What can we know about the world of atoms?

At the end of April 1926, the then only twenty-five-year-old Werner Heisenberg held a lecture at the prestigious Physics Symposium at the University of Berlin. The title of his speech had attracted all the eminent German physicists of the time, among others the already very famous Albert Einstein. In front of this demanding audience, the young physicist presented a new theory on the behavior of atomic particles that he had recently developed in cooperation with his other young colleagues. Even though everyone was interested to hear what kind of theory these young scientists had come up with, the lecture turned out to be quite unusual.

At the time, what physicists discussed at great lengths was how to explain the unusual behavior of microscopic particles which sometimes acted as usual particles, and at other times as waves. How to explain this strange double nature of atomic particles was the question to which nobody could provide a satisfactory answer. What was so unusual about Heisenberg’s lecture was that the young physicist seemed to be trying very hard not to even mention what supposedly happened inside the atoms themselves. He limited himself strictly to demonstrating the mathematical theory of calculating the predictions of the results of experiments on atoms, without giving any explanation of what actually happened in the world of atoms. That was because the physicist himself did not know the answer to the burning question of physics of that time, but he had succeeded in finding a way to calculate the predictions for the results of atomic particle experiments.

After the lecture, Einstein himself came up to the young physicist and invited him to accompany him on his way home. Of course, Heisenberg was ecstatic about the offer. He was certain that Einstein would be very pleased with his approach to the problem of quantum physics, as this field of science had been named, because he had used a similar approach when he had been working on his theory of relativity. Just as Heisenberg intentionally avoided delving into what actually happened inside the atoms and restricted himself to the characteristics of atomic activity that could be measured and calculated, Einstein, some decades earlier, when dealing with the question of time and space had systematically limited himself to individual readings and direct measurements, leaving the deeper questions of what time and space actually were on the side.

“It is the theory that determines what can be observed”

The innovative approach with which Einstein restricted himself to what could actually be measured, temporarily leaving other questions aside, enabled him to start a veritable revolution in physics and to completely redefine the discussion about the nature of time, space, energy and matter. Heisenberg hoped that, by applying this method to the world of quantum particles, he could make a similar breakthrough in understanding nature as his idol had succeeded in doing at the beginning of the twentieth century.

Surprisingly, Heisenberg’s idea to avoid establishing models of what was really going on in the world of atoms and limit his work only to what he could actually observe did not please Einstein at all. It is interesting that his doubts did not stem from the concern that a strictly mathematical theory was insufficient to explain what happened in nature, but from his opinion that even when relying merely on physical experience, which is directly accessible, one should still apply different scientific theories when, for example, explaining a movement registered by a measuring device as the result of the collision of an atomic particle into the instrument. Einstein claimed that explaining even completely direct physical experiences requires the application of a number of different theories and that such a thing as the direct observation of the world, completely independent of any theory, can not exist.

As Heisenberg later wrote down in his memoirs, one of things Einstein said was: “It is fundamentally wrong to attempt to confirm a theory merely on the basis of observable quantities. In reality, what is true is quite the opposite. It is the theory that determines what can be observed. /…/ Only theory, that is the understanding of natural laws, allows us to link an experience to its cause.”

Heisenberg defended his newly discovered theory of quantum mechanics, but he and Einstein quickly reached the conclusion that they still knew far too little about what went on in the world of atoms to reach any important conclusions. It was also apparent that, because of the great age difference – Einstein was almost twice his younger colleague’s age – they were unable to have a completely relaxed discussion. In the following years it was Niels Bohr, an older Danish physicist closer to Einstein’s age, that took over the debate on the important issues raised by the new field of quantum physics and also became one of the key scientists that greatly contributed to the exploration of this new physics of the world of atoms. The discussion between Einstein and Bohr is believed to be one of the greatest intellectual debates of the twentieth century. It lasted almost thirty years, from the 5^th Solvay Conference until Einstein’s death in 1955.

Einstein would then become a little upset …

In September 1927, at the Como Congress in Italy, Bohr presented his principal idea for explaining the world of atoms to his colleagues. Einstein was not present at this meeting, but he supposedly did not miss much, because Bohr’s lecture, according to those that were present, was so condensed that nobody could actually understand it very well. Today, however, this very lecture is considered to be one of the milestones in the history of physics, because it established the central idea around which the interpretation of quantum mechanics is focused, and still has a place in many physics textbooks today.

According to Bohr, physics can only base its theories on what we can say about the world and not on what the world itself really is. While Heisenberg ignored the problem of how to imagine the world of atoms, Bohr made another step forward and showed that one can get a relatively good idea about what is going on by combining the two opposing models explaining the nature of atoms. Bohr’s principal idea was that the world of atoms can not be described using one consistent model only, but by applying several together.

