A Lifetime of Chemistry

Tim Clark is a jolly looking fellow: he’s tall, he’s round, and his beard is white. When he speaks, a low rumble overtakes the room and you listen to what he has to say. Tonight, he’s telling stories of Professor Paul von Ragué Schleyer.

Paul Schleyer, at the age of 83, is still a practicing chemist. He has several students and teaches a graduate course in the fall. He’s written many technical books–along with one, as of yet, unpublished memoir–and has published over a thousand papers. He is an expert in synthesis and computational chemistry. It’s fair to say, he’s had a good career.

Tim Clark was there when he left Princeton for a small German university–a move that confused many. “I know what lured him,” Clark says. “I’ve seen her.” The next slide shows a large computer in a cabinet. Clark tells us that it has 0.2 MB of memory. This is what Schleyer had left the prominent university for: a machine with the computing power of a modern wristwatch. The switch was, obviously, successful. Schleyer’s reputation only increased as he tackled the new field of computational chemistry.

After discussing some of the work he and Schleyer had done together, Clark showed a series of quotes by famous scientists. Most were mocking chemists. The crowd had a good laugh. The final slide had this quote from Justus von Liebig, “The loveliest theories are being overthrown by these damned experiments; it’s no fun being a chemist anymore.”

Schleyer followed Clark with a short speech thanking him for the presentation. He told the story of how Clark came to work for him on adamantane, but never got around to it. He read a passage from a technical book by Norman Allinger which contained an anecdote of Clark being impressed by the speed of molecular mechanics. He ended his speech with a sentence that typifies his research career, “I am still a strong proponent for fundamental research; I think its natural home is in universities.”

Does Government-forced Open-access Help Science?

As scientists along with government officials in the House and Senate work to pass bills that force government-funded research to be freely accessible, one question pops to mind: Will peer review–the principal standard in scientific research–work with open-access?

With current subscription based journals, the publication process involves an editor, who is paid, a number of reviewers, who are not paid, and a boat-load of people formatting, producing and distributing the content–all paid. With open-access format, how do publications get reviewed or formatted or distributed? At the very least someone needs to coordinate reviewers maintain a website.

Will the government finance current publishers or will government-funded research go strictly in government-funded journals? Since most research is funded by government grants–judging from the funding sources listed at the end of academic papers–the later would force many publishers out of business. The specificity of smaller journals would be lost, and all research may get lumped together–though I suppose they’d separate fields like physics and psychology. Publishers, of course, are calling the open-access bills “unnecessary and a waste of federal resources.”

And who would keep track of citations? Right now, there is an intricate bookkeeping system keeping track of citations for each author–for a fun dick-measuring game of who has the most citations–and an overall “impact factor” of the journal–another game to see which journal is most cited. Though I call these games, keeping track of citations is important. It (kind of) shows which scientists and journals publish meaningful work.

While I like the idea of open-access–in a romantic sense–I’m not sure it is compatible with the current structure of scientific publication. If these bills pass, a dramatic overhaul of the entire system will have to occur. If–or when–that happens, we must preserve the peer review process even if all else is lost.

Coming Soon: 3D Printing

Three-dimensional printing may be the “next big thing” in the technology sector. President Obama, in his State of the Union address, praised White House efforts to establish manufacturing labs saying 3D printing “has the potential to revolutionize the way we make almost everything.” He promised the launch of three new hubs–though the locations are as of yet undisclosed.

Three-dimensional printing started with clunky plastic, but has now evolved to include a variety other materials–including cartilage for prosthetic ears. Products are first designed by computer aided design (CAD) software which is commonly used by engineers to test-build a variety of devices and mechanical parts before actual manufacturing. Once the design is optimized, it’s sliced into cross-sections–similar to how computer images are split into pixels. Raw material–powder, liquid, or any other form–is loaded into the printer and prepared for deposition, often by heating. The printer lays down material layer-by-layer until the entire 3D structure is completed. Typical layer thickness is in the micrometers, small enough to create relatively smooth edges.

