Monday, January 4, 2016

Science and Serendipity: My best day in the lab

My best day in the lab was a day of creation. Actually, it began in a bar.

Science can be a process of discovery, in which observations are made and hypotheses formulated, tested, rened, and repeated ad innitum, or until the scientist gets bored and moves on to the next subject. A scientist working on a problem - What are the molecular steps that initiate cancer when cells are exposed to carcinogens? - will focus on a small part of the universe, like a cell, or double-stranded DNA. But science is also creative: can we design and build molecules that will selectively deliver anti-cancer drugs only to cancer cells in the brain? This science creationism employs the tools of science to make devices, polymers, microscopic machines and a whole host of novel materials.

Sports enthusiasts like to regale each other with stories of a great game, often over beer. Chemists do too, except the game is synthesis, the players molecules, and the field, the laboratory. My labmate had made a new and interesting molecule - it was interesting because, if the common bonding models we had were correct, it had the wrong shape, and it didn't rust in air (like it should). Following this discovery, as was a common practice in my lab, we retired to the campus pub to celebrate our victory and plot our next move. I had solved the structure - figured out, using X-ray crystallography, the 3-dimensional organization of atoms in the molecule - and proposed a theory for why the molecule was stable and I thought at the time, "If we can make that molecule with osmium, can we make a copy using tungsten instead?" The periodic table is full of such what ifs, and we - fun science, in my experience, is collaborative - spent 20 minutes pouring over our beer and writing on my bar napkin (an old professor's words - I learned more chemistry talking in bars than I ever learned in the lab - were prophetic).

Later the next day - it's not good to drink and synthesize - I looked through the stock room to see if the compounds I envisioned were available. In synthesis, as in a good episode of MacGyver, you sometimes have to go with what you have on hand. I was able to locate adequate chemical substitutes for my synthetic plan.

... It worked.

Monday, July 18, 2011

Heat and Light

Benoît Paul Émile Clapeyron, 19th century French Engineer and Physicist is generally credited with developing what we know to be the 2nd law of thermodynamics, and his work has allowed us to evaluate the upper limit of efficiency in an internal combustion engine (hint: combustion engines are not particularly efficient).  But, to my knowledge, there is no historical record of him ever baking a Madeleine cake so, well, he can’t have been all that great.

There’s been quite a lot of fuss about light bulbs lately.  Some people don’t like the new, energy efficient ones because they look weird and take longer to illuminate to full brightness.  It is true that it can be little tricky to attach a lamp shade to the new design (but do we really think this is an unsolvable problem?  Really?), and the new ones don’t generate enough heat to drive an Easy-Bake oven but they do two things well: light up a room and use less energy when they do so.  The shape is actually necessary because, unlike an incandescent bulb where the light emanates from a white-hot filament (typically tungsten; thorium, a radioactive isotope is often produced during the fabrication of tungsten filaments – oops!), the new bulbs generate light at the surface of the bulb only and you get more light out when the surface area is higher – which it is in the curly shape.  But there’s a little more to it than that.  The bulb is really a twisted fluorescent lamp in which UV light from excited gas atoms inside the tube excites a fluorescent compound painted onto the surface of the bulb.  In fluorescence, typically higher energy light goes in (in this case UV) and lower energy light comes out (in this case visible/white light).  It sounds weird that you put in one kind of light to get another kind but you can see lots of examples – black lights, which emit ultraviolet light, will cause fluorescent paints to “glow” in the dark (next time you’re in a disco, make sure that you brush your teeth and wear something brightly colored – it will be dark, but you’ll see what I’m talking about.).

We need both, sure, but there’s a time for each.  Light informs, illuminates, opens the doors and reveals the details for all to see.  Heat, not so much.

Less heat.  More light.  Please.  The good news is that reasonable people seem to be leaving the drama to Broadway, and Glee (here is a recent NY Times story on the subject).

Wednesday, March 2, 2011

Where are the science experts?

When you have questions about health and science, some people go to the internet while others, like my brother-in-law, call me.  I used to think he wanted to know the answers to the questions (what are stem cells and why are they important?) but, lately, I have been thinking that he wants to keep me from getting bored during the holidays.  Am I dull?  Really?  Save that thought…

What happens when the President or the Congress have questions about science?  I mean, surely they have must have questions.  Don’t get me wrong, President Obama (B.A. Columbia University, J.D. Harvard University) is pretty bright and a number congressmen and women have advanced degrees but do they know about the way the ozone hole works?  Or what the differences are between adult and embryonic stem cells.  What do they know about climate change, or greenhouse gases?  Do they know why CO2 is a greenhouse gas and why N2 is not?  Are they scared of bisphenol A?  Where do they go for help?  What about judges who are often asked to evaluate arguments of a scientific nature (do breast implants adversely affect human health?).