Naturally, Einstein strongly disapproved of Bohr’s idea, so he decided to put all his efforts into revealing a paradox between his theory of relativity and the claims made by the new, quantum physics. This is how Heisenberg remembered the events that took place at the 5^th Solvay Conference in Brussels in 1927: “Everybody was staying at the same hotel. However, it was not in the conference hall where the most passionate debates took place, but during meals in the hotel restaurant. /…/ The discussion often began early in the morning when Einstein would explain some new theoretical attempt which, according to him, invalidated the principle of non-specificity. Of course, everyone immediately started to analyze what he had proposed, and on the way to the conference room, to where I usually accompanied Bohr and Einstein, we had already clarified the first question and claim. Throughout the day we continued to discuss this at length and, before the evening, we had come far enough that at dinner Niels Bohr could already prove to Einstein that even in the example that he had suggested, it was impossible to avoid the principle of non-specificity. Einstein would then become a little upset, but by breakfast the next morning he would already have prepared a new theoretical test, even more complex than the previous one. By the evening, however, this test proved to be no more resistant than the first one, and the game would continue for another couple of days.”                

Can we learn more about atoms?

In 1930, Einstein arrived to the 6^th Solvay Conference with an elaborate and carefully designed theoretical test which he had prepared in advance and was supposed to prove that something was wrong with quantum mechanics. However, after a detailed analysis, Bohr quickly discovered that this time Einstein had failed to take into consideration the effect of his own general theory of relativity which had caused him to think he had found an error in quantum physics. If he would have taken the general theory of relativity into account, there would be no inconsistency.

After another failure Einstein no longer tried to prove that quantum mechanics itself was incorrect, but went at the problem from a different angle. He tried to prove that quantum theory was incomplete. In other words, he wanted to show that, in theory, it would be possible to say more about atoms themselves than quantum physics would allow. He wished to show that atomic particles had characteristics that can not be explained by quantum physics, but could possibly fit into a different theory and could be measured as well.

He needed no less than seven years to find a way that could theoretically prove that quantum physics was an incomplete theory which did not take account of all the characteristics of atomic particles. In 1935, he and his colleagues Boris Podolsky and Nathan Rosen, now already at Princeton, United States, published a paper in which they described a theoretical experiment to prove that nature has to know more about itself than what the equations of quantum physics can reveal.

When Bohr found out about Einstein’s new paper, he immediately dropped everything he was doing and dedicated himself to finding an error in Einstein’s theoretical experiment. Three months later, an article with Bohr’s answer to Einstein was already published. Nevertheless, Einstein did not agree with Bohr’s defense of quantum physics and their debate came to a standstill. Both were certain that it was more or less a matter of a “philosophical” debate. A few decades later, though, another physicist, while reading Einstein’s paper, got the idea how it would be possible to experimentally verify whether quantum physics was a complete theory or not. But that is another story.

Why desert comes last

When it comes to doing a great number of things, it is difficult to imagine doing them any other way than how we are used to. It feels as if our most deeply rooted habits were something natural and predetermined. The same goes for preparing and consuming food. Many would be surprised to learn that the order of courses in a meal as well as the established combinations of tastes in an average European meal today have its origins in the middle of the seventeenth century. It was at that time that the wealthier Europeans made significant changes to their eating habits, habits that have been taken for granted to this day. The reason for changing the established diet was a new scientific theory about how digestion works and what healthy nutrition really means.

Nature as one big kitchen

Since ancient times, people have been aware of the fact that their health depends greatly on the food they consume. In the time of the High Middle Ages and Renaissance there was a rule defining the health of an individual as a state in which his bodily fluids are in just the right proportions. Food was an important factor in maintaining physical balance as the doctors of the time could not rely on many methods with which the balance between bodily fluids could be regulated. When someone was severely ill, they would try to reestablish the balance within the body by controlled blood-letting. That is why the wealthier part of the population that could afford to choose the kind of food they would eat, usually followed the principles of healthy nutrition.

According to ancient medical tradition which was based mostly on the works of the Hippocratic Corpus, Aristotle’s essays and Galen’s treatises, digestion was viewed as food being cooked inside the human body. Just as, in nature, the sun heats the earth so that plants grow from it and bear fruits, the inner flames of the human body were believed to “cook” the ingested food further until it was transformed into bodily fluids, while the remains were disposed of in the form of excrements which would then fertilize the earth, and the natural cycle could repeat.

The image of the cosmos as a big kitchen in which natural flames induce the growth of living nature and the circulation of matter was reflected in the image of the human body as a miniature version of this cosmic kitchen in which the inner flames cook the ingested food. According to this model of nature and man, the most frequent advice doctors gave their patients was that they should boil their food as much as possible, ensuring that their digestive mechanisms are put under less stress, and that they should consume balanced food. Of course, this balance should be viewed according to the way nutrients were classified at the time.

