August 22, 2006

One Death is a Tragedy

Mood: raging against the unfairness of it all

The body of an aquaintance of mine turned up in the N. Saskatchewan River this morning after he'd been missing for two weeks. This isn't someone I knew especially well, but he was on the UofT ACM Programming Competition team, so I saw him at practices twice a week for a period of about six months. We ate pizza and talked about programming problems.

Normally I'm not one to talk about my feelings, but I have to find some sort of outlet this time. There's no word yet on whether the death was accidental or not, but either way, I'm angry. I'm pretty sure this isn't the PC reaction, judging from the flood of almost identically worded email messages expressing condolences and sympathy being sent to the family. If I were in their shoes, those messages would make me feel worse, not better, so I'm not sending one myself. Maybe this is the wrong way to react, since some members of the family probably feel differently than I do about the expressions of support, but it has the virtue of being honest and heartfelt. And maybe some of them do feel the same as I do.


Yes, upset, very upset. But not the hysterical, falling apart kind of upset. The kind that motivates you to go out, find out exactly what happened, and do something to stop it from ever happening again.

August 19, 2006

The Means of Production of Energy in Living Organisms

Hans Krebs and W. A. Johnson, The Role of Citric Acid in Intermediate Metabolism in Animal Tissues, 1937

In the era of DNA sequencing and proteomics, it's sometimes difficult to remember that only in the past century have biologists finally put to rest the idea that living matter obeys different laws than nonliving matter. Biochemistry proved to be the key to detailed understanding of the internal processes of living organisms. Rather than being animated by some sort of life-force present only in living tissue, cells and tissues turn out to run on chemical reactions that obey the same laws that govern non-organic chemical reactions.

What is a chemical reaction, precisely? In short, if one or more molecules have their bonds rearranged, a chemical reaction has occurred. This usually happens when the molecules involved collide, disturbing the delicate balances of repulsion and attraction that form the bonds. During the resulting chaos, bonds are rearranged and energy is transferred between bonds and molecular motion. As you might expect, stable arrangements are more likely to result than unstable ones. Things get interesting when you realize that the word "energy" is being used here as a synonym for "unstability". The more energy needed to construct a molecule, the more unstable, and unlikely, it is. By comparing the energy contained in the molecules on each side of a reaction, you can figure out which way the reaction is going to go (towards the stable, lower energy side), how much heat is going to be released (the difference between the two sides), and even precise equilibrium concentrations.

That last deserves elaboration. Every reaction is, in theory, reversible. Although the lower energy side of the reaction is more likely, if molecules collide hard enough, the stable configurations can be bumped up into higher energy configurations. For example, if you start with a beaker full of substance AB, and conditions are right for it to begin breaking down into A + B, as soon as the products appear in the beaker, some of them will start colliding and reforming into substance AB. This reaction may still favour A + B over AB, but as the concentrations change, the forward and backwards reactions will eventually be proceeding at the same rate, and equilibrium will be achieved; e.g. 10% AB and 90% A + B. Chemists can predict exactly what the equilibrium concentrations will be if they know the energy needed to construct the molecules A, B, and AB.

Things get even more interesting when you consider interactions between lots of chemical reactions. If the products of a reaction get sucked away into another reaction, or moved across a membrane, or removed from the picture in any other way, the reactions will shift to replace the lost products until equilibrium is achieved again. Similarly, when reactants are added, they will react until there are enough products to balance them.

Living systems are, at bottom, a vast network of interconnected chemical reactions. The products of one reaction feed into the next; membranes block the movement of some molecules, let others through, and actively pump still others to one side or the other; catalysts make highly unlikely reactions possible, even probable, greatly speeding up the rate at which equilibrium is reached.

Hans Krebs helped figure out one of the most important and wide-spread chains of reactions present in living tissue, an eight-step cycle that breaks down food and stores its energy in a form a cell can use. Previous work had demonstrated that two three-step chains existed:
citrate→aconitate→isocitrate→α-oxoglutarate, and

These reactions all add or remove H2O, H+, and CO2 from the main molecules, and can all be replicated in a test tube. However, in a test tube, they quickly reach equilibrium, effectively grinding to a halt. Krebs showed that both these sets of reactions will continue for far longer than expected in living tissue (specifically, pigeon flight muscles), implying that the reactants are regenerated somehow. It was already known that α-oxoglutarate will react with an atom of oxygen to form succinate and CO2, and Krebs showed that a known inhibitor of the succinate→fumarate step in the second chain causes the citrate chain to grind to a halt in living tissues. This strongly implies that there is a single continuous chain from citrate to oxaloacetate. He then showed that pigeon muscle creates new citrate in the presence of oxaloacetate, closing the circle.