A Kickstarter project by Formlabs recently raised almost $3 million to develop low-cost 3D printers–their original goal was only $100,000. The printer, called Form 1, promises small, at-home printers for enthusiasts to create their own plastic sculptures made from an undisclosed gray liquid. Printed examples included a chess-piece castle, the Eiffel tower, and quarter sized bird cage.

3D molds

Three-dimensional prints from Formlabs come in a variety of shapes and sizes.

Three-dimensional printing is attractive to both enthusiasts and manufactures, although techniques such as injection molding are still more affordable if printing large quantities. As of now, most printing has been done by hobbyists in the form of toy modelsworking clocks, and edible chocolate turtles. As costs for 3D printing decrease, printers and materials will become more widespread. One day we may be printing car replacements parts or children’s toys at home from our own design.

Accidently Winning the Nobel Prize

Another topic Professor Zhengwei Pan spoke of in the lecture I previously mentioned was being timely with research. He emphasized that immediately analyzing unexpected results was key to a new discovery.

As an example, he told the story of Buckminsterfullerene, a soccer-ball shaped molecule that won its discoverers the 1996 Nobel Prize in Chemistry. A buckyball–the pet name that’s caught on with the scientific community–is made up of sixty carbons arranged into twenty hexagons and twelve pentagons with a carbon at each vertex and a bond along each edge.

The discovery–like many major discoveries–came about accidently. Harry Kroto and his collaborator Robert Curl were studying unsaturated carbons in space dust. In order to characterize the molecules they were seeing in the dust clouds, they needed to make them here on Earth. This was a task neither was up to, so Curl called his coworker Richard Smalley, an expert in experimental physical chemistry. Smalley set out to make unsaturated carbon chains by hitting a sheet of graphite with a laser, but he ended up finding large clusters of 60 and 70 carbons. When analyzing the molecules with mass spectrometry, Smalley found the clusters were spherical–or as close to spherical as a molecule can get.

The threesome was surprised, since they were aiming to make carbons plasmas found in space not stable molecules. After much discussion, they came up with the highly symmetric soccer-ball reminiscent of the geometric come-like architecture of Buckminster Fuller. They named the molecule after their muse, published the paper and collected their prize.

Because the group analysed their unknown results, they walked away with the most famous prize in all of science. What would have happened if they had shelved those results because it wasn’t what they set out to find? Someone else would have discovered C60 and come to the same geometric conclusion. The prize would have been lost to Kroto, Smalley, and Curl.

So maybe it’s time to reopen that “failed” project that gave you such strange results. Who knows? You may have stumbled onto something new.

Finding the Story in Science

Last Friday, I attended a lecture by Professor Zhengwei Pan on how to write a successful scientific paper. Prof. Pan has published in both Science and Nature, and has been featured on nine journal covers–including Nature Materials–so he’s an experienced guide for a group of graduate students who have written few, if any, papers. Instead of taking us step by step through the process–”Here is the discussion. This is where you write your results.”–he focused on finding the right story. He said once you find the right story, the paper is reduced to writing about the figures. I should mention Prof. Pan works heavily with microscopy, so he has a bounty of beautiful pictures.

Finding the story is the hardest part of any research project. What you did and how you did it doesn’t matter as much as what does it mean, and every scientist wants to do meaningful work. We all want to discover something new or make the biggest and the best. But how? How do you stumble onto a major discovery? Prof. Pan said the biggest discoveries come by accident. Not the kind of accident that comes from being clumsy or careless in your work, but the happy accident that comes from being diligent and hard working, from taking careful notes.

He told a story about his own discovery of using germanium as a catalyst to grow zinc oxide nanowires. As a post-doc at Oak Ridge National Laboratories, Prof.–then just Dr.–Pan was tasked with synthesizing semiconducting nanowires–this was in 2005 when nanowires were the exciting new material for electronics research. Pan tried numerous times to grow zinc oxide by a traditional method (vapor-liquid-solid crystal growth) with no luck. But suddenly, miraculously, it worked! Pan ran to the scanning electron microscope–an instrument which takes nanometer-sized “pictures” using a beam of electrons–and shoved his sample into the beam. Instead of thin, uniform wires, Pan’s wires had a round head.