Established by President Lincoln in 1963, the U.S. National Academies today includes the National Academy of Sciences (or just NAS) the Institute of Medicine (IOM), the National Academy of Engineering (NAE), and the National Research Council (NRC).  The legislation introduced by Senator Henry Wilson of Massachusetts set forth – in my opinion sensibly - the following principles:

[T]he Academy shall, whenever called upon by any department of the Government, investigate, examine, experiment, and report upon any subject of science or art, the actual expense of such investigations, examinations, experiments, and reports to be paid from appropriations which may be made for the purpose, but the Academy shall receive no compensation whatever for any services to the Government of the United States.
An Act to Incorporate the National Academy of Sciences (NAS)  

Initially, the academy was stocked, kind of like a trout pond, with 50 members and, later, members (like Spencer Baird, American icthyologist) were added by a nomination and election of current members.  Today, about 2,000 scientists, doctors, and engineers are members of this elite institution.  How elite?  About 200 Nobel prizes have been awarded to Academy members.  Membership doesn’t pave the way for a Nobel Prize any more than winning a Screen Actors Guild award leads to an Oscar.  Both the Nobel committee and the Academy are looking for the brightest minds to help advise the World, the President and the Congress to help them solve the big problems of our time.  In 1916, when the National Research Council (NRC) was added, that “problem,” for which the nations needs were greater than the NAS and NAE (established in 1864) could accommodate, was the [first] World War.  

I love going to the National Academy of Science web site ( and looking at reports that address issues of research in biotechnology, medicine, education, and natural resources.  While somewhat longer than the brief snippets that get out to the popular press, many are written in very accessible language. There are 600 “projects” under investigation today, spanning Agriculture (Sustainable Development of Algal Biofuels) to Biodiversity (A to B?).  In the area of nuclear security, the U.S. Department of Homeland Security (DHS) wanted to use new radiation detectors to screen cargo containers for nuclear/radiological material at US ports and border crossings, so Congress told DHS to ask the NRC to advise them on testing, analysis, costs, and benefits.  One neat side effect is that the results of all these Congressional “homework assignments” is a report that you can buy (for the bound copy) or download for… wait for it… free!

The NAS, NAE, and IOM also publishes (along with the University of Texas at Dallas) a monthly magazine Issues in Science and Technology that you can read online.

Don’t like reports?  Magazines?  The National Academies feel your pain.  They’ve also got lots of informative booklets (most of which can be downloaded for free) on a number of critically important topics like:

More information on publications of the National Academies can be found at

The legislature and the President had the wisdom to establish the National Academies.  They knew that the problems facing the nation were too big and complex for legislators to solve them alone, and in one sweeping step, they harnessed the energy of the best and brightest minds to study, explain, and help us to tackle them.  

UpdateThe FBI asked the NAS to evaluate their scientific investigation of the anthrax letters from 2001. In their report, which was peer-reviewed - a critical step in good science - before its release on February 15th, the NAS commended the FBI for drawing on the expertise of government and private-sector in building a novel Anthrax repository but suggested that recently-developed techniques could have increased the strength of their conclusions.  I have oversimplified the extensive investigation that the NAS conducted.  For more information on this, check out the report.

Tuesday, February 1, 2011

Ready, Set, Communicate!

At times, I have lamented what I think is the reluctance of scientists to weigh in on matters of science policy and the fact that the void left by this reluctance is too readily filled by charlatans promoting policies without a scientific foundation.  Yet there are numerous ways that science is available for public consumption. Here are some of the resources that are worth your time: Science News chronicles, in brief read-it-while-you’re-waiting-for the-next-train-format, little snippets highlighting science across a broad spectrum of areas. A brief sampling of today’s listings include stories on invisibility cloaks, transforming skin cells into heart cells, the positive effects of aerobic exercise on memory and the dark side of a “love” hormone. 

