Tuesday, September 27, 2011

The flame of life and death: My favorite (insufferable) chemical reaction

For me, the most astounding thing about science has always been the almost unimaginably far-reaching and profound influence that the most trite truths about the universe can have on our existence. We may think that we are in charge of our lives through our seemingly sure control of things like food, water, energy and material substances and we pride the ability of our species to stave off the worst ravages of the natural environment such as disease, starvation and environmental catastrophe. We have done such a good job of sequestering ourselves from the raw power of nature that it's all too easy to take our apparent triumph over the elements for granted. But the truth is that we are all without exception critically and pitifully beholden to a few numbers and a few laws of physics.

And a few simple chemical reactions. Which brings me to my favorite reaction for this month's blog carnival. It's a reaction so elementary that it will occupy barely a tenth of the space on a napkin or t-shirt and which could (and should) be productively explained to every human being on the planet. And it's a reaction so important that it both sustains life and very much has the potential to end it.

By now you might have guessed it. It's the humble combination of hydrocarbons with oxygen, known to all of us as combustion.

First the reaction itself which is bleedingly simple:

CnH2n+2 + (3n+1)/2 O2 → (n+1) H2O + n CO2 + Energy

That's all there is to it. There, in one line, is a statement about our world that packs at least as much information into itself as all of humanity's accumulated wisdom and follies. A hydrocarbon with a general formula CnH2n+2 reacts with oxygen to produce carbon dioxide, water and energy. That's it. You want a pithy, multifaceted (or two-faced, take your pick) take on the human condition, there you have it. While serving as the fundamental energy source for life and all the glory of evolution, it's also one that drives wars, makes enemies out of friends, divides and builds ties between nations and will without a doubt be responsible for the rise, fall and future of human civilization. Faust himself could have appeared in Goethe's dream and begged him to use this reaction in his great work.

First, the hydrocarbon itself. Humanity launched itself onto a momentous trajectory when it learnt how to dig carbon out of the ground and use it as fuel. Since then we have been biding our time for better or worse. The laws of quantum mechanics could not have supplied us with a more appropriate substance. Carbon in stable hydrocarbons is in its most reduced state, which means that you can get a bigger bang out of your buck by oxidizing it compared to almost any other substance. What billions of controlled experiments over the years in oil and natural gas refineries and coal plants have proven is that you really can't do better than carbon when it comes to balancing energy density against availability, cost, ease of handling and transportation and safety. In its solid form you can burn it to stay warm and to produce electricity, in its liquid form you can pump it into an incredibly efficient and compact gas tank. For better or worse we are probably going to be stuck with carbon as a fuel (although the energy source can wildly differ).

The second component of the chemical equation is oxygen. Carbon is very fortunate in not requiring a pure source of oxygen to burn; if it burned, say, only in an environment with 70% or more oxygen that would have been the end of modern civilization as we know it. Air is good enough for combusting carbon. In fact the element can burn under a wide range of oxygen concentrations, which is a blessing because it means that we can safely burn it in a very controlled manner. Varying the amount of oxygen can also lead to different products and can minimize the amount of soot and toxic byproducts. The marriage of carbon and oxygen is a wonderfully tolerant and productive one and we have gained enormously from this union

The right side of the combustion equation is where our troubles begin. First off, water. It may seem like a trivial, harmless byproduct of the reaction but it's precisely its benign nature that allows us to use combustion so widely. Just imagine if the combustion of carbon had produced some godforsaken toxic substance in addition to carbon dioxide as a byproduct. Making energy from combustion would then have turned into a woefully expensive activity, with special facilities required to sequester the poisonous waste. This would likely have radically altered the global production and distribution of energy and human development would have been decidedly hampered. We may then have been forced to pick alternative sources of energy early on in our history, and the face of politics, economics and technology would consequently have been very different.

