all over the world AND therefore they deserve the best in available infrastructure resources.

In many locations, from Singapore to Saudi Arabia, the desalination plants are being co-located in areas with power plants, conventional and nuclear. This allows the wastewater from the power plant (conventional or nuclear) to be mixed with the hyperconcentrated effluent (called "brine") solution containing the filtered particles from the desalination plant. This can be safely released back into the ocean, and scientists then monitor its impact on local species, studying the environmental impact at the same time. Second, there are currently studies being done on how feasible it is to hook up solar panels to either large or small-scale desalination facilities. Scientists in London published a study in 2006 in the International Journal of Low Carbon Technologies examining the parameters

I want to put one more example out into cyberspace, lest we think California's plant is somehow so innovative that it is hard to replicate or that it is the only place in the United States with a problem of this magnitude. Neither are true. The largest desalination plant in the United States is in Tampa Bay, Florida. There in 2003, a privately-owned and constructed desalination became fully owned by the local government, and continues to pump millions of gallons today. Although there was a performance glitch which required reconstruction in 2005, this story is very similar to what is going on in Carlsbad - the plant is co-located with the local power plant, which produces operational costs savings, and the un-filtered water from the desalination plant is diluted in a ratio which makes the environmental impact minimal. In other words every gallon of un-filtered water from the desalination plant is mixed with **70** gallons of cooling water from the power plant before being released into Tampa Bay.

Shortly after the start of the 21st century, these plans were put in place in the form of public-private partnerships, here in the United States. Private business involvement makes sense from the point of view of efficient construction and innovation - it's always important to use the latest technology, and easier for private business to bear the initial risk associated with the development and initial stages of functioning of the plant. Don't misunderstand - none of this takes place without regulatory oversight according to EPA standards, as well as the local government's health department and environmental oversight agency. Then, when it is determined that the project is running effectively and efficiently, it can be sold, to be managed by the local government. In a non-competitive way the municipality is the only entity that should bear the operational responsibility that the drinking water is healthy, reliable and safe. There is a ton of room for both to maneuver. Private industry can continue to be successful at the construction and efficiencies created when these plants are essentially replicated all over the world; public interest can take over, once it is determined that the plant can be effectively and steadily managed to meet local needs, and the incentive for profit changes.

In terms of high-tech, I've said very little. Sure, there are always advances in filtration technology (which we will look at), and power-usage efficiencies that can be developed, but the fact is that this solution to this problem is ready-made for what we are going to need in the 21st century, and it dovetails nearly perfectly with what we've been discussing. In the 1960s, John Kennedy spoke about the fact that the ocean contains the water we need to solve our problems. By 1998, the civic planning and regulatory oversight needed to get these plants up and running started to take place, and by the time the 21st century rolled around, we have numerous examples of workable solutions to the problem of a lack of clean water.






April 01, 2009

Magnetism and Data Storage Using Perpendicular Nanomolecules

By Red Sox Steve

Nanotechnology is fast approaching the point where it will touch all aspects of human life. As we've discussed here before, from medical technologies to improvements in semiconductor function, miniaturization to the scale of a single crystal or subatomic particle will lead to developments in the way things function in our world. One of the most obvious examples of the advantage of electronic miniaturization is found in the way electronic data is stored.

As it exists now, computer hard disks use a system called "longtitudinal recording" to store data. What this means is that on the surface of a disk, each "bit" is laid flat. There are a couple of limitations to this orientation. First, each bit is activated by the application of a magnetic field - the stored data is recalled because the bits are "directionally magnetized". In other words, data is read and interpreted according to its orientation on the platter. Because the bits have been laid down on the platter's surface, there is a physical limitation to the amount of data that can be stored on a given sized platter.

Recording Head

The problem with continuing to store bits (in the form of metal nanoparticles) flat is that as more bits are placed on the platter's surface, there is a greater chance each will randomly "flip" its respective orientation. If this happens, then when the data is read by what is known as the hard drive's "actuator", it will have already been corrupted, and therefore become useless. When a magnetic field of nanoparticles influences the magnetic moment of nanoparticles in their surroundings, this is known as the "superparamagnetic effect" - the superparamagnetic effect may cause a random flipping of nanoparticles which will corrupt and destroy the data stored on a hard disk. One way to overcome the superparamagnetic effect is to store bits perpendicularly on a hard drive's platter. In other words, the major axis of the nanomolecule would be perpendicular to the surface of the platter. Perpendicular storage of bits in the form of nanoparticles can be more dense and therefore more powerful.

Scientists have been studying the possibility of using Nickel as a nanoparticle which can be magnetized and serve as a base metallic layer onto which another metal can be deposited. With the application of an external magnetic field, Nickel by itself can become "ferromagnetic". What this means is that it can have a permanent "magnetic moment". If a magnetic field is brought close to Nickel, Nickel will change the orientation of some of its electrons so they all spin in the same direction. Recall that electrons like to pair with each other; when they do, their "spins" cancel each other out - as a result, an atom where all electrons are paired has no magnetic moment. In the case of Nickel and Nickel-Cobalt, a magnetic moment is created when it is brought into the proximity of a magnetic field because some of its electrons begin to spin in the same direction. "Magnetization" therefore, is the sum total of unidirectional electron spins exhibited by a given material.

Scientists are currently studying the possibility of using Ni-Co attached to a surface layered with organic (carbon-based) molecules called "polyimides". Let's not dwell on the structure of polyimides - for our purposes, let's keep in mind that the substrate's surface is carbon-based and flat and that scientists are attempting to layer metal crystals on the surface in a perpendicular fashion.