Pan's ZnO Nanowires

Taken from Angewandte Chemie International Edition 44 274-278.


“What was going on?” Pan asked himself. Never before had he seen single-material nanowires look like this. He used another technique, called energy-dispersive X-ray spectroscopy, to find the chemical composition of his new material. The length of the wire was zinc oxide, as he expected, but the head was made of gallium. He hadn’t added any gallium to his quartz tube, where he grew the wires. How could the heads be made of gallium? He carefully poured through his lab notebook looking for any hint at what that circular head could be. Finally, he realized that he had previously used that quartz tube to grow gallium oxide nanowires. The next time he went to grow zinc oxide nanowires, he threw a little gallium into the tube. The rounded heads appeared. He had accidently discovered a new material.

So, researchers, do careful work, but always look for the unexpected. If something goes wrong, find out why. You may come out of it with an interesting story of your own.

Turn that radio down, it’s too bright!

Noise comes in many colors. We’re all familiar with white noise–the static on the radio and TV–but unless you work with electronics, you may not have heard about other colors of noise.

Contrary to what you might think, meaningless random noise is not always the same. Different kinds of noise make different sounds and images, so to keep track of the different types they are named after colors, typically in reference to light with a similar spectra. For example, the frequency spectrum of white noise is relatively flat–you’re likely to find the same amount of noise at all frequencies. White light contains equal amounts of every color and also has a flat spectrum. Essentially, if we could translate the flat, even noise into color, it would be white.

If noise is essentially meaningless, why do we care about distinguishing different kinds? Well, as Dan Ellis, a professor at Columbia University, says, “The technical challenges in, say, building a cell phone system, or an ultrasound machine, come from trying to extract a desired information ‘signal’ from a background of unwanted ‘noise’.” Each color of noise has a certain post-processing method to decrease or remove the signal from the actual, desired data. But sometimes random noise is useful. White noise can block out other sounds which helps some people–especially those in crowded cities–get a good nights rest.

The other colors of noise are not flat, but concentrated at specific frequencies. Blue noise, for example, increases with increasing frequency. This is useful in graphics engineering to trick the eye into seeing a continuous color gradient instead of the actual quantized pixels. In audio, blue noise is more annoying than useful because of the high-frequency hiss. Pink noise is the exact opposite, it decreases with increasing frequency. Since pink noise is concentrated at the low end of the spectra, it’s often used in auto to increase the bass and cut down on high-frequency notes. On its own, pink noise sounds like the low hum you hear on an airplane.

Brown noise–confusingly also known as red noise or more comically “drunkard’s walk” noise–lies between pink and white noise. It’s called brown not in reference to the color, but because it can be generated by mimicking Brownian motion. Brown noise is a more pleasant version of white noise with lower-frequency notes reminiscent of waves on the beach or a windy day.

There are also several other unofficial colors–orange, black and green–but white, blue, pink and brown are the most useful. So next time you’re assailed by a blast of static or mechanical rumbling think of what color you’re hearing. Maybe you’ll finally get some sleep on that next red-eye flight back home.


Goodnight, Sweet Prince

Today the Large Hadron Collider (LHC for short) will close its doors for two years to make much-needed upgrades, possibly to start exploration into the existence of dark matter and extra dimensions.

The LHC represents everything science should be. Physicists and Engineers from over 100 countries joined together to build the $9 billion particle collider with the sole purpose of answering fundamental questions of the universe. And, boy, did they. Even with a set back only nine days after opening–a magnetic quench that took over a year to fix–the machine has detected new fundamental particles, the Higgs boson being the most important.

Physicists have been using the Standard Model since the 1970s to explain all sorts of natural phenomena, with the catch that no one has proven the model to be experimentally correct. The LHC tests fundamental aspects of the Standard Model, but doesn’t take a side on whether it is right or wrong. There are even some scientists out there that hope the LHC finds something new and unexpected to turn the physics community on its head. But last November, the LHC (tentatively) found what the majority of scientists had crossed their fingers for: the Higgs boson, the particle that gives everything mass.