The American Chemical Society, in celebration of the International Year of Chemistry (IYC2011) has posted daily science tidbits to capture your imagination. The site boasts links to interesting and short articles about energy, the environment, health and materials.  For example, a few days ago, they focused on the ozone later (SPOILER ALERT: if the ozone layer goes away, you’ll have to wear sun-bloc with SPF 10,000!).  And you can read ahead and see that June 8th will highlight the critical issue of nuclear waste storage and disposal

The journal Nature, in addition to their chemistry blog from the editors of Nature Chemistry  has also added a special section to celebrate IYC2011

The American Association for the Advancement of Science publishes a daily news section with short, interesting tidbits across the entire scientific spectrum (OK, if visible light goes from Red to Violet, what is the spectrum of science?  Would philosophy be on the left or the right?).  As an example a recent article focused on how tree leaves can fight pollution.  Apparently, when trees are stressed by increased ozone, their capacity to absorb pollution from cars is also increased.  Ozone absorbed by trees?  But I thought ozone was in the stratosphere.  Actually, ozone, although the same molecule in each location is often referred to as “bad” when it occurs in the troposphere (where we live) and “good” when it occurs in the stratosphere (where it shields us from ultra-violet light).  As elaborated on the National Center for Atmospheric Research (NCAR) web site, tropospheric ozone is formed when sunlight shines on a mixture of nitrogen oxides and volatile organic compounds.  This is sometimes referred to as "photochemical smog." These chemicals that fuel the fog come from vehicle exhaust, industrial emissions and gasoline vapors.  There are natural sources too: ozone is formed during electric discharge (it is the acrid smell around electric motors) and during lightning strikes. 

I remain convinced that there is a wealth of science out there for the taking.  Not only will you impress your friends with these tidbits, but you'll help them to see the value of science to health, the environment, and society.  Enjoy!  And if you know of interesting science-related web sites, feel free to post a link in the “comments” section and I’ll add it to this column.

Update: Many newspapers and magazines also have special weekly sections dedicated to science, including The New York Times (Science Times), The Washington Post (Science News), and The Economist (Science & Technology).

Thursday, January 27, 2011

Chemistry is all around

If you don’t think that chemistry is everywhere, consider the following news items from the past few days:

Oil dispersant still remains in Gulf – January 26th

In a study released yesterday by the Woods Hole Oceanographic Institute, researchers looked for evidence of sodium dioctylsodiumsulfosuccinate (DOSS), the dispersant used to break up the oil spill at Deep Horizon last year.  DOSS is a major component of the mixture, called Corexit, that is a common dispersant used for oil cleanups, and manufactured by Nalco.  In addition to DOSS, Corexit contains 2-butoxyethanol and propylene glycol.  Do you need a degree in organic chemistry to follow what’s going on?  Not really.  The key to the chemistry behind dispersion derives from the fact that water and oil are immiscible (look at a bottle of oil and vinegar salad dressing some time…) because, while the bonds in water (O–H) are polar, the bonds in oil (C–H) are not.  The adage “like dissolves like” comes into play here: polar or ionic substances will dissolve more readily in polar solvents; non-polar substances dissolve more readily in non-polar solvents.  At any rate, this is where surfactants come in.  Surfactants tend to be long chain molecules with a hydrophilic (“water loving”) section containing a charged – or at least polar – group that is miscible with water, and a non-polar hydrophobic ("water fearing") section that is miscible with oil.  The combination of these two features allows surfactants to break up large oil samples into small microscopic droplets.  Bacteria have an easier time metabolizing small droplets (yes there are bacteria that can live off oil!) and dispersing the oil slick is a critical first step in remediation.  That there is still some DOSS in the ocean is important, as it appears not to have undergone biodegradation.  That said, the quantities of DOSS measured are approximately 1/1000th of what would be considered toxic.  Whether these concentrations will have a deleterious impact on the Gulf ecosystem remains to be seen.

State of the Union Address – January 25th     

In his State of the Union Address, President Obama called for the following science initiatives:
  1. Put 1,000,000 Electric Cars on US highways in 5 years.
  2. Obtain 80% of our energy from “clean” sources in 35 years.
  3. Establish eight "Blue-Sky" research centers.
  4. Train 100,000 science teachers 

Of course, these items are are related.  A division of the Department of Energy called ARPA-E is interested in funding 8 centers for research into our energy future, each with a price tag of about $25 million dollars.  The DOE believe that an infusion of $$ into the academic and national laboratories of the best and brightest offers attractive prospects for addressing our future energy needs.  25 million dollars sounds like a lot of money, but it is only a fraction of the money that we currently spend on oil.  Given that the supply of oil on the earth is finite, it is only logical that we should pursue other means of energy generation (solar, nuclear, biomass, etc.) and hopefully, the ARPA-E centers will usher in a new wave of innovation.  In case you didn’t know, in a 40-ish gallon barrel of oil, we burn about 87% to move cars and trucks around on highways and to heat our homes, leaving only 1 ¼ gallons of oil left to make things.  When the price of oil goes up, gasoline prices go up to, but so do the prices of everything else that is made from oil-based sources (plastic, for instance).  And, owing to increased pressure on our oil supply, these prices can only continue to go up.  Research in energy will make it possible to build better electric cars as well as the electric grid to charge them efficiently.  Science teachers will make it possible for the next generation of scientists to be ready for the challenges that they will face.