Using a microlithographic (microlithography - layering a substance onto a surface with a thickness on a nanometer scale) process called "spin coating", a Nickel compound was layered onto a polyimide surface at a desired thickness of 40 nm. On top of that, a layer of Cobalt was deposited over the Nickel. Part of the process of annealing the Cobalt onto the Nickel was using 500 Watt halogen lamps at approximately 400-600 °C for 30 seconds. After examining the result with Transmission Electron Microscopy and X-ray Spectroscopy, scientists were able to confirm a few things. First, the Cobalt atoms had formed Ni-Co "islands" over the substrate's surface - it didn't form a monocrystalline layer which would have defeated the purpose of using discrete Ni-Co particles for data storage. Furthermore, scientists found that Nickel and Cobalt existed on the sample surface in approximately equal amounts. Since there was no evidence of Cobalt forming separate homogenous clusters within the sample, it is reasonable to assume that each single Cobalt atom bonded to a single Nickel atom.

According to this study, Nickel-Cobalt exhibited a higher Magnetization saturation than pure Nickel when exposed to similar magnetic fields. It was also noted that over a given range of applied magnetic fields, Ni-Co reacted more strongly to both the presence AND lack of a magnetic field as compared to Ni nanoparticles. Much of the reason had to do with the increased size of the Ni-Co particles as well as the enhanced magnetic interactions between them. Larger particles impose a much more pronounced magnetic moment when exposed to a magnetic field and become strongly demagnetized as a result of the lack of an external magnetic field.

The magnetic field created by neighboring bits on a platter is a key determinant in the amount and stability of data that can be stored on a given sized platter (aka "hard drive"). Up to now, conventional storage methods consisted of laying nanoparticles ("bits" in the computer world) flat along the surface of a platter. However, using nanoscale properties like magnetization and magnetic moment along with nano-level manufacturing methods such as spin coating has given scientists the ability to orient nanoparticles in a perpendicular fashion. By utilizing flexibility at the nano level, scientists are increasing their ability to very specifically control atomic behavior; in this case, the ability to change the orientation of a tiny particle from "laying down" to "standing up" means that science is on its way to making computing more powerful than ever before.

Citation:

- Monolayered Ni–Co alloy nanoparticles template fabricated using a Ni nanoparticle array, APPLIED PHYSICS LETTERS 88, 163102 2006
- Wikipedia





March 31, 2009

Can't You Hear the Whistle Blowing?

By Red Sox Steve

We took a look here at the train systems of China and Japan on Saturday. China has the fastest train in the world, and plans to spend billions on future construction. Japan started constructing a foundation for high-speed passenger rail with the Shinkansen starting in the 1960s, and continues to improve the backbone of its system even today.

Now, we need to take a look at the United States and Europe. A majority of all the money on earth is currently circulating in each of these four geographic areas, and if the US and Europe are going to continue to remain competitive with both each other and Asia in the war for global capital and new ideas, they'll need to figure out a way to get the most value out of their respective transportation dollars.

Just after the US Civil War ended, westward expansion of the US territory again became a priority for the government. In 1869, the last spike was driven for America's transcontinental railroad, edifying America's desire to traverse and settle the vast continent that was hers. With the subsequent economic boom and bust of the 1870s, the nation moved itself westward, and aside from horse and carriage, railroad was the main form of transportation between developed areas.

As the industrial revolution took hold, rail was critical to the movement of goods and people - it was the fastest, cheapest, safest, most efficient and comfortable way to get from city to city until approximately the 1950s. During the first half of the 20th century, mass production of the automobile and the creation of an airline industry began to take place, which would later serve as alternatives to every form of "wheel-on-rail" travel available during that time. Major airline companies both in Europe and the US were formed as a result of the technology used in World War I, however their expansion was slowed as a result of the economic downturn of the 1930s.

After the end of the Korean War in the 1950s, President Eisenhower signed the Federal Highway Act of 1956. Under the auspices of national security, an expansive effort was made to link America's cities via highway - cities which were previously only linked by railroad tracks and single-lane roads at best. This begat a major expansion of both the automobile industry and the suburban lifestyle which have been major drivers of the US economy, until now.

"Despite a slow growth in jobs and travel in 2003, congestion caused 3.7 billion hours of travel delay and 2.3 billion gallons of wasted fuel, an increase of 79 million hours and 69 million gallons from 2002 to a total cost of more than $63 billion."

“The 2005 Urban Mobility Report”, a report of 85 major metropolitan areas in the US by Texas A&M University.

The rail industry that exists in the United States today is a fraction of what it once was. Although the United States has the largest economy in the world, the 2007 revenue generated by the rail industry was a paltry $63 billion (compare that number to the hundreds of billions that go straight to the Saudi Prince, Iran, Venezuela and Russia every year!), compared with the $170 billion generated in Europe and the $400 billion generated in Asia. According to an August 2008 report on the US rail industry by Datamonitor, over 85% of the revenue generated in the industry was due to freight transport, not passenger travel, in 2007. According to an industry report by Plunkett's, about 1 million people were employed by U.S. railroads in 1955, compared to about 225,000 in 2006.

Combine this with the fact that many of the industrial customers of two of the leading rail-freight companies in the US (BNSF and UPRR) use rail to transport mass-manufactured goods and agricultural products, and you've got an economically unsustainable situation on your hands - when demand for these goods dries up, the demand for rail service will decline, and unless there is an increase in passenger traffic, you'll continue to see declines in the revenue that the rail industry generates. The US rail industry is clearly not on the right track.

