THE BIOLOGY OF THE VISIBLE AND THE INVISIBLE
MANILA, SEPTEMBER 5, 2007 (STAR) STAR SCIENCE By Eduardo A. Padlan, Ph.D. - One need not be a scientist to teach science. As Jimmy Abad said in an article in this series, science and literature share a number of things, one of which is the quest for reality. Indeed, when teaching literature, one could also be teaching science. This could be true of the other disciplines as well. The language may be different, but the end result could be the same.
This article was excerpted from a talk of the same title that I delivered at the Concepcion D. Dadufalza Award ceremony held in UP Diliman last July 17. Concepcion D. Dadufalza was a well-liked, well-respected professor of English at UP and to this day has many loyal disciples. Here, I will try to show that, while teaching English, Ms. Dadufalza, consciously or unconsciously (I cannot know — she passed away in 2004), was actually teaching fundamental concepts in Chemistry and Biology.
In her English classes, Ms. Dadufalza made extensive use of The Little Prince, a children’s book written by Antoine de Saint-Exupéry. Yes, a children’s book! The most famous line in that book is: “L’essential est invisible pour les yeux” in the original French, which translates to “What is essential is invisible to the eyes.”
That statement seems to be so contrary to biology. We do use expressions like “gut feeling,” “mind over matter,” “heart-felt” whatever, etc., which imply the importance of things inside us that cannot be seen by the eyes. But what is essential cannot all be invisible. For instance, recognition is the hallmark of biology. Moreover, biological entities, whether whole animals or molecules, primarily recognize each other through their surface features, that is, their “visible” features. Let me illustrate.
We have keen senses. We can know, from the way a man looks or from the way he looks at us, if he presents a danger to ourselves. We judge the attractiveness of a woman from the symmetry of her face and from the smoothness of her skin — among other things.
Sight is not the only sense that we use to interpret situations from a distance. Men put out a certain smell when angry and ready to fight. If we had a keen enough sense of smell, we could truly say, even at some distance from an angry man, that we “smell trouble.” (A dog’s sense of smell is many times better than ours. Dogs can smell fear. Some dogs have been shown to be able to smell certain diseases in human patients.) And, of course, we can recognize anger, affection, and other emotions from the sounds which usually accompany those emotions.
Our senses have been honed through millions of years of evolution so that we can judge situations — both good and bad — without getting too close. We give considerable importance to first impressions — for good reason (it could mean our lives). Our initial judgment is made on the basis of what we can immediately sense — what’s on the surface.
Even atomic and molecular interactions involve surface features. Every atom has a nucleus and a cloud of electrons swirling around it. Thus, an atom’s surface is made up of electrons. When atoms interact, they interact via those electrons, not their nuclei.
The critical importance of even a single electron in the electron cloud is illustrated by the way hemoglobins bind oxygen reversibly.
The hemoglobin in our blood is an “oxygen carrier” — it picks up oxygen in the lungs and delivers it to the tissues. We have hemoglobins in our tissues, for example, the myoglobin in our muscles and the neuroglobin in our nerve cells that accept the oxygen and store it for times of need. Other organisms have hemoglobin. All vertebrates and many invertebrates, including various worms, insects, mollusks, and others, have hemoglobin. Even some microorganisms, like some yeast and bacteria, have hemoglobin. And hemoglobin is found in some plants, too. All hemoglobins bind oxygen reversibly.
The structure of hemoglobins from various organisms, including the ones from bacteria and plants, has been determined and all hemoglobins have been found to have the same basic structure. The mechanism by which oxygen is bound reversibly is shared by all these hemoglobins. How does this mechanism lend support to the notion that surface features are critical to molecular function?
The basic components of all hemoglobins are the heme and the globin, the latter being a protein that surrounds the heme. Centrally located in the heme is an iron atom and it is this iron atom that binds oxygen. The iron atom has to be in the ferrous state (Fe++). If an electron is removed from the iron atom to make it ferric (Fe+++), it can no longer bind oxygen reversibly and the hemoglobin can no longer perform its vital function. The nucleus remains the same; it is just the electron cloud that changes, and the consequence of the change in the iron atom’s surface feature is quite drastic.
Molecules are made up of atoms and molecules interact with other molecules, or with atoms, also via their surfaces. We see this very clearly in the interaction of antibodies with antigens.
Whenever a foreign substance (an antigen) manages to enter our body, our immune system produces cells and molecules that would get rid of that substance. One of the molecules that the immune system produces is the antibody. The antibody that is produced is specific for the antigen and it binds to the antigen tightly. The antigen could be venom from a bee sting, or it could be a molecule on the surface of a virus, or a bacterium, or a parasitic worm. The binding of antibody to antigen results in the latter being destroyed, or eliminated, by normal processes (involving specialized cells or other molecules).
How does the body produce specific antibodies to the million or so different antigens that we encounter in our lifetime? Antibodies can discriminate between two antigens that differ only slightly, for example, two proteins that differ by only one amino-acid residue. What makes the binding of antibody to an antigen so exquisitely specific?
The structure of a number of antibody:antigen complexes have been determined and the structural basis for the high specificity of the binding of antibody to antigen, as well as the seemingly limitless diversity of antibody specificities, have become well-understood.
The specificity of antibody binding to antigen is found to be due to the complementarity of the interacting surfaces, one on the antibody and the other on the antigen. For every bump on one surface, there is a corresponding depression on the other. Frequently also, if one surface has a positive charge on it, the other surface has a negative charge opposite it. It is this complementarity in physicochemical properties that results in tight binding.
Clearly, in the case of molecules also, recognition of one molecule by another and their interaction are determined by surface features. But what determines the nature of the surface of a molecule? It is the “structure” of the molecule.
The structure of a molecule is what distinguishes it from other molecules and gives it its unique properties. It is the scaffold that supports the surface of the molecule and underlies the molecule’s surface properties. It is the part of a molecule that other molecules do not see. But it is the part of the molecule that determines what other molecules see. It is an essential, nay, critical, part of the molecule.
Thus, in molecular interactions, the “invisible” is clearly essential.
Even the basic interaction between atoms is determined by features that are invisible. Although atoms interact via their electrons, it is the nucleus, hidden from view by the electron cloud, which determines where and how those electrons swirl in space, and thereby, how they can interact with other electrons.
The attractiveness of a woman, likewise, is determined by things that we cannot see. Her physical attributes are a manifestation of her health and her genes — again, things that we cannot see with just our eyes.
Antoine de Saint-Exupéry was right. Something may be invisible, but it is nonetheless essential. But he was only partly right. We know that the parts which are visible are just as important as those which are invisible. Nevertheless, it is clear that Antoine de Saint-Exupéry had some understanding of biology.
And Ms. Dadufalza, in using the Little Prince extensively in her English classes, was actually teaching a very fundamental concept in Chemistry and Biology.
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Eduardo A. Padlan has a Ph.D. in Biophysics and was a research scientist at the (US) National Institutes of Health until his retirement in 2000. He is currently an Adjunct Professor in the Marine Science Institute, College of Science, University of the Philippines Diliman. He is a corresponding member of the NAST. He can be reached at firstname.lastname@example.org.
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