It’s interesting to think that while we were building computers and walking on the Moon, no one knew why particles had mass, just that they did. With the Standard Model, scientists believe that the particles we know–electrons, quarks, etc.–get their mass from interaction with a Higgs field and the amount of interaction with that field determines the mass; more interaction means a more massive particle.

But how do we know a Higgs field exists? If the field is given enough energy to “excite” it, a Higgs particle will pop into existence. Because the particle is so massive, it quickly decays–in fractions of fractions of a second–into two streams of electrons and hadrons, the building blocks of protons and neutrons. The LHC hopes to see these decay streams after smashing protons and bare lead nuclei together at ultra-high speeds. The decay streams will only be seen for a small fraction of collisions–1 possible Higgs boson for 10 billion collisions–and many decays need to be observed to guarantee a discovery. But with around 600 million collisions per second, the LHC should be able to see roughly one event every half hour.

Currently, scientists at the LHC think they saw enough decays to confirm the existence of the Higgs boson, though it will take a while to analyse the massive amount of data coming from the collider. Now is the opportune time for the LHC to shut down and make upgrades. While we won’t hear of any experiments for close to two years, there is still much to look forward to from the outcome of past runs.

How to Accidently Ruin the Environment

Scientists mean well. Of course I can’t speak for everyone, but most of us want to do good–good for science, good for humanity, good for the environment. Thomas Midgley, Jr., an especially prolific inventor with over a hundred patents, wanted to prevent the impending fuel crisis following World War I.  While he achieved his goal which led to more powerful engines–an advantage in World War II–he also caused more irrevocable environmental damage than any other person in history.

Knock–that worrisome metallic ping! your car makes when accelerating hard in hot weather–was thought to come from a flaw in the design of internal combustion engines. Without knowing how to prevent knock, advancement had plateaued. No one could make the powerful, fuel-efficient engine America needed. Midgley, ever the innovator, soon discovered that knock actually came from a problem with the fuel, not the engine. Working for General Motors, Midgley led a trial-and-error search for an additive to prevent knocking.

The solution was to add a small amount of tetraethyl lead to current gasoline. The product was quickly put on the market and advertised as a superior alternative to ethanol-blended fuels–coincidently, ethanol-blended fuels were much more expensive for General Motors to produce. A year after the discovery, the American Chemical Society recognized Midgley’s work with the Nichols Medal–an 18 carat gold representation of “outstanding achievement in chemical research”.

General Motors along with the company now known as ExxonMobil formed the Ethyl Gasoline Corporation to mass-produce their new fuel additive. Not two months after the opening of the first tetraethyl lead chemical plant, five workers died and many others suffered from lead poisoning, hallucinations and insanity. To curtail the public backlash, Midgley participated in a press conference where he demonstrated the “safety” of tetraethyl lead by deeply inhaling its vapors for a full minute. Soon after he contracted lead poisoning, and sought treatment in Europe.

Although doping started in the 1920s, leaded gasoline remained the standard for many decades. It wasn’t until the 1970s with a study by Philip J. Landrigan where the dangers of lead additives were fully exposed. Landrigan, a pediatrician, tested the blood of children living near a smelting plant in El Paso, Texas.  Sixty percent of the children were found to have elevated levels of lead in their blood. The public outrage forced the government to head Landrigan’s warnings and phase out the use of lead additives for more environmentally-friendly alternatives.

If inciting millions of motorists to shoot flumes of poisonous vapor into the air for close to fifty years isn’t enough damage for you, let’s look at Midgley’s other famous invention: Freon. Again Midgley meant well, at the time–again in the 20s–air conditioning and refrigeration units cooled their systems with flammable, toxic reagents such as ammonia and propane. Still with General Motors, Midgley was tasked to find a safe alternative. A good refrigerant must be volatile and chemically inert, and halogenated hydrocarbons were the obvious choice. He settled on dichlorofluoromethane, a small molecule with three halogens–a fluorine and two chlorines–bound to a carbon center. This compound, commonly called Freon 21, and similar chlorofluorocarbons refrigerants were, like leaded-gasoline, a huge success. They quickly became widespread in not only air conditioning and refrigeration but also in aerosol sprays–maybe you recognize the abbreviation for chlorofluorocarbon: CFC.

