Nature’s experiments

Nature experiments and will probably continue to experiment for as long as there is life on Earth. But the experiments do not appear to be well-conceived; rather, they are probably more appropriately described as simple trial and error. Let’s look at how Nature experiments with protein molecules.

Protein molecules come in a wide variety of shapes and sizes, reactivities and functions, and associations with other molecules, including nucleic acids, lipids, carbohydrates, and other proteins. When we compare the structures of proteins with the same function, we find that, except in very rare occasions, the structures are very similar. It would seem like Nature, through trial and error, had chanced upon a structure that served a useful function and had kept it, even when species diverged, allowing only small structural variations. We see that in enzymes that serve critical functions, for example, the digestive enzymes. The mammalian acid proteases (pepsin is one of them) have very similar structures and their structures are very similar to those of the acid proteases of plants, molds, and other organisms, including the AIDS virus (!). We see that also in the hemoglobins — oxygen binders — which have similar structures, whether the molecule comes from man, fish, clams, worms, insects, bacteria, or plants. It is the three-dimensional structure that Nature preserves, not necessarily the amino acid sequence.

But while Nature preserves critical structures, it also experiments on them. Of course, it cannot play with the structure too much lest the molecule lose its critical function (and cause the demise of the organism). To avoid such a catastrophe, Nature first makes a copy — it duplicates the gene that codes for the protein. Nature can then experiment with the copy with impunity. So now, we find proteins with similar structures, but with different functions. The best example of this is the immunoglobulins — the family of proteins which includes antibodies and various other molecules of the immune system, and a variety of receptors found on the surface of cells. The immunoglobulins are usually in the circulation, or exposed to blood, so that they are subject to the threat of attack by the digestive enzymes which are present in blood. Probably not surprising is the fact that the immunoglobulin structure is one that will not collapse even if it is cleaved by enzymes. In this case, Nature has chosen to preserve and diversify a structure that is stable under conditions that demand great stability.

When it is advantageous to have great diversity, Nature makes many copies of the same gene and experiments will all of them.  Here again, the best example would be the antibodies (and some immune system receptors). Antibodies are molecules that we produce to bind, neutralize, and otherwise get rid of foreign substances (antigens), like toxins and molecules on the surface of germs and parasites that manage to get into our body. Antibodies (and some immune system receptors) are critical for our very survival. Since there are a large number of possible antigens, we must be able to produce also a large number of different antibodies. So, Nature has provided us with many different antibody genes and that, together with various genetic mechanisms that result in further diversification, allows us to produce a very large number of different antibodies — every day.

Usually, Nature is parsimonious. If it can do with less, it will do with as little as possible. But if something is critical for survival of the individual or of the species, Nature can be very wasteful. The example given above with antibodies is a prime example of this wastefulness. We produce a very large number of different antibodies every day, just in case we come under attack that day. Another example is in reproduction (clearly critical for the survival of the species). Man produces and delivers several hundred million sperm cells per reproductive encounter, when just one cell will do (under ideal conditions). These examples must have been the result of Nature’s experimentation. An individual, who is unable to cope with the onslaught of germs and parasites, will most probably die. A species that takes chances in maintaining an optimum number of member individuals, might soon be extinct.

What we are today — and what all animals, plants, and other creatures are today — is the result of Nature’s continuing experimentation, often under changing conditions. (Most people would call this “evolution.”) We and all the animals, plants, and other creatures that are in existence today are the best results, so far, of Nature’s experimentation. We should be happy — I think.

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Eduardo A. Padlan is a corresponding member of the NAST and is an adjunct professor in the Marine Science Institute, College of Science, University of the Philippines Diliman. He can be reached at [email protected].