Molecular basis of life, chapter 1
SUBJECT AND METHOD OF BIOLOGY
1. Subject of biology: living systems
1.1. What is life
The subject of biology is shown in its name – "biology" means "science of life" in Greek. It studies living systems. The most fundamental and fastest developing branches of biology are known today as “life sciences”. What is life, however? It is easier to recognize living things than to describe their characteristics. On our planet, we are surrounded by them and take them for granted. To see how extraordinary life is, it helps to look at a place where it is not present.
Top: Mars landscape, photo copied from Astronomy Picture of the Day, original source NASA, with their kind permission. Bottom: typical Earth landscape for comparison, own photo.
Life can be defined as the ability of an object to maintain and expand an identity of its own, resisting the tendency towards maximum thermodynamic stability. 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.
Unlike the crystals, living things try to avoid damage. They will move away from the damaging agent, or grow in the opposite direction, or enhance their metabolism to endure the assault, or, on the contrary, fall into a quiescent state until the hard time is over. In short, while non-living things are inert under any circumstances, living systems defend themselves actively. While the non-living object does not care whether it will exist or not, the living thing resists destruction. For any living system, the environment is not neutral. It is a set of problems that the living thing must solve in order to survive, grow and reproduce.
1.2. Life functions
Living things (organisms) can be recognized because they do some things that non-living objects cannot do. These "things" are called life processes or functions. Here are the most important of them:
- self-perpetuation: as long as it lives, the organism retains its characteristic identity (perpetuates itself) by maintaining a relatively stable steady state (self-regulation). This is achieved not by immobilization of the molecules forming its body, but by their periodic exchange (self-renewal) while preserving their general arrangement.
- Growth and reproduction: the organism expands its identity onto the surrounding matter by including it into its own body (growth) and into similar new organisms (reproduction).
- Metabolism and energy flow: 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).
- Sensitivity: the organism detects changes in the environment (also known as stimuli) and reacts to them by appropriate changes in its life processes (sensitivity).
1.3. Life structure (organization)
Living organisms can perform everything listed above because they are built appropriately. The way non-living objects are built, on the contrary, makes the life processes a priori impossible. Hence, life is characterized not only by functions but also by corresponding structures.
All living structures have several important characteristics:
- They are highly ordered, i.e. it is very 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, a phenomenon called self-assembly or self-organization.
The smallest living system (i.e. the smallest structure performing all life functions) is the cell. Subcellular structures, called organelles, possess some but not all of the characteristics of life. In other words, the integrity of life is lost at subcellular level. Therefore the cell is considered a basic structural and functional unit of living systems, "atom" of life. Organisms are either single cells or groups of cells.
Viruses are small objects that are not cellular but are nevertheless often considered living. They have no metabolism of their own and do not look alive outside their host cells. On the other hand, viruses possess the most important feature of life, that is, preservation and expansion of their identity. To avoid pointless discussions whether viruses are living or not, they are classified separately from all (other) organisms as special, acellular, "honorary" forms of life.
1.4. Hereditary program (genotype)
Observing the "efforts" of organisms to survive and reproduce, we should not jump to the conclusion that all life is conscious. Obviously, some organisms are conscious and we are among them. However, 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 the organism, (both structure and function), is contained in every cell. We call it hereditary program or hereditary information, because it is transmitted to the organism's progeny during reproduction. It consists of discrete commands called genes and is encoded as a linear script in one or more DNA molecules called chromosomes. The hereditary program of a particular organism is also known as its genotype.
Each organism carefully protects its hereditary program from damage and change. Nevertheless, random changes called mutations occasionally appear in the genotype. In the long run, mutations are needed for the preservation and diversification of the living world. However, their immediate effect on the organism is more likely to be deleterious than beneficial. Therefore mutations are not welcomed by the organism. They appear accidentally and despite the "efforts" of every cell to keep its hereditary information unchanged.
Most of the time, the organism guards its genotype not only against mutations but also against mixing with genotypes of other organisms. Sometimes, however, gene transfer between organisms takes place, e.g. in sexual reproduction. Mutations and gene transfer change genotypes and so cause hereditary variation. This way, genetic diversity is created among organisms that originally were very similar.
Reproduction soon creates too many organisms. It is impossible for all of them to survive, a situation called struggle for existence. In most cases, the organisms struggling for existence have different hereditary programs as a result of mutations and gene transfer. Those whose program is more appropriate for the moment have a higher chance to survive and reproduce. The result is differential preservation of genotypes, which we call natural selection.
Under the combined action of mutations and natural selection, as time passes, groups of organisms undergo irreversible progressive change called evolution. It is considered a characteristic of organisms, like life functions, but unlike the life functions it "happens by itself", without being written in the hereditary program (there are no genes for evolution). As a result of evolution, organisms match their environment, a phenomenon called adaptation.
2. Methodological basis of biology: scientific method
2.1. Natural sciences
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 way of 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 such as mathematics, logic and philosophy. 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 these are sciences at all.