Amtrak is the only passenger rail service in the nation, and, from personal experience I can tell you that it is NOT the most economical way to travel the Northeast corridor. Consider the fact that a bus trip from New York to Providence cost $40, while the cheapest train ride cost $54 (Acela costs $89 - there is no premium alternative on the bus); because of the geography of northeast travel, the distances are roughly the same - both modes of transportation run along the coastal area for a great majority of the trip. Furthermore, the train only gets in a little quicker than the bus (about 30-45 minutes according to the published schedule); the train has a much LESS frequent departure schedule, and you can take ANY bus with ANY ticket (can't do that with a train unless you wait in a line to change your ticket...)! Add it all up, and I've taken the bus 95% of the time for the last 5 years, and have probably saved myself hundreds of dollars in the process!

The good news is with the 2009 Economic Recovery and Reinvestment Act (yep, the "stimulus"), we're putting some funds towards rail travel... we're going to spend $8 billion for high-speed rail, and $1.3 billion for Amtrak upgrades. It's hard to take that effort seriously when China is going to spend $63 billion on its system... and it already has the fastest train in the world, which cost $1.2 billion to construct.

I've got to report to you, however, that we have a maglev project in the works right here: Transrapid USA. In 1998, Congress established the Maglev Deployment Program as part of the Transportation Equity Act for the 21st Century, but - despite the numerous proposals (Baltimore to Atlanta, Anaheim to Vegas, etc.) - we aren't even close to building a maglev train here. Unfortunately, the only place I find discussion of any proposed maglev developments in the US is on this website, so aside from this self-promotional effort, it's difficult to talk more extensively about how these projects may actually work.

After WWII, the British, French and West German auto industries began to expand, but with that, a system of on-street trolley cars and mass transportation continued to be part of the urban landscape. Britain's trajectory is similar to the United States - although on-street tram cars and trolleys were widespread even before the 1950s, by the 1960s this form of mass transportation had succumbed to considerable pressures and the service it provided had been severely diminished, giving way to the automobile and bus systems. France opened its first high-speed rail system in 1981, the TGV (train à grande vitesse - French for "high-speed train"), running between Paris and Lyon, as a result of the research done by rail operators GEC-Alsthom and SNCF (one of the largest railroad companies in Europe) in the 1970s. In Germany during the 1980s, a number of rail lines ran at 200 km/h, and in 1991, the ICE (InterCityExchange) started running between Hannover and W'urzburg with a top speed of 250 km/h. Britain, France and Germany have disparate 20th century histories, to be sure. I'm going to try to work in some of the highlights and major differences here, so we get an idea of what we are dealing with.

In 1994, when the Eurostar line made its maiden voyage through Europe, it was the French infrastructure that performed the best and even today has surplus track capacity, while it was the English rails that were the most outdated and congested around major cities. Also, please note, with all this discussion of maglev train technology being the latest and greatest, some reports state that it was a FRENCH scientist, Emile Bachelet, studying in BRITAIN, that came up with the relevant technology; other articles name Hermann Kemper, a GERMAN scientist that received the needed patents! France. Britain. Germany. Both scientists contributed something, and looking at the position these nations are in today, it's no coincidence.

In Europe today, the French and Germans have dominant high-speed train service, with more to come. Some reports state that France will upgrade its TGV in 2010 to a train with a record-breaking 357 mph performance in test trials. Spain is in the process of constructing 1,400 miles of new high-speed lines, and trains can go 186 mph on a line between Barcelona and Madrid. In 2002, the German company Deutsche Bahn constructed a train that travels above 180 mph between Frankfurt and Brussels. Oh, and all the technology behind the trains in China? Spreken zie deutsch? You guessed it! Mostly German - Siemens, ThyssenKrupp & Transrapid International (the JV between Siemens and ThyssenKrupp) developed the maglev technology, and ThyssenKrupp and Max Bogl constructed the guideways!

"If you ask inward investors who did not invest in the UK but instead chose one of our competitors, 80 per cent of them would give you transport infrastructure as a key reason why they chose another place to go - it's hurting, everybody recognises something needs to be done."

Dr. Earl James, in an interview with the Engineer, April 24, 2006

It is hard, after doing all this research to NOT be impressed by the UK Ultraspeed project. When the Chinese were faced with the option of either upgrading existing technology or "leapfrogging" all existing technology, and instead focusing on a state of the art approach, they chose maglev. State of the art. Dr. James, the project manager for the UK maglev upgrade, is preaching that the same approach be taken in the UK. The maglev proposal put forward by UK Ultraspeed focuses on the fact that there need not be a circuitous system or an east-west axis. Instead, it is one line travelling North-South, from Scotland to London, stopping at all major airports along the way. The maglev advantages conferred by the system in Shanghai would be similar, if not exactly the same: speed, cost, safety, efficiency, comfort (actually, these are the same reasons Americans started using train service in the 1800s!). If and when they put this system in place, the British would have the best system on the planet.

As the 21st century develops, mankind will need to figure out how to move people using less of our natural resources, and more of our technology. We can see that in China and Japan, a constant commitment to development and an effort to use the latest technological advances have created a sustainable and successful rail structure. Although the Europeans are playing catch up to the Chinese even today, they are doing so with the wind at their back: their respective histories provide a framework under which they can operate, and, in the case of the UK Ultraspeed project, abandon when necesssary. The United States is in a very different position - as previously discussed here, we've pursued a commitment to highway development and what we can now call planned obsolescence: a political, cultural, and economic commitment to the growth of an auto industry that utilizes the world's finite supply of metals and fossil fuels, funneling billions of dollars each year to petro-states that mean us harm.