As I wrote in an earlier blog (Parents matter in science education), we’re in a tough spot when it comes to the level of preparation of science students (only 2% of high school students nationwide were found to be “advanced” in their preparation of science).  Some have argued that the focus of testing on reading and math, to the exclusion of science, has contributed to this deficiency.  Whatever the cause, we have to turn that number around.

International Year of Chemistry - January 1st 

In case you weren’t already aware, 2011 has been declared the “International Year of Chemistry” which is, in my opinion, totally cool.  There are a wide array of sources with interesting tidbits but, for starters, go to the IYC web site for links to upcoming events and history.  But that’s not all: there are pages from other scientific societies and publishers like the American Chemical Society and the journal Nature that are chock full of chemistry nuggets.  For example, the ACS web site identifies January 23rd, 2011 the date (in 1911) that Marie Curie was denied membership to the men-only French Academy of Sciences (this was after she had received her 1st Nobel Prize).  I recently read a wonderful biography of Dr. Curie written by Barbara Goldsmith (Obsessive Genius: The Inner World of Marie Curie, Norton, 2004), recommend it highly, and I will likely devote a future blog to the Curie family and their contributions to nuclear chemistry.

There is much to enjoy and discover in chemistry, if not in science.  I hope you will enjoy the journey.

Wednesday, January 26, 2011

George Washington was a microbiologist

True story.  I am completely not making this up.

George Washington, commander of the revolutionary army and the first President of the United States, performed some of the earliest documented experiments in microbiology, when he and a team of collaborators, including Thomas Paine, paddled out into the Millstone River in central New Jersey to perform an experiment.  Paine, who wrote Common Sense, went to see General Washington with a letter of introduction from Ben Franklin who had hoped to secure a pension from the US Congress for Mr. Paine.  For inspiration, Washington had selections from Paine's writings read aloud to his troops each night in the hopes that it would inspire them during the war.  At any rate, Paine had heard that there were sections of the river that could be set on fire so, one night, he, Washington and some troops paddled out into the river. As Paine wrote of the incident in a letter on November 5th of 1783:

We had several times been told that the [Millstone] river… might be set on fire… When the mud at the bottom was disturbed by poles, the air bubbles rose fast, and I saw the fire take from General Washington’s light and descend to the surface of the water... This was demonstrative evidence that what was called setting the river on fire was setting on fire the inflammable air that arose out of the mud.

But Washington wasn't alone in these early experiments.  At approximately the same time, Allesandro Volta, the Italian scientist for whom the term volt is named, wrote to Father Carlo Campi in November 1776 (7 years before the Washington-Paine experiment) of conducting similar experiments on Lake Maggiore in the Italian Alps:

So, on the 3rd of this month, with my head full of such ideas, and being in a little boat on Lake Maggiore, and passing close to an area covered with reeds, I started to poke and stir the bottom with my cane.  So much air emerged that I decided to collect a quantity in a large glass container… This air burns with a beautiful blue flame.

The “flammable gas” referred to in these experiments was “swamp gas,” of which a large component is methane, a little molecule in which one carbon is bonded to four hydrogens.  Chemical formula: CH4.

You may wonder where the "microbiology" comes in.  Here's how:

There are a group of microscopic organisms that derive chemical energy from the conversion of carbon in a variety of sources into methane.  These methanogens (“methane making”) are not classified as bacteria but, rather, come from a separate kingdom, Archaea, which derives from the Greek word 'arcaia' which means “ancient things” (archaic has the same root). Typically, methanogens live in mud on the bottoms of relatively quiet rivers and ponds.  You don’t have to do anything to get them to grow except create conditions in which they can flourish.  Typically that means (a) remove the oxygen (these environments are called “anoxic”) and (b) provide a nice source of carbon, usually in the form of decaying organic matter (tree leaves, for instance).  Other natural sources include carbon dioxide, methanol, acetic acid (among others), and halocarbons (there is some evidence that methanogens can help to detoxify chemical wastes, so this chemistry has implications beyond historical interest).