Moving on we come to what's almost ubiquitously regarded as a villain these days- carbon dioxide. If carbon dioxide were as harmless as water we would live in a very different world. Sadly it's not and its properties again underscore the profound influence that a few elementary facts of physics and chemistry can have on our fate. The one property of CO2 that causes us so much agony is the fact that it's opaque to long-wavelength infrared radiation and absorbs it, thus warming the surroundings. This is not a post to discuss global warming but it's obvious to anyone not living in a cave that the issue has divided the world like no other. We still don't know for sure what it will do, either by itself or because of the actions taken by human beings from merely perceiving its effects. But whatever it is, it will profoundly alter the landscape of human civilization for better or worse. We can all collectively curse the day that the laws of physics and chemistry decided to produce carbon dioxide as a product of combustion.

Finally we come to the piece de resistance. None of this would have mattered if it weren't for the most important thing combustion produces- energy (in fact we wouldn't have been around to give a fig). In this context combustion is exactly like nuclear fission; twentieth-century history would have been very different if all uranium did was break up into two pieces. Energy production from combustion is what drives life and human greed. We stay alive by eating carbon-rich compounds - especially glucose - which are then burned in a spectacularly controlled manner to provide us with energy. The energy liberated cannot be used directly for our actions and thoughts. Instead it is used to construct devilishly clever chemical packages of ATP (adenosine triphosphate) which then serves as the energy currency.

Our bodies (and those of other creatures) are staggeringly efficient at squeezing oxidation-derived energy out of compounds like glucose; for instance in the aerobic oxidation of glucose, a single glucose molecule can generate 32 molecules of ATP. Put another way, the oxidation of a gram of glucose yields about 4 kilocalories of energy. This may not seem like a lot until we realize that the detonation of a gram of TNT yields only about 1 kilocalorie (the reason the latter seems so violent is because all the energy is liberated almost instantaneously). Clearly it is the all-important energy term in the combustion equation that has made life on earth possible. We are generously contributing to this term these days by virtue of quarter pounders and supersizing but our abuse does not diminish its importance.

The same term of course is responsible for our energy triumphs and problems. Fossil fuel plants are nowhere as efficient in extracting energy from carbon-rich hydrocarbons as our bodies, but what matters is whether they are cheap enough. It's primarily the cost of digging, transporting, storing and burning carbon that has dictated the calculus of energy. Whatever climate change does, of one thing we can be sure; we will continue to pay the cheapest price for our fuel. Considering the many advantages of carbon, it doesn't seem like anything is going to substitute its extraordinarily fortuitous properties anytime soon. We will simply have to find some way to work around, over or through its abundance and advantages.

If we think about it then, the implications of combustion for our little planet and its denizens are overwhelming and sometimes it's hard to take it all in. At such times we only need to take a deep breath and remember the last words spoken by Kevin Spacey's character from "American Beauty":

"Sometimes I feel like I'm seeing it all at once, and it's too much, my heart fills up like a balloon that's about to burst... And then I remember to relax, and stop trying to hold on to it, and then it flows through me like rain and I can't feel anything but gratitude for every single moment of my stupid little life..."

That's right. Let's have it flow through us like rain. And watch it burn.

Image source

Monday, September 19, 2011

Book Review: "Feynman"

With his colorful personality and constant propensity to get into all kinds of adventures, Richard Feynman is probably the perfect scientific character to commit to comic book form, so in one way this graphic novel is long due. What is remarkable is how powerfully Jim Ottaviani and Leland Myrick harness this unique medium to accurately dramatize the life and qualities of this genius. Both authors are uniquely qualified for this endeavor, having already penned graphic portraits of Niels Bohr, Robert Oppenheimer and Leo Szilard.

Ottaviani and Myrick manage to capture the essential characteristics that made Feynman such a cherished teacher, scientist, friend, colleague, and public personality. Most importantly, the book succeeds in vividly bringing out Feynman's quintessential quality of almost obsessively staking out his own iconoclastic path both in science and in life. The biography is really a memoir akin to "Surely You're Joking Mr. Feynman" since it features Feynman's own account of his life, work and intellectual development. The great strength of the book is that it uses close-ups and color to highlight key words and moments from Feynman's life. While the biographical information in the book has been covered in other works and most notably in Feynman's own memoirs, the comic book form has a very different impact because of the combined literary-visual effect it has on the viewer.