The theory of four elements

At the time, different types of food were classified according to Aristotle’s established theory of four elements from which the world was believed to have been created. Individual elements had been attributed corresponding characteristics. Fire was hot and dry, water was moist and cold, air was hot and moist, and earth was dry and cold. Food was classified in accordance with these four characteristics; pepper, for example, was put into the category of fire while melons, mushrooms and fish were classified under water. Because it was believed that the human body should ideally be moderately warm and moderately moist, meals were planned accordingly. A healthy diet meant eating food which came as close as possible to the ideal ratio of individual elements in the body.

The ideal meal was believed to be a sort of warm and relatively squishy porridge, because it contained all the characteristics that were supposedly best for the body. It is interesting that raw vegetables were, consistent with the principles of the time, considered unhealthy and appropriate merely as food for the poor. On the other hand, sugar was believed to be a very healthy nutrient and an ideal food additive which was also sold in pharmacies. Because it was relatively expensive, it was usually kept safe or even locked up in the kitchen.

New science, new menu

In the 17^th century, however, the diet of wealthier Europeans underwent a significant change. The ideals of nutrition had changed and so had advices for a healthy diet. In her books and articles, Rachel Laudan, a science historian researching the history of relations between science, medicine and nutrition, has come up with several convincing arguments which indicate that the change in the eating habits of the rich around the year 1650 happened mostly because of new scientific discoveries. The main reason for these changes was a new scientific theory about how human digestion worked and how, in nature, one substance changed into another. If scholars before mostly compared the happening in nature and the human body to the process of cooking, which supposedly causes substance to change, the central natural process now became fermentation. In the most general terms, fermentation is a chemical process in which carbohydrates, like sugars, are transformed into alcohol and acids. With the fermentation of yeast, for example, one can produce wine, beer and vinegar. With the fermentation of lactic acid bacteria, milk changes into yogurt and other dairy products. Fermentation also contributes to the bread rising process, releasing carbon dioxide which leavens the dough by creating the bubbly structure typical of bread.

The chemistry of tastes

Scholars that, a few centuries ago, studied the branch of science today known as chemistry, used fermentation and distillation to isolate individual key ingredients of plants and search for new active healing ingredients. Because fermentation was present throughout nature as well, the theory was quickly established that the essence of human digestion was not some extended process of cooking food that takes place in the stomach, but the process of fermentation itself.

The system of food classification was quickly adapted to the new theory of digestion. Aristotle’s four elements with their usual characteristics were replaced by a system of classification according to three new ideals of pure substances which were first introduced in chemistry. The three ideal substances were salt, oil and quicksilver. However, these are not to be understood in the modern sense of the words, but the more (al)chemical sense, pertaining to the roles of these substances in the processes of fermentation and distillation. The chemists of the time discovered that in the process of distillation substances are usually separated into three parts: volatile liquids, “oily” substances and solid residues.

Sugar becomes poison

Oil was the term used to designate substances that did not evaporate during the boiling process, in contrast to alcohol which was classified as one of the “quicksilver” substances. Among the food items that could be found in the kitchen, butter, lard and olive oil were the closest to the “element of oil”. Apart from regular salt, flour and similar solid substances were part of the “salt” group. The typical representatives of the “quicksilver” group were vinegar, wine and other alcoholic beverages, as well as certain flavors of meat and fish. With the new division of food, oils especially gained importance, becoming the key ingredient of a variety of sauces. The new food classification system caused a noticeable change in eating habits.

As for sugar, doctors began to realize that it was far from the ideal nutrient it was once believed to be. They discovered, for example, that it damaged teeth, and was also found in the urine of several patients which was later attributed to diabetes. According to the new division of nutrients, sugar was no longer believed to be an ideal type of food, and some doctors came close to describing it as poison. That is why during the last few centuries our main courses have no longer contained excessive amounts of sugar, and sweets have only been consumed in small quantities at the end of the meal.

Cell police

Once upon a time, long ago when our planet was still uninhabited by plants and animals, single-celled organisms had developed an effective method to defend against the attacks of pesky viruses that even then caused epidemics. It is only a few years ago, that scientists discovered that the same mechanism single-celled organisms had developed as a defense system against viruses several millions of years ago, is still active in most living beings inhabiting Earth today, including people. A deeper insight into the workings of this mechanism could enable us to successfully treat severe diseases. That is why it came as no surprise when the 2006 Nobel Prize in Medicine was awarded to the very scientists, who had, several years earlier, discovered how this primeval, but still very effective cell mechanism built into most of our planet’s living beings worked.