Did Paine know about Volta's experiments?  Seems unlikely, but it’s interesting to note that, over a century before quantum mechanics, citizen-farmer-statesmen-scientists were studying the natural world to understand the how and why.  They may not have known about atoms, molecules, or the scientific method as practiced in the 21st century but, like any good scientist, they each designed an experiment that tested a hypothesis, collected their data, and analyzed their results.

Incidentally, methane is produced in landfills, by termites, and the rumens of cows – all regions where methanogens are allowed to flourish – and it is produced in enormous quantities.  Some estimates suggest that a billion tons of methane are released into the atmosphere annually where some of it is oxidized back to carbon dioxide and absorbed during plant metabolism, but it’s influence doesn’t stop there.  Methane is an important greenhouse gas.  It isn’t present to as great an extent as CO2, but it has a higher heat capacity than carbon dioxide.

Tuesday, January 25, 2011

Parents matter to science education

When I tell people that I'm a chemist or that I teach chemistry, they usually say one of three things: (a) I hated or was never good at chemistry (90%), (b) I never took chemistry (5%) or (c) I am a chemist too! (< 1%)  I would expect to see similar numbers with other science subjects although perhaps more people would have liked biology, but I sure would like to see the poor impression of chemistry and the hard sciences fade away.  The future advances in our nation - our ability to cure disease and to develop new technology that addresses our growing energy needs - is intimately connected to science education.  At the moment, we're not doing a very good job at this.  As reported in today's New York Times, a Department of Education report indicates that only one-fifth of high school seniors are graduating at or above a merely "competent" level (and only 2% are earning an "advanced" ranking).  In response to the NAEP - 2009 Report, U.S. Secretary of Education Arne Duncan said "When only 1 or 2 percent of children score at the advanced levels on NAEP, the next generation will not be ready to be world-class inventors, doctors, and engineers."  1/5th?  2%?  Yikes! 

As our national workforce evolves away from a manufacturing base, we lament the loss of these jobs, but rationalize this loss in terms of better, “new economy” jobs that will be available to Americans.  Unfortunately, as documented by the National Academy of Sciences in Rising Above the Gathering Storm (revised in 2010), we are also losing forward-looking technologies in the energy sector like fuel cells, energy storage, and wind power.  Moreover, our capacity to compete for the 21st century jobs we envision is undermined by our failure to adequately prepare students in science, technology, engineering, and mathematics.  In choosing a 21st century economy, we must commit to educating our students so that they are prepared to drive it.  As a college chemistry teacher, science fair judge, and high school science mentor, it has been my observation that the impressions and aptitude of college students toward science depend less on the college curriculum than from their science experiences during the K-12 years.  College science courses are essential for training of young scientists, but the students who arrive with a strong pre-college science background have a tremendous advantage over students whose exposure is weaker, and they are more likely to pursue these courses and professions.  Moreover, the attitudes of families and parents are critical.  Almost to a person in my experience, children who either aren't interested or think they aren't good at science have parents who share these attitudes.  Coincidence?  I think not.  Students inherit their fear or love of science and math from their parents as surely as any genetic attribute.  The challenge, then, is two-fold: we must teach parents the value of science as we teach science to their children.  We target parents in public health initiatives to stem childhood obesity and decrease the incidence of type 2 diabetes.  We should also try to make parents more effective partners in their children’s science education.

What can parents do?  Do they have to become expert in chemistry or physics or biology, and to hover over the kitchen table with their children slogging through homework assignments? They can but, if nothing else, they should encourage their children to take on hard subjects and recognize that there are advantages to having more doors open rather than less.  Parents can ask questions about the subject, talk to the teachers, and read the many resources available for the lay audience that are out there, go to the science fair, or the magic show at the local college, or the new exhibit at the science museum.  My parents were not scientists, but they saw how important it was to me and they encouraged me to pursue it, with a steady stream of science kits, microscopes and, well, by not getting upset when I had frozen rodents in the basement refrigerator (they were for feeding the snakes...).  My Ph.D. thesis (on the chemistry of multiply-bonded metal complexes - pure poetry!) sat in their living room.  They never read it, and we didn't talk about it at length, but they sure were proud of it.  Thanks, Mom and Dad!

Scientists helped fight infection during the war by teaming up with engineers, building huge-scale fermenters in a Brooklyn factory to culture mold that would make penicillin.  More recently, bioengineers cloned the spider silk gene into goats so that when they produce milk, they also produce silk for the manufacture of incredibly strong fibers.  How cool is that?  Who wouldn't want to know about that?