2.2. Philosophical basis of science
It is characteristic for natural sciences that they study only natural phenomena and invoke only natural explanations for them. This is called mechanistic materialism or methodological naturalism. The people engaged in science are strictly bound to its restrictions. In other words, the scientist in his private life can believe in God, a pantheon of gods, nature spirits, astrology, black magic and anything else he wishes, but while doing science, he must never "explain" natural phenomena by supernatural forces or entities.
A good explanation of the philosophical basis of science was given in 2005 by the US judge John Jones. He had to decide whether the so called "intelligent design" should be studied in public schools. Motivating his decision, namely, that "intelligent design" is religion rather than science and hence teaching it in US public schools is unconstitutional, the judge said: "Since the scientific revolution of the 16th and 17th centuries, science has been limited to the search for natural causes to explain natural phenomena… While supernatural explanations may be important and have merit, they are not part of science. This self-imposed convention of science, which limits inquiry to testable, natural explanations about the natural world, is referred to by philosophers as "methodological naturalism" and is sometimes known as the scientific method. Methodological naturalism is a "ground rule" of science today which requires scientists to seek explanations in the world around us based upon what we can observe, test, replicate, and verify."
2.3. Facts and theories
The observed (empirical) phenomena studied by natural sciences are called facts, data or evidence. Observing them, the scientist seeks regularities. When he finds a regularity, or at least thinks so, he describes it in a construction of thought called theory. In a nutshell, science is about creating, testing and improving theories.
There is no recipe for creating theories. Newton conceived the theory of gravity after he observed the fall of an apple. (Contrary to popular belief, the apple did not fall on his head.) Theories cannot be derived from facts. Rather, it is the other way round: every description of facts and every observation is inevitably done within the frame of a theory, although the observer may not formulate it explicitly and may be even unaware of it. However, theories must be in agreement with known facts. Good theories also have some prognostic value, i.e. they are able to make predictions about yet unknown facts. Astronomy gives excellent examples of this by its precise predictions of future solar and lunar eclipses, but the predictive value of theories in other scientific fields is much more modest.
2.4. Testing theories
Once created, theories are tested and enriched by checking how they relate to new facts. For this purpose, the researcher either studies phenomena occurring spontaneously in nature (observation), or creates an environment where he can trigger and to a large degree control the phenomena (experiment). Experiments are usually carried out in a special, properly equipped facility called laboratory.
A new theory that has not yet been tested is called hypothesis. If it turns out to contradict the results of the new observation or experiment, it is revised or rejected. If, on the contrary, the hypothesis is in agreement with the empirical data, this is good for it and it can now be called theory; but the tests will continue. They are best done by by different scientists in different laboratories and not only by the researchers who have developed the theory and are partial to it. Even if a theory has been corroborated by thousands of facts, if it clashes with some new facts, it must be reconsidered. The creation and testing of theories comprises the scientific method. By its application, theories are gradually improved and this improvement is the essence of scientific progress.
In order to be critically examined by observations and experiments, theories must be testable and falsifiable. Falsifiability means that for every theory, we must be able to list facts that, if observed, will prove the theory wrong. A theory that cannot be proven wrong has zero information value. It cannot explain anything and is not really a theory. (When asked what evidence would disprove the theory of evolution, the geneticist J. Haldane reportedly replied, "Fossil rabbits in Precambrian rocks.")
The distinctive feature of science, critical thinking, manifests itself in the testing rather than the creation of theories. This is not widely known, because theories are almost always taught in a dogmatic fashion, without the scientific method. The currently accepted theories are presented if they are literally true and will stay forever. The old, rejected theories are portrayed as evident delusions that could be supported only by stupid individuals. Scientists are described as people familiar with the known facts and believing in the "correct" theories explaining them. In reality, the scientist is defined not by what he believes in but by the reasons why he believes in it. He supports the currently accepted theories only because they are the best available explanations of known facts and is ready to abandon them if they clash with new facts. As the author of the Photon in the Darkness blog puts it: "The average person thinks that a scientist is just a huge repository of "facts", since that was what their "science" classes in high school were all about. That couldn't be farther from the truth. A real scientist has to learn a prodigious amount of information, true enough, but the real emphasis is on learning how to think. It is much easier to teach a student the Periodic Table than it is to teach them how to formulate a testable hypothesis. And it is far easier to teach the Krebs Cycle than it is to teach how to draw an accurate and supportable conclusion from experimental data."
It must be admitted that the mere mortals who are actually doing science often deviate from the ideal of a scientist. 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. Emotionally, it is easier to turn a blind eye to new facts than to abandon a favorite theory. 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. In some cases, acceptance of the new theory requires change of generations.
On the other hand, we must keep in mind also the far more numerous examples of conservatives proven 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 by repeating (reproducibility), preferably by different researchers and in different laboratories. Measurements are done using the best equipment available (precision). This is important because we can err not only in the theory but also in what we consider facts. After all, we perceive not the natural phenomena themselves but some version of them as provided by our senses and equipment, and this version is only as accurate as the senses and the available equipment.
When we design an experiment, together with the test sample for which we do not know what we shall obtain, we prepare a similar sample called control in which the unknown factor is replaced by a known one. We can set the control in a way to include all conditions needed for some phenomenon