For instance, in describing Feynman's time at Los Alamos, one can actually see people's bewildered faces as they struggled to comprehend both his genius in solving intractable physics problems and his wildly successful attempts at safe-breaking. There are evocative close-ups of Feynman's father teaching him to appreciate and truly understand nature during walks in the park, of Feynman encouraging his sister to learn science and his wonderful and tragic relationship with his first wife. Also included are Feynman's strip-club forays (during which he solved physics problems), his famous dunking of the Challenger space shuttle's O-rings into a glass of cold water to demonstrate their failure (again rendered much more dramatic by the graphic medium) and some fairly detailed albeit brief discussions of his pioneering work in quantum mechanics.

I was especially convinced of the power of the graphic form during the parts dealing with Feynman's lectures about scientific wonder and humility. As he paced the podium at Caltech and stressed the importance of holding oneself to an absolute standard of integrity, successive panels of the book zoomed in on his face. This device which is commonly employed in comic books imparts a heightened sense of importance to the words in a way that would not be evident on simply reading them. The other idea used in the comic medium is to intersperse the narrative with divergent panels; for instance, Feynman's eloquent description of science as a great game of chess intersects with snapshots of a chess game played by two people in a park where his father has taken him for a walk.

The minor gripe I have with this comic account is that the faces of different characters are sometimes not easily distinguishable. In addition the narrative would have had a bigger impact if the characters resembled their real life counterparts. But these minor points detract little from the volume's novelty. Ottaviani and Myrick have done a wonderful job in making a unique scientist and human being come alive in these pages. With the mountains of literature written about Feynman one would think that there's nothing new that could be said or done. But this "dramatic picture" of Richard Feynman, as his friend Freeman Dyson calls it, will occupy a proud place on the shelves of Feynman fans. Knowing his fondness for fun, Dick would undoubtedly have approved.


Thursday, September 08, 2011

Nobel Prizes 2011

So it's that time of the year again, the time when just like Richard Feynman and Paul Dirac, three lucky people get to mull over whether they will incur more publicity by accepting the Nobel Prize or rejecting it.

Predicting the Nobel Prizes gets easier every year ((I said
predicting, not getting your predictions right) since there's very little you can add in the previous year's list, although there are a few changes; the Plucky Palladists can now happily be struck off the list. As before, I am dividing categories into 'easy', and 'difficult' and assigning pros and cons to every prediction.

The easy ones are those regarding discoveries whose importance is (now) ‘obvious’; these discoveries inevitably make it to lists everywhere each year and the palladists clearly fell into this category. The difficult predictions would either be discoveries which have been predicted by few others or ones that that are ‘non-obvious’. But what exactly is a discovery of ‘non-obvious’ importance? Well, one of the criteria in my mind for a ‘non-obvious’ Nobel Prize is one that is awarded to an individual for general achievements in a field rather than for specific discoveries, much like the lifetime achievement Academy Awards given out to men and women with canes. Such predictions are somewhat harder to make simply because fields are honored by prizes much less frequently than specific discoveries.

Anyway, here's the N-list

2. Computational chemistry and biochemistry (Difficult):
Pros: Computational chemistry as a field has not been recognized since 1999 so the time seems due. One obvious candidate would be Martin Karplus.
Cons: This would definitely be a lifetime achievement award. Karplus did do the first MD simulation of a protein ever but that by itself wouldn’t command a Nobel Prize. The other question is regarding what field exactly the prize would honor. If it’s specifically applications to biochemistry, then Karplus alone would probably suffice. But if the prize is for computational methods and applications in general, then others would also have to be considered, most notably Ken Houk who has been foremost in applying such methods to organic chemistry. Another interesting candidate is David Baker whose program Rosetta has really produced some fantastic results in predicting protein structure and folding. It even spawned a cool game. But the field is probably too new for a prize.