Like a country with strict regulations

The living cell is a highly complex mechanism in which many precisely planned and controlled chemical processes take place. It could be compared to a country in which everything happens strictly according to regulations. Carefully stored in the central palace of the country is a massive collection of laws and regulations containing the exact instructions for everything that may happen within its borders. There is only one version of the “code”, so it can never leave the central palace. However, the inhabitants of the country need precise instructions in order to produce anything, so there is a large number of scribes working in the palace, constantly transcribing recipes for creating individual products from the code and sending them around the country. When one of these copies of instructions is delivered to a citizen of the country, he immediately goes to work. If the citizen who receives the instruction were a cook, he would simply make the dish as described in the recipe.

Using the metaphor of a country where everything happens in accordance with strict regulations, we have roughly described the way a living cell functions. The unique code containing all the information necessary for the functioning of the country is of course a metaphor for the genetic code which is carefully stored in the DNA molecule and never leaves the cell nucleus. The copies of instructions for building individual products are molecules of messenger RNA (mRNA) that carry information from the nucleus to different parts of the cell, while the diligent scribes making the copies of the code in the central palace are enzymes called RNA polymerases (the 2006 Nobel Prize in Medicine was awarded for the research of this very enzyme).

The copies containing the recipes, or molecules of mRNA, can easily leave the cell nucleus and move freely throughout the cell. As we have mentioned, when the recipe reaches a cook, he reads it and makes whatever the instructions are for. In actual cells, the cooks that use recipes to make different dishes are called ribosomes. Their job is to use the information contained in the messenger RNA to build a certain protein which, in turn, performs specific tasks in the cell. This is how most of the cells of all living beings on Earth work.

When a cell is attacked by terrorists

However, a country in which everything happens strictly according to regulations does have its faults. Evil terrorists can smuggle in their own recipes which are not copies from the central palace code. When a cook happens to get such a “terrorist” recipe, he has no way of telling that the instructions did not come from the country’s code. That is why he has no difficulties with following the terrorist recipes. Unconsciously, he works for the enemy of the state and can, without even knowing it, build a deadly murder weapon. These evil terrorists that infiltrate cells and abuse their mechanisms are known as viruses. They are extremely cunning and well adjusted to living this pirate’s life.

Anti-terrorist squads

In response, cells had quickly developed a method to fight such malevolent terrorist attacks. When terrorists enter a cell they first try to multiply or, in the terms of our metaphor, to produce as many recipes for creating a murder weapon as possible, and spread them throughout the cell. However, when they multiply, they spend a few moments in the form of a double RNA helix. One could say that for a short fragment of time the recipe and its copy remain attached. And it is in this very moment, when the instructions and its copy are still glued together, that a cell can detect the recipe as potentially dangerous and sends its special police units after it. The anti-terrorist cell police does not only destroy the instructions with the copy attached, but also starts to eradicate all other recipes in the cell which contain the same instructions.

The technical term for anti-terrorist units that can detect recipes carrying their own copies and destroy them is RNA interference or RNAi. For their fundamental contribution to understanding the functioning of the mechanism of cell resistance against viruses, which is also an effective mechanism for controlling the expression of individual genes, the Americans Andrew Fire and Craig C. Mello were awarded the 2006 Nobel Prize in Medicine.

The petunia mystery

As is the case with most important scientific discoveries, the first encounter with the RNAi mechanism was completely accidental. In 1986 a small California biotech company wanted to create a special flower. They tried to create a petunia that would have extremely vibrant violet petals. They knew which gene was responsible for the production of violet color, so they tried to enhance its expression by injecting more instructions for creating violet color into the plant’s genetic code.

The results of the experiment were surprising. Instead of becoming even more intensely violet, the flowers of this genetically modified petunia were now completely white. Naturally, the researchers thought they must have made some kind of mistake, but after carefully reviewing the entire process found out that there was no error. The answer to the question of why the petunia flowers turned completely white and not more violet than usual became the mystery that many brilliant minds spent more than a decade solving.

Unlimited anti-terrorist awareness

Today, we know that when the new genes were being injected into the plant, the RNAi mechanism was turned on, recognizing the presence of the artificially added genes as an enemy virus attack and destroying all recipes similar to those that scientists had tried to infiltrate into the cell. Because the newly added recipes were identical to the ones that the cell had already produced itself, the cell’s anti-terrorist squad started to destroy both the artificially injected recipes and the ones that had been naturally transcribed by the scribes working within the cell nucleus. The cell police was successful in destroying all the recipes for producing the color violet, so the petals turned out white.

For now, the discovery of the RNAi method has proven to be useful mostly in scientific research of individual genes, but it will soon become important in the treatment or at least in the diagnosis of various severe diseases. The cell’s anti-terrorist squads can be taught to destroy specific recipes within cells which contain the instructions for the production of individual proteins. A number of diseases occur exactly because cells produce an excess of a specific cell product. Different methods are already being tested to use the RNAi mechanism in treating the various forms of hepatitis, Huntington’s disease and AIDS as well as some forms of cancer.