Krebs didn't know the precise nature of the final step of the pathway, but he knew that it had to involve adding C2H4O2 to the oxaloacetate. As it turns out, the Krebs cycle forms the last two thirds of glucose breakdown, the part that requires oxygen. The first third is a more ancient, anaerobic, metabolic pathway that breaks glucose into C2H3O, which then feeds into the Krebs cycle along with HO-.

What, then, is the purpose of this cycle of reactions? Its net effect seems to be to break C2H3O, 2H2O, and HO- into 2CO2 and 8H+. The whole purpose of the cycle turns out to be to generate those H+ ions. The Krebs cycle occurs inside mitochondria, and there's a protein complex embedded in mitochondrial cell walls that acts like a miniature turbine as H+ ions flow through it. The "turbine" is ATP synthase, which generates the primary energy-carrying molecule in known life.

More than just glucose feeds into this cycle: carbohydrates get broken down into glucose, and proteins and fats get broken down into C2H3O, so that practically all food we eat gets funnled into this reaction. In addition, the oxygen entering the Krebs cycle turns out to enter our cells from our blood, and, ultimately, our lungs. We die when we stop breathing because this metabolic pathway grinds to a halt, and we stop producing ATP. Every cell in every aerobic organism requires oxygen just to power this reaction.

Lots of other metabolic pathways have been discovered, but the Krebs cycle usually shows up in the center of any serious diagram. In my opinion, the only other metabolic pathway that even approaches its importance is photosynthesis, the pathway that put all that free oxygen into our atmosphere in the first place.

August 10, 2006


Alexander Fleming, On the Antibacterial Action of Cultures of a Penicillium, With Special Reference to Their Use in the Isolation of B. Influenzæ, 1929

Alexander Fleming's "serendipitous" discovery was actually quite likely, given his work habits. One description of his laboratory had him "completely surrounded by plates and dishes of bacterial colonies -- growing quilts of reds, greens, and yellows. Other culture dishes were stacked up at random in corners. Test tubes and glass slides littered the counters." Fleming liked to leave his dishes of bacteria lying about for weeks at a time. One day he looked at one of his petri dishes and saw this:

He immediately used his skills in bacteriology to start answering questions. Which moulds created antibacterial compounds? (Only one of 13 strains he tested.) Which bacteria were affected? (Several groups were vulnerable, but a lot weren't.) How effective was the substance, quantitatively? What were its properties? Perhaps most importantly, he injected it into rabbits and mice, and found that it was completely non-toxic.

His discovery took over a decade to mature. A method for manufacturing a concentrated form of the active molecule was not discovered until 1938, just in time for WWII. Penicillin's success led to the discovery of new antibiotics, including streptomycin, which can cure tuberculosis and the plague, in 1943.

Many great advances are triggered by the discovery of new observational tools, which can suddenly give access to a flood of new information. The increasing skill of Dutch lens-makers in the 1600s lead to the creation of the telescope, and then, equally important, the microscope. Suddenly exposed to the eye was a whole new ecology of microorganisms: tiny multicellular plants, animals, and fungi, single-celled protozoa, and bacteria, much simpler, older, and hardier than protozoa.

By the 1920s many diseases were known to be caused by specific microorganisms, and two types of tools had been created to combat them. One was very simple: use toxic chemicals to kill the microorganisms, and hope that the patient can recover from the damage caused once the self-replicating disease has been eradicated. The other was very sophisticated: use bits and pieces of dead disease organisms to trigger the body's immune system, allowing it to build up strong defenses without opposition. Chemotherapy was crude, but had one great advantage over vaccination: it could save patients that were already infected.

Fleming discovered a new strategy, one which fell between chemotherapy and vaccination in sophistication. In the microecology, as in the ecology we can study with the naked eye, there is plenty of competition. Fleming found that we could borrow a substance being used by one microorganism to kill others without harming itself.

Chemotherapy, which once used substances such as mercury, arsenic compounds, and carbolic acid, usually kills everything in the infected area, including the patient's own immune cells. Penicillin, on the other hand, is targetted: it affects specific species of bacteria, and only those bacteria. It was discovered later that penicillin blocks the production of a key component of bacterial cell walls, causing them to dissolve.

Penicillin, and antibiotics in general, are not a magic bullet that has ended all disease. They have no effect on diseases caused by genetic defects, viruses, protozoa, or multicellular parasites. Nonetheless, Penicillin has been a major benefit to humanity. It kills bacteria which cause strep throat, meningitis, pneumonia, gonorrhea, and diphtheria, all of which have practically been eradicated in the developed world. It has also led to the development of further antibiotics, which cure many other bacterial diseases, including typhus, tuberculosis, and the plague, and to an ongoing search for targetted antimicrobial drugs which disrupt disease causing microorganisms without causing collateral damage.