3. Chemical biology and chemical genetics (Easy)
Another favorite for years, with Stuart Schreiber and Peter Schultz being touted as leading candidates.
Pros: The general field has had a significant impact on basic and applied science
Cons: This again would be more of a lifetime achievement award which is rare. Plus, there are several individuals in recent years (Cravatt, Bertozzi, Shokat) who have contributed to the field. It may make some sense to award Schreiber a ‘pioneer’ award for raising ‘awareness’ but that’s sure going to make a lot of people unhappy. Also, a prize for chemical biology might be yet another one whose time has just passed.

4. Single-molecule spectroscopy (Easy)
Pros: The field has obviously matured and is now a powerful tool for exploring everything from nanoparticles to DNA. It’s been touted as a candidate for years. The frontrunners seem to be W E Moerner and M Orrit, although Richard Zare has also been floated often.
Cons: The only con I can think of is that the field might yet be too new for a prize

5. Electron transfer in biological systems (Easy)
Pros: Another field which has matured and has been well-validated. Gray and Bard seem to be leading candidates.

Among other fields, I don’t really see a prize for the long lionized birth pill and Carl Djerassi; although we might yet be surprised, the time just seems to have passed. Then there are fields which seem too immature for the prize; among these are molecular machines (Stoddart et al.) and solar cells (Gratzel).


1. Nuclear receptors (Easy)
Pros: The importance of these proteins is unquestioned. Most predictors seem to converge on the names of Chambon/Jensen/Evans.

2. Statins (Difficult)
Akira Endo’s name does not seem to have been discussed much. Endo discovered the first statin. Although this particular compound was not a blockbuster drug, since then statins have revolutionized the treatment of heart disease.
Pros: The “importance” as described in Nobel’s will is obvious since statins have become the best-selling drugs in history. It also might be a nice statement to award the prize to the discovery of a drug for a change. Who knows, it might even boost the image of a much maligned pharmaceutical industry...
Cons: The committee is not really known for awarding actual drug discovery. Precedents like Alexander Fleming (antibiotics), James Black (beta blockers, antiulcer drugs) and Gertrude Elion (immunosuppresants, anticancer agents) exist but are far and few in between. On the other hand this fact might make a prize for drug discovery overdue.

2. Genomics (Difficult)
A lot of people say that Venter should get the prize, but it’s not clear exactly for what. Not for the human genome, which others would deserve too. If a prize was to be given out for synthetic biology, it’s almost certainly premature. Venter’s synthetic organisms from last year may rule the world, but for now we humans still prevail. On the other hand, a possible prize for genomics may rope in people like Carruthers and Hood who pioneered methods for DNA synthesis.

3. DNA diagnostics (Difficult)
Now this seems to me to be a field whose time is very much due. The impact of DNA fingerprinting and Western and Southern Blots on pure and applied science, everything from discovering new drugs to hunting down serial killers, is at least as big as the prizeworthy PCR. I think the committee would be doing itself a favor by honoring Jeffreys, Stark, Burnette and Southern.

4. Stem Cells (Easy)
This seems to be yet another favorite. McCulloch and Till are often listed.
Pros: Surely one of the most important biological discoveries of the last 50 years, promising fascinating advances in human health and disease.
Cons: Politically controversial (although we hope the committee can rise above this). Plus, a 2007 Nobel was awarded for work on embryonic stem cells using gene targeting strategies so there’s a recent precedent.

4. Membrane vesicle trafficking (Easy)
Rothman and Schekman
Pros: Clearly important. The last trafficking/transport prize was given out in 1999 (Blobel) so another one is due and Rothman and Schekman seem to be the most likely canidates. Plus, they have already won the Lasker Award which in the past has been a good indicator of the Nobel.


I am not a physicist
But if I were
I would dare
To shout from my lair
“Give Hawking and Penrose the Prize!”
For being rock stars of humungous size

Also, Anton Zeilinger, John Clauser and Alain Aspect probably deserve it for bringing the unbelievably weird phenomenon of quantum entanglement to the masses. Zeilinger's book "Dance of the Photons" presents an informative and revealing account of this book.

I have also always wondered whether non-linear dynamics and chaos deserves a prize. The proliferation and importance of the field certainly seems to warrant one; the problem is that there are way too many deserving recipients (and Mandelbrot is dead).