Characteristics of living things

Chapter 1

THE SUBJECT OF BIOLOGY – CHARACTERISTICS OF LIVING THINGS. THE SCIENTIFIC METHOD

1. Universal laws of life

         It brings some danger to devote a whole chapter to the subject and the method of biology, especially Chapter 1. The author knows from experience that the more dubious, poorly taught and ot little use for the students is a discipline, the more time is devoted to explain what the subject of this discipline is and why, how important it is and what extensive ties it has with other sciences. I realize that if the present text arouses suspicions of this kind, the reader will close the page and never open any page from this site. However, it seems necessary to describe life in general – not only because this item is included in our program, but also because it is really important. It is significant that the physicist Schroedinger, author of the Schroedinger equation, wrote a book titled What is life.

         The subject of biology is shown in its name – "biology" means "science of life" in Greek. Life can be defined as the ability of an object to maintain and expand an identity ot its own, resisting the pressure directed toward maximum thermodynamic stability. Living objects (organisms) can be recognized because they do some things non-living objects cannot do. These "things" are called life processes or functions. Here are the most important of them:

as long as it lives, the organism maintains a relatively stable steady state (self-perpetuation or self-regulation), and this is achieved not by immobilization of the molecules in its body, but by their periodic exchange (self-renewal) while preserving the general way they are arranged;

the organism expands its identity onto the surrounding matter by including it into its own body (growth) and into similar new organisms (reproduction);

to perform these processes, the organism absorbs exogenous free energy (energy flow) and substances (flow of matter) and changes these substances within its body (metabolism);

the organism absorbs information from the environment (information flow) and reacts by appropriate changes in its life processes (reactivity).

         Living organisms can do all these things because they are appropriately made. The way non-living objects are made, on the contrary, makes the life processes a priori impossible. Hence, life is characterized not only by functions but also by corresponding structures. They are ordered, i.e. it is highly unlikely that the molecules of an organism will arrange themselves in this way by chance. This order is not imposed by an external force, but by mutual recognition between the most important molecules – self-assembly (self-organization).

         It is interesting to compare organisms to crystals, which superficially resemble some properties of life. Like organisms, crystals have an ordered structure and can grow, including new particles from the environment. If a crystal is broken apart by an external force, the parts can grow on their own. However, the crystal has no spontaneous "reproduction". It can take particles from the surrounding solution or leave particles there, but does nothing akin to metabolism. And, perhaps most important, when we damage a crystal, it does not resist, while each organism tries to avoid damage. The organism will move away from the damaging agent, or grow in the opposite direction, or enhance its metabolism to endure the assault, or, on the contrary, fall into quiescent state until the hard time is over. In short, while non-living things are inert under any circumstances, organisms defend themselves actively. While the non-living object does not care whether it will exist or not, the living thing wants to exist. For any organism the environment is not neutral. It is a set of problems the organism has to solve in order to survive and reproduce. This does not mean that life as such is conscious. Obviously some organisms are conscious – we are among them, after all. But as far as we can judge, the vast majority of organisms are not conscious and care for themselves and their progeny just because they are programmed to do so.

         This program, which determines the identity of each organism, (both structure and function), is contained within the organism. We call it hereditary program or hereditary information, because during reproduction it is transmitted to the organism's progeny. It consists of discrete commands called genes.

         Sometimes the organism takes part in what we call sexual process and trades genes with a similar organism. With the exception of this strictly controlled exchange, each organism carefully protects its hereditary program from damage, change or mixing with that of another organism. Sometimes, however, changes appear in the hereditary program. We call them mutations. Although mutations are needed for the preservation and diversification of the living world, they are not welcomed by the organism. Instead, they appear accidentally and despite the efforts to keep the hereditary information unchanged.

         Reproduction soon creates too many organisms. It is impossible for all of them to survive – a situation called struggle for existence. Usually the organisms struggling for existence have different hereditary programs (because of mutations and sexual processes). Those whose program is more appropriate for the moment have a higher chance to survive. The result is differential preservation of different hereditary programs, a process we call natural selection. By this mechanism, as time passes, groups of organisms undergo irreversible development called evolution. It is considered a property of organisms, like life functions, but unlike the functions it "happens by itself", without being written in the hereditary program. The evolution of organisms makes them match their environment – a process called adaptation.

         For now, we are interested only in the general characteristics of living things and we will not discuss their specific features such as size, composition and structure. These specific features will be dealt with in later chapters.

2. The scientific method

         After the subject of biology, we will briefly discuss its method. In the later chapters, when we talk about a "biological method", we will mean some specific procedure, e.g. dissection, microscopic observation or electrophoresis. But for now, we will talk about the method which is used throughout biology and encompasses not only the diverse specific methods, but also the appropriate thinking. It is called scientific method.

         Apart from biology, the scientific method is used by physics and chemistry. These three sciences are called natural and their subject is everything that can be studied by the scientific method. Outside the method remain the arts, the ideologies, the religions and the purely deductive realms of thought – mathematics, logics and phylosophy. The scientific method is inductive, i.e. oriented towards the outside world. The so-called social sciences also try to use it, but with many restrictions and variable success, therefore we look at them with self-confident disregard and, in a low voice, doubt whether those are sciences at all.

         Natural sciences describe the world by constructions of thought called theories. This is possible because the human mind seeks regularities and finds them, no matter whether they really exist. Every scientific theory is compared to the observed phenomena, called facts or data. If they contradict the theory, it is revised or rejected.