Phew, that was a mouthful! Point is, the Chinese and Japanese have state of the art European technology, which has been contributing to the success of each of their respective industrial and infrastructure pursuits for a long long time, while the US has been all but eliminated from the overall picture. Unless the US manages to act swiftly and decisively in this arena, we will see yet another opportunity to align ourselves with the world's economic, political and military powers pass us by. To our detriment. Not theirs.






March 27, 2009

Going off the rails on a Guangzhou train!

By Red Sox Steve

After the dust settles from this economic crisis, the stimulus money is spent, the regulators start using magnifying glasses to scrutinize the finance industry, and, most importantly, hard working men and women get back to work, the 21st century world will come into clearer focus. It's already on TV and the internet... energy efficiency in homes and cars, "feed the pig" ads reminding us to save money, the Obama speech about "clean coal" stimulating Appalachian economies (NOT going to happen), free Skype calls between computers (Hi Mom, Dad, Mary, and Matt!), and all the other ideas we have to sort through. We've got to use that intensely powerful apparatus between our ears to try to figure out what's what, and where we go from here.

I have my thoughts about where we are going, but what I've been looking into is how we are going to get there. How are the coal mines in Datong (Shanxi Province of China) connected to Qinghuangdao, the port city in the Hebei Province? How do we improve the link between San Francisco and LA? How do we speed up travel from Manchester to Liverpool? Tokyo to Nagano?

The answer: TRAINS! Not just any trains, but high-speed trains, and even faster than high-speed trains, magnetically levitated, electrically propelled trains!

There are hundreds of thousands of miles of train tracks all around the world, and money is being spent in Asia, Europe, and the United States to improve what is already in place.

In 2006, the Chinese completed the Qinghai-Tibet line, going up to Llhasa, high in the Himalayan mountains - the trains travel to such high altitudes that engineers and scientists had to figure out how to capture oxygen from outside for passengers and how to prevent the tracks from being disturbed by the thawing taking place just below the permafrost layer. The Chinese stimulus, unveiled in Nov. 2008, designated some funds towards railway-related expenditures: $17.6 billion on a passenger rail line in northwest China, $22 billion on a network of freight rail lines in north central China, and $24 billion on a high-speed passenger railroad from Beijing to Guangzhou.

UK Ultraspeed is a British infrastructure project designed to link major cities there with high-speed trains; thing is, it's based on the Shanghai-Pudong airport 500km/h magnetic levitation train...

The distance from Shanghai to Pudong Airport is 19 miles. The fastest way to traverse this distance is via a magnetic levitation ("maglev" for short) train. This video does an excellent job of describing the concept and the technology being used. Essentially, an electric motor uses current to create a mechanical force. In the tech used on maglev trains, the electrical motor's coil is unwound and laid along the track - as the electrical field is applied along the track, the train will move. There is no friction created where the electrical field is applied. One part of the motor is attached to the track, and the other part is attached to the train car - for the length of the journey, these pieces remain 1 cm apart. The Transrapid gets you to the airport from downtown Shanghai in 8 minutes.

The Transrapid only needs 2 minutes to travel 5km before it reaches a speed of 300km/h; a typical high-speed train needs at least 30 km to reach 300km/h. Yes. Seriously.

Here are some quotes taken from an October 16, 2006 piece in the Engineer by Dr. Alan James, chief executive of UK Ultraspeed:

- "This exceptional performance makes the Shanghai Transrapid not only the fastest, but also the most reliable transport system in daily service on Earth."

- "At UK Ultraspeed, too, we still firmly believe that Transrapid maglev technology can fundamentally transform Britain's economy, enhance Britain's environment and transform Britain's transport."

Maglev technology means these trains are typically also the most energy efficient form of travel, using less energy than a car, an airplane, and a typical high-speed ("wheels on rails") train; they also produce slightly more noise than a loud vaccum (69 dbA) when travelling at 240 km/h.

The Chinese weren't the ones who first came up with the idea of maglev trains. The Japanese bullet train system is locally known as the Shinkansen ("bullet train") and it serves as the base for Japan's rail transportation network. The system first opened in 1964 with the Tokaido line between Tokyo and Osaka, and now there are eight Shinkansen lines carrying over 400,000 passengers per day.

Japanese engineers are currently working on a number of projects: the High Speed Surface Transport (HSST), being developed by Japan Airlines and Nagoya Railroad Co., a Magnetic Levitation Unit (MLU) being developed by Nippon Rail, and an "electrodynamic suspension" technology that utilizes super-cooled superconducting electromagnets to levitate a train by almost four inches. This technology will be used in the Chuo Shinkansen project, which will run between Tokyo and Osaka through Nagoya, cost about $44 billion and be completed by 2025.

While it was the Japanese who first explored the possibility of high-speed rail, China, with the Transrapid system has overtaken everyone in terms of utilization of the technology. Both of these nations, along with the United States and Europe (which we'll discuss later), are conducting research into the feasibility of implementing the latest technology into their high-speed rail systems. I've been told that traveling through developed Asia and urban China is like a journey into the future. Chinese expenditure on infrastructure is much higher than the United States, for example; Beijing's airport was designed to accommodate 10 million people per year, while Japan has an extensive, nationwide bullet train system that covers a huge part of the country, the research and construction into which started in the 1960s. These two nations have been serious about building for the future for a long time, and the technology they are implementing and the funds they are putting aside to do so proves the point: this type of development and constant commitment to innovation serves as a model for how a 21st century economy should develop and function.






March 20, 2009

Water: The Scope of the Problem

We've spoken in this space about mankind's need for infrastructure development - what kinds of demands future infrastructure will be under, what kinds of problems infrastructure projects will solve, and the fact that as we move forward in the 21st century, humanity is becoming more and more urban every day necessitating a need for persistent attention to the situation.