CFCs were standard in military aircraft as fire extinguishers beginning in World War II and transfered over to civil aircraft soon after. By the 1960s, these dry, powerless extinguishers were prevalent in computer rooms, laboratories, museums and anywhere with water-sensitive property. Along with refrigerant and propellant products, CFCs were everywhere.

At the peak of CFCs, an independent scientist, James Lovelock, fired up an electron capture detector–his own invention–and found fluorinated compounds in 50 separate air samples. Soon after, Mario J. Molina and his professor F. Sherwood Rowland discovered CFCs in the upper atmosphere are destroyed by solar radiation, creating chlorine radicals that destroy the ozone layer. Instead of burying this research in academic journals, the pair warned news media and politicians of the environmental damage done by CFCs. Regulation of these materials started in the 1990s, and by 2007 two hundred countries had agreed to eliminate CFCs entirely. Molina and Rowland, along with Paul J. Crutzen, won the 1995 Nobel Prize for Chemistry for their discovery of the destructive properties of CFCs.

So where is Thomas Midgley now? How does he feel knowing he created two of the most environmentally-damaging, mass-produced products to date? In 1940, Midgley contracted polio and was left unable to walk. He invented a system of string and pulleys to lift him out of bed, but in 1944 at the age of 55 Midgley was caught in his own device and strangled to death. He never knew the harm his inventions caused, which is probably for the best.

Martian Time

Earthlings are meticulous about tracking time from the moment we get out of bed–to stop that blaring alarm clock–to the moment we get back in–when we reset that hated alarm. But how do we define time on other planets? For most of us, little could matter less, but for scientists involved in missions to Mars, little could matter more.

Astronomers mark the average length of a Martian day as 24 hours 39 minutes and 35 seconds. To set a Mars Local Time for use in exploratory missions, NASA developed a “Mars clock” based on the terrestrial 24 hour system, but with longer seconds, minutes and hours. Notable robots such as the Mars Pathfinder, the Mars Exploration Rovers, and the Phoenix and their mission controllers have operated on Mars time, rather than Earth time. The ever-shifting time gap between Earth and Mars required Earth-based controllers to advance their schedules by forty minutes each day–many calibrated their wristwatches to Mars time.

“You’re always jet-lagged,” Deborah Bass, the Deputy Project Scientist for the NASA Jet Propulsion Laboratory’s Phoenix Scout Mission, told Popular Science. “It’s only a little bit, because an hour–who cares, that’s not so bad. But it starts to take its toll.”

Many of the current rovers run on solar power–meager solar power at that. Rovers have only a four-hour period around local noon before their clocks run down. Scientists controlling the rover’s actions must be hyper-aware of the time on Mars. To make time keeping more complicated, five of the six successfully-landed rovers defined their own time zone. Only the Mars Pathfinder kept “local true solar time” set to the Martian midnight hour. The twin Mars Exploration Rovers, Spirit and Opportunity, used a “hybrid local solar time” to sync the true solar time with mission operations. For us, hybrid time is like using a watch set for Eastern Standard Time in central California–confusing, but it still counts passing minutes.

Though the length of a Martian day is close to a day here on Earth, the length of a year is almost twice as long on Mars. If months are kept to 28 Martian days to roughly align with Earth months, a year would have 24 months. But what would we call those extra months? Would there be a first December followed by a second December? Would we, as some enthusiasts suggest, alternate Earthly calendar months with Zodiac constellations or maybe science fiction authors? Or should months not be evenly spaced, since the orbit of Mars is not even itself? Mars wobbles around the sun in such a way that spring is the longest season at around 193 Martian days, while autumn is the shortest at around 143 Martian days. Do months need to reflect natural seasons and constellation cycles, or in this modern age are human economic and social patterns more important?

Unfortunately, most of us probably won’t stick around long enough to find out how humanity settles this question, but in the mean time it’s fun to think about.