         The researcher registers the facts either as they appear spontaneously in nature (observation) or in a laboratory where he has some control over them (experiment). Each observation or experiment must answer some question, to solve some problem concerning a critical examination of a theory. If the researcher has just one theory, the question usually is whether it applies also to some poorly studied facts; if there are two or more alternative theories, the question is which of them better explains these facts.

         If no theory has been proposed for the studied phenomenon, or the researcher dislikes the theories of other scientists, he can create a new theory of his own. It is usually called a hypothesis and is used like any other theory.

         The described series of thoughts and actions forms the scientific method. The scientific progress can be defined as gradual improvement of theories by the scientific method.

         The theories are created by "dogmatic" thinking, i.e. the same type of thinking that creates myths and legends. The distinctive feature of science is the critical thinking. It is a purely destructive instrument; it cannot create a hypothesis, it can just disprove it. This is rarely said, because in schools only the theories are taught, without the method, and in a dogmatic way. The theories accepted now are presented as if they are proved 100 per cent and will remain forever. The older, rejected theories are presented as evident delusions, and we wonder how people could be so stupid to believe in them. The impression is that the scientist is a person who has learned the facts known to date and believes in the "correct" theories explaining them.

         In fact, what distinguishes the scientist is not in what he believes, but why he believes in it. He believes in the accepted theories just because they are the best available explanations of facts and is ready to renounce any theory, if it clashes with new facts. Therefore, there is no principal difference between a theory and a hypothesis. Each theory, even if supported by thousands of facts, can be disproved partially or wholly by the next fact to come. However, the tradition is to call hypotheses the newly presented views, and theories – those who have endured at least several serious critical examinations.

         People outside natural sciences often think that the job of a scientist is to find out facts objectively. This opinion is wrong. First, it implies that the facts found out are really found out, i.e. equals facts to truth. But although scientists always seek the truth, they must never say they have found it, even for elementary things. We perceive not the facts themselves, but some idea of them, provided by our senses and instruments. (See above – we defined the facts not as phenomena, but as "observed phenomena"). This means that a mistake is always possible. Let's just remind the obvious "fact" that Sun revolves around Earth.

         Second, facts can be found out only by being included in theories. The theory can remain without explicit formulation, it can even be subconscious, but it dominates each description of facts and each observation. Suppose somebody observes by electron microscopy spermatozoa form some species not yet described in the scientific literature. This investigation looks like "collecting facts without a theory", but is it really? No matter whether the observer realizes it or not, he has a theory in his head – that the sperm cells he sees for first time are in many respects similar to sperm cells from other animals he knows. Without this theory the observer will get no facts, because he will not know which section is transverse and which – longitudinal, which is a head and which is a tail.

         Let's take for example an actual study of this type, investigation of the spermatozoal ultrastructure of the bowfin Amia calva, a fish belonging to the Holostei group. The authors explicitly write in the Introduction chapter of their article: "The objective of the study was to examine the bowfin spermatozoon in order to determine if it shares similarities with the spermatozoon of the other holost genus, Lepisosteus, or with the spermatozoa of primitive teleosts" (Afzelius & Mims, 1995).

         A better example how "facts are collected without a theory" is the microscopic observation by a person with little experience in microscopy and scarce knowledge of the object. Every 1^st year student sometimes cannot see an object which, as his colleagues say, is right in front of his eyes; and when the unexperienced observer finally sees the object, he cannot say what color it is and asks other observers about it. The unbiased, theory-free observation is fruitless even in the rare cases when it is possible at all. It is like observation without brain and leads nowhere.

         In fact, contrary to what is accepted, the researcher is not obliged to be and usually cannot be unbiased. If he has two or more theories at his disposal, he chooses one of them just because he likes it more. When a theory clashes with some new data, its proponents do not renounce it immediately. Instead, they first demand confirmation of the new facts, saying that their opponents most likely have done errors in their experiments, or have misinterpreted the results. The history of science is full of examples how good new theories, consistent with all known facts, have been accepted by the scientific community only after being rejected for years.

         On the other side, history of science rarely mentions the far more numerous examples of the conservatives proving to be right. Challenging unexpected scientific reports is good for science. It indeed hinders good new theories but also rarely allows an accepted theory to be replaced by any of the bad new theories being proposed all the time. Besides, the perspective to face opponents improves the quality of research. To be accepted, new results must be confirmed (reproducibility), preferably by different researchers and in different laboratories. Measurements are done using the best equipment available (precision). Together with the experimental sample, a similar sample called control is prepared, in which the unknown factor is replaced by a known one. Then results from the experimental and control samples are compared. These are the technical details of the scientific method.

Main references

        Villee C.A., V.G. Dethier. Biological Principles and Processes. W.B. Saunders Co., Philadelphia, 1971.

        Markov G. The secrets of the cell (Bulgarian). 3^rd revised edition. Narodna Prosveta, Sofia, 1984.

        Popper K.R. Unended Quest: An Intellectual Autobiography. Open Court, La Salle, Illinois, 1982.

        Weisz Р.В. The science of biology. 3. edn. McGraw-Hill Inc., USA, 1967.

The article used as an example of a scientific work:

        Afzelius B.A., S.D. Mims (1995). Sperm structure of the bowfin, Amia calva L. J. Submicrosc. Cytol. Pathol. 27: 291-294.

URL http://www.mayamarkova.com/biology/B1Life/B1Life.htm

Published in 2006

Copyright © Maya Markova

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