There is another need common to all of mankind, something that we all benefit from, but that we don't have enough of: Water. There are environmental, social, commercial, and even political and military implications all related to the presence - or lack - of water.

Some things about water are easily understood: clean water is a key to human health, waste management, and disease prevention; access to oceans and deep water ports is essential for thriving global trade; water is used in every agricultural and many industrial processes; and last, but certainly NOT least, water covers 75% of the earth. It is critical that globally oriented citizens and investors understand this is only the proverbial "tip of the iceberg". Just like any other problem, we first need to understand what it is before we can work on solving it. Prepare yourself for a monumental task.

In anticipation of the 5th World Water Forum held in Istanbul, Turkey from March 16 - 22, the UN published its third report on the condition of the world's water supply entitled: "Water in a Changing World".

According to this report:

1) The 10 countries which use the most water are India, China, the United States, Pakistan, Japan, Thailand, Indonesia, Bangladesh, Mexico and the Russian Federation.

2) Globally, agriculture is the most consumptive of all water needs. Irrigated agriculture accounts for 70% of water withdrawals (gross amount of water extracted from the environment), and although increasing in urbanized economies, industrial (including energy) use accounts for 20% of total water use and domestic use for 10%.

3) Half of the world's population is under 25, and the rate of slum formation is nearly the same as the rate of urban growth.

4) Directly quoting: "Coal consumes about 2 cubic metres (m^3) of water per megawatt hour of electricity generated, nuclear power about 2.5 m^3 and petroleum about 4 m^3. Extracting petroleum from Canada’s tar sands, consumes an estimated 20-45 m^3 of water per megawatt hour, nearly 10 times that for conventional oil extraction."

This 349 page report (yes, I skimmed some chapters, but 1, 2, 3, 4, and 7 were the most interesting!) sets the stage for the variety of problems 21st century humans will have to deal with. We can already tell from the list of the world's most water-consumptive economies that no particular economic or political ideology will dominate the solution. Furthermore, because of the migratory and demographic trends of the world's population, the problem will be around for quite a while. Solutions will not only be found by local and national politicians, but by scientists and engineers as well - public and private funding efforts will be made, and when they are, all of humanity - present and future - will benefit from the discoveries. Because water has a wide variety of uses, the scope of the problem may only be rivaled by a lack of oxygen or sunlight. In other words, everyone in the world knows that everyone else in the world needs water, and no benefit is conferred on the larger world when a particular nation or group goes without it.

Speaking of which, let's discuss another water-related problem which, if left unattended, will affect every part of the globe: the divergence of interests which require and desire access to the Indian Ocean.

From my reading of a recent article in Foreign Affairs Magazine ("Center stage for the twenty-first century: power plays in the Indian Ocean", March April 2009, by Robert Kaplan), half of the world's container traffic and 70 percent of total petroleum products pass through the Indian Ocean. Some oil tankers pass through the world's principal oil shipping lanes, including the Gulfs of Aden and Oman, Bab el Mandeb and the Straits of Hormuz and Malacca. Forty percent of world trade passes through the Strait of Malacca; 40 percent of all traded crude oil passes through the Strait of Hormuz.

The Indian Ocean serves multiple nations with varying economies, ideologies, and interests, including Somalia, Pakistan, India, Bangladesh, Iran and Indonesia. In constructing ports and military "listening posts" on coastal Pakistan, the Chinese are undoubtedly attuned to the critical role the Indian Ocean has on their economy and security. The relationships between these countries as well as the role the United States will play in facilitating the peaceful rise of India and China is extremely complex: Pakistan and India don't get along. Although India is a democracy and Burma is controlled by the military, Burma also holds a great deal of mineral and fossil fuel wealth needed by India. Pakistan and Iran are ideologically aligned via Islam against the secular world India, China and the United States are trying to create, although India is constructing a natural gas pipeline through Pakistan to get natural gas from Iran. Indonesia has the world's largest Muslim population, but little else in common with Pakistan and Somalia and benefits economically from its relationship with China. Round and round we go while trying to navigate the treacherous waters of the Indian Ocean and the complicated relationships of eastern Africa, the Middle East, and the Asian sub-continent.

I've only needed to consult two published sources to gather facts that give us an idea of the scope of the problem. All of mankind needs water. All of mankind is impacted by the presence and function of an ocean. Those are things that can be easily understood by any 6 year old anywhere from Cranston to Caracas to Cape Town. However, with over half the world's population living within 100km of an ocean, what we better need to understand is how life impacts water and how water impacts life, and how we can solve the problems that will be created by the 21st century.



March 14, 2009

21st Century Infrastructure: A Bridge to Somewhere

By Red Sox Steve

Between the developed and developing world, there are disparities - education, lifestyle, health, wealth, technology. These gaps are closing - more and more workers worldwide will continue to join the white collar workforce, competing for resources with those in the developed world in the process. Technology - computer, medical, military will continue to make its way around the globe, and with that, there is the constant threat that it will fall into the "wrong hands". "Needs" based on lifestyles and consumption habits will continue to increase - no, not in the short term, we are dealing with a cyclical global economic crisis after all - in the long term. People are moving from rural to urban, and as of 2008, for the first time in human history according to a UN report, more of the world lives in urban places versus rural ones.

Population growth and urban migration rates in developing countries will continue to outpace those in more developed places. Public and private money will be spent to support secular migration trends in all places around the world. If we want to talk business in this space, we've got to follow the money, and that directs us towards infrastructure. Infrastructure means everything from power generation to roads to rail to shipping ports to airports. In short, we ain't getting nowhere and ain't nothing coming our way without infrastructure.

The US, China, and Japan have the three largest construction markets in the world, in that order. Furthermore, the demand risk (Demand risk - the likelihood that the projects will be fully utilized when constructed) is a major factor in determining whether a project is viable for construction. In other words, high speed rail, water and sanitation systems, and clean power generation are especially important in areas with highly concentrated urban populations - places like Tokyo, Beijing, Mexico City, Sao Paulo, Delhi. The global downturn in commercial and residential real estate means the services construction companies provide can be had on the cheap; here are a few more facts we can ponder (2, 3, & 4 are courtesy of Business Monitor International Ltd.):

1) India is the 5th largest consumer of oil in the world, and in 2008 its parliament agreed to cooperate with the United States in participating in a civilian nuclear energy program (this treaty is still subject to further approvals). According to a Feb 13, 2009 Euromonitor report, 3% of India's power comes from nuclear energy. If the Indian economy is to grow (just like ANY OTHER economy in the world), another type of energy source must supplant oil, and at this point, it looks as if that will be at least partly nuclear. India will continue to harness nuclear energy technology through foreign sources subject to governmental approval processes yet to be completed.

2) Beijing currently has a metro system comprising 142km of subway track, with plans to expand to 560km by 2020.

3) Japan has 145 airports with paved runways, 23,500km of railways, 949,000km of roadways, and 10 major ports.

4) The US has the largest highway network in the world, totalling 6.33mn km in length, of which 3.73mn km (59%) is paved. By length of paved highway, the US is first in the world ranking. Its network is larger than those of the second-, third-, fourth-, and fifth-ranked countries all combined (India, France, Spain, and Japan). The railway network, at 194,731km is also the largest in the world, ahead of Russia (87,157km) and China (71,600km). The majority of train usage is by freight while passenger usage is significantly below other developed nations such as Japan and the EU. There are 14,801 airports around the country, of which 5,131 have paved runways. The airport network serves 29 large hub areas across the country.

5) According to a 2007 Euromonitor International report, there are currently 20 cities in the world with more than 10 million inhabitants, and it is estimated that 180,000 people are added to the world's urban population every day.

The massive and dense amount of humankind confined to small urban spaces also creates a number of problems: diseases spread faster, waste (liquid and solid) builds up more quickly in a smaller space, air and noise pollution become more concentrated and harmful; if these issues continue unabated, public health and economic competitiveness become seriously threatened.

To the positive, urban places provide many more paid employment opportunities than rural places. Female labour force participation is also greater in cities because of the nature of urban job opportunities which require fewer strenuous physical demands. Cities also generate more wealth per person than rural areas. For example, the per capita productivity of Shanghai (US$10,000) was six times higher than China's national per capita productivity (US$1,663) in 2000; this leads to higher incomes and higher household expenditures.

Taking all this information into account leads me to believe that we will see (and are already seeing) massive shifts in financial resources - both public and private - to an extent we have never seen before. The 20th century helped to sort out most of the world: there were the capitalists, the socialists, the communists, the non-aligned; even the colonialists and their colonies. There was the first world, the second world, and the third world. There was the League of Nations, the UN, NATO, CENTO, SEATO, ASEAN, Caricom. Fewer and fewer of those particular categorizations matter every day. Countries of all stripes played off their relative positions and advantages to try to secure the most advantageous overall position possible - similar to one opponent playing multiple, simultaneous chess matches and then totalling each individual "score" to get a final "score" - an indicator of overall performance.

The 21st century game will be a little different. The players - the United States, Europe, Brazil, the Chinese, the Japanese, Mexico, and all the rest - are slowly being compelled to forget the results of that 20th century game, and instead work to create a new world. The current economic crisis is simply a transition, the burden of which is being borne by every nation around the globe (AND borrowed from the future in the form of debt). Massive efforts are being undertaken everywhere from Eastern Europe (by Japanese construction companies) to California (north-south and east-west rail systems) to La Paz (cross-continental highway construction from Brazil to Chile, through Bolivia) to literally construct the 21st century world mankind will inhabit and utilize.

Infrastructure projects and government spending tell a global investor a great deal about a nation's willingness to control a stake in its own future, and to give its citizens a right to control a stake in theirs. Things like science, engineering, and technology-based businesses will be the types of businesses that solve some of the problems (discussed above) of the 21st and 22nd centuries. The rural-urban shift taking place is simply humanity molting its agrarian, industrial-revolution based skin in favor of a new set of economic opportunities, which will affect the lives of citizens around the globe. The gaps that we all recognize, whether as "beneficiaries" of differences in standards, or as "victims" on the other side of a seemingly insuperable divide, will continue to close. We must pay attention to opportunities, like infrastructure-based spending and development, that are created in the process.


March 08, 2009

MEMS in the Wii, iPhone and Cell Phones; Nano to Stop Bullets

By Red Sox Steve

How does the iPhone know which way is up? How does your Wii know to swing the tennis racket on the TV screen as hard as you?

The nanotechnology (we'll call it "nano" here) tree has a number of branches and roots, some, which we've discussed in recent articles, we need to expound upon, and others are completely new. Nano is rooted in MEMS (Micro Electro Mechanical Systems), which we talked about last time, and it branches into biology & health sciences, chemistry, physics & energy, electrical engineering & computing.

MEMS technology was born out of Honeywell's research into pressure sensors in the late 1960s. MEMS operate on a scale (one one millionth of a meter) larger than the nano (one one billionth of a meter) by a factor of 1,000. MEMS development is based on the type of technology used to construct an IC (Integrated Circuit). The various switches, sensors and mirrors that encompass MEMS are etched onto silicon wafers by the thousands - MEMS can be constructed that sense changes in gas pressure, change function in the presence of light, and measure changes in magnitude and direction of an object.

Nintendo's Wii controller (and the iPhone) uses an accelerometer (a type of MEMS) to know where the device is and where it is going. Essentially, accelerometers account for the pull of gravity, and then respond to changes in orientation based on acceleration in any given direction. When the accelerometer is being pulled in a certain direction, the mass within the system is displaced by a certain amount; the displacement indicates the direction of the object and its acceleration, which is then translated by the MEMS into what is seen on the TV screen. Swinging your controller in Wii tennis gives the console the message: this is where I am going, and this is how fast I am getting there. These types of devices are also useful in any system where it is necessary to measure vibration: a fan, an engine, a rocket, or even a pedometer!

MEMS functionality is not only manifested in the physical world, but is on display in the telecommunications world as well. One of the major problems with cell phones is the power consumption of an LCD screen. Qualcomm is using MEMS technology to improve the energy efficiency of the display screens on personal mobile devices.

A limitation of LCD displays is their inability to contrast, as ambient ("background") light changes. The human eye, when looking at a reflective object like a sheet of paper, sees differences in the contrast the ambient light makes with objects on the page; when looking at an emissive object, the human eye is seeing the light emitted FROM the object, like a computer or TV screen. In situations where there is more ambient light, it is easier to see a reflective object, and harder to see an emissive object. This explains why a person must "cover" the display of their portable device when outdoors in bright sunlight - to shield the amount of ambient light and see the emissive light coming from the device's screen.

IMOD (Interferometric Modulator) technology can counteract these issues: "As ambient light levels increase, so does the IMOD display’s white-state reflectivity. As a result, an IMOD display offers a superior contrast ratio in brightly lit environments. In darker environments, supplemental illumination is provided by a low-power frontlight." IMOD-based displays compensate for the amount of ambient light in ways that LCD displays are currently unable - these devices are easier to use in conditions of varying light, and consume less energy by moderating their own light production in the process.

According to a Plunkett's report, as of 2007 there were 200 to 300 companies manufacturing MEMS, including Hewlett-Packard, Texas Instruments, Bosch, Epson and Lexmark and the MEMS market reached $8 billion. Some of the latest and greatest developments in MEMS are being developed by a company called MEMX, in collaboration with the Sandia National Laboratory in New Mexico. Essentially, MEMX is using various circuit design methods to meet the current challenge of trying to pack as many MEMS as will fit onto a silicon wafer chip: MEMX is working on putting 10 million micro devices onto a chip!

The technology gets smaller and smaller - MEMS are the predecessors to nano and scientists are able to discover and manipulate nano-level phenomena using MEMS technology; MEMS technology is also used in the scanning tunneling microscope, which made it possible to discover nano behavior in the first place!

Is it possible to construct lighter yet stronger bulletproof vests?

In October 2007, a study published by The Centre for Advanced Materials Technology at the University of Sydney, Australia studied how carbon nanotubes are impacted by bullets and weapons fragments.

Essentially, a bullet proof vest uses its tensile strength or a hard metal plate to stop bullets and bomb fragments from harming the torso and abdomen. The substances used can be quite heavy: ceramic plates and titanium can be used to cover the body. Another well known bulletproofing material is Kevlar, the marketing name for what is known as a para-amid synthetic fiber (a carbon-based molecule linked by carbon-nitrogen as well as hydrogen-oxygen and hydrogen-nitrogen bonds). The tensile strength of Kevlar is five times stronger than that of steel. Unfortunately, it is possible for bullets to penetrate these substances and cause harm and even death.

Science has known about the relative strength and conductivity of carbon nanotubes for almost 20 years, and now its resistance to ballistic impact is being examined. The goal the scientists are working towards is to construct fabric which contain enough layers of carbon nanotubes to absorb bullets without the bullet either penetrating the fabric or causing blunt force trauma to the area of impact.

Scientists have found that the radius of the nanotube is a key factor in determining how much energy a given tube can absorb by a travelling bullet. Further investigations found that subsequent (and successive) bullet impacts on a nanotube structure did not cause additional damage, because the nanotube had returned to full tensile strength in enough time to fully absorb the energy of the subsequent bullet (on the order of trillionths of a second).

Smaller, more energy efficient, stronger, tougher, more adaptable. The role that MEMS and carbon nanotubes will play in 21st century life grows every day. Scientists operating in both the public and private sector are using technology to improve various aspects of human life. The information presented above needs little conclusion; the tiny, yet awesome, magnitude of these investigations and discoveries will change our lives forever.



March 03, 2009

'Oliver's Army': New Life for a New Century

By Matthew

'Don't start that talking
I could talk all night
My mind goes sleepwalking
While I'm putting the world to right
Call careers information
Have you got yourself an occupation?'

'Oliver's Army' - Elvis Costello

Oliver

There is a place in Texas, called 'Primarily Primates'.

(It's been the source of some conflict between PETA, the State of Texas and its founder. Those issues are murky and are not the subject for this discussion, but I did not want to gloss over the matter.)

They provide habitat for Chimpanzees and Lemurs, including Oliver, the upright-walking 'Humanzee'.

Oliver is genetically similar to Chimpanzees, with 48 Chromosomes (humans have 46) but his genetic code is distinct from Chimpanzees.

He's a mutant.

New life.

How'd he get this way?

That, we don't know. He isn't a Human Hybrid, not entirely...but his features, behavior, posture and cognition are not of chimps. The position of his head, legs and genitals is in line with a walking Human male. He is bald. His ears are positioned higher and shaped differently from Chimpanzees.

He has no interest in Chimpanzee females. He is attracted to Human females. He is not recognized socially within the Chimpanzee group and does not show any interest in their social activities.

Whether from 'Natural Selection' or through some anonymous genetic experimentation, Oliver is FACT.

And he is Fifty One years old.

Life happens and it doesn't make a bit of difference how. There are no barriers to the hybridization of Chimpanzees and Humans, little doubt that it has occurred in some laboratory somewhere or that it WILL happen.

The Science exists.

Oliver MAY be a result of such Science, more than five decades ago. Or he may be an entirely organic mutation, a trial balloon of structure organized by the unseen hand of genetic evolution.

He is a harbinger of new species of Primates. We do not know if Oliver is a blueprint for what we will find with actual hyrbidization, but we DO know that the next Century will feature new classifications of Primates. Human/Chimp hybrids, sub-species mutations.

Perhaps both.

Or more.

Oscar

Oscar Pistorius is a 22 year-old South African. He was born without legs below his knees (Fibula) and had his useless, boneless legs amputated as a child. Fitted with progressively more sophisticated prosthetics, he has grown into a world class runner (missed qualifying for the OLYMPICS by a mere 1.0 second, running 3rd in South Africa's Olympic Trials for the 400 Meters). He dominated the Paralympics instead, winning the 100, 200 and 400 Meters.

He is known as 'The Fastest Man on No Legs'.

As with Oliver, their are layers of political, ethical, cultural and social questions related to Oscar.

And, as with Oliver, those are not of any interest to us here. Oscar is HERE, he is young, his prosthetics are mere prototypes. He will be faster. He will do more.

And he was born with a genetic disposition for this form of hybridization, as Oscar was. With no legs, ever, and no sensation of balance relating to the use of human legs - Oscar is a blank slate for the new balance his prosthetics require. He intuits what is the only locomotion he can know. And then?


He upgrades.

And re-learns.

He too, is a mutant.

More importantly, he is also a Cyborg. A Cybernetic Organism that contains natural and artificial systems. Cybernetics is a HUGE field, and applies to many more interdisciplinary studies in an almost limitless number of applications. These feedback loops between the elements of Oscar are self-perpetuating - he gets new legs, uses them and the information he receives from that usage generates the design of new legs.

His brain and his legs are growing together, becoming accustomed to one another.

Oscar Pistorius is New Life.


Prosthetics evolve in these feedback loops, can be genetically grown in laboratories, can be fashioned artificially and can be linked to the brain and central nervous system.

'Moore's Law', like Oliver, refers to something born in 1958 - the Integrated Circuit.

In 1965, Gordon Moore, co-founder of Intel, observed that the number of transistors that can be placed on an integrated circuit without extraordinary expense increases exponentially and doubles approximately every two years.

All those labs, working on all those body parts, genetics, cybernetics, digital loops that improve exponentially...we don't know the details, they literally will not exist until they develop cybernetically between the various interfaces. But we DO know that the next Century will feature waves of Cyborgs.

Repliee Q1Expo

An Actroid with this name is a Japanese Robot, more precisely - an Android.

A humanoid Robot.

Japan is the global leader in Robotics and is obsessively pushing the science forward, from robotic construction workers, who do not need sleep, or compensation...are many times as strong as a human and cannot be 'hurt' to Actroid Androids - Female Robots with Artificial Intelligences, lifelike human appearances and sensor arrays that allow it to 'feel', react, understand stimuli and respond appropriately - even listen and speak, not from a script - from THOUGHT.

Like the Cyborg, Androids benefit both from the Cybernetic Feedback loops in its systems AND from the exponential increase in computing power, based upon 'Moore's Law'. Instead of an interface between organic and artificial systems, the data exchange is experiential WITHIN artificial systems.

Turn it on, it works, it learns, it reports, it can be improved and can improve on its OWN.

It's Human handlers are simultaneously processing the same data and incorporating it's lessons into later stage designs.

All that digital data, self-perpetuating, driven by both human and artificial intelligences.

This too, is New Life. The new Century will feature an incalculable number of Robots, some Android, others not.

New Life is on the way. New Industries. New lifestyles. New social structures, ethical quandaries, political realities.

Listen to the 'debate' being held about Athletes and Steroids, then contemplate this discussion.

A child born today, athlete or not is more likely to have supplemental improvements that are administered;

*chemically, through drugs...

*genetically, through biological implants...

*cybernetically, through artificial implants or augmentation...

*digitally, through computer processing implementation...

...than not.

There will be those who resist, luddite-like, and they will maintain 'Natural Human Societies', faith systems will follow, cultural conflicts, perhaps even violence between the different life forms.

Unaugmented humans may play 'Natural' Baseball, the way non-Steroid using BodyBuilders are known as 'Natural Bodybuilders', none of that is new, by the way, some guy talked openly about such topics in a movie filmed in 1975.

That guy is now the Governor of California.

Doesn't change the reality of this new Century.

It's called 'The Twenty FIRST Century' and you are living in it now, although for us in America, it is probably best understood as being lived thus far in the last Eight years of the LAST Century with an eight year detour back to the 19th and 20th under 'The Crawford Crusade'.

It's beginning again in America, it never stopped elsewhere and, where even the 20th Century never happened, it won't make a bit of difference.

All the changes of history pale in comparison to the ones that are coming, if not in your lifetime, certainly in your children's, and they will seem antiquated to their own Fifteen year olds.

There is a lesson in all of this - and here it is;

Don't spend TOO much time bemoaning the World that no longer is. That world has actually been gone for longandlong...the new World is HERE and its fascinating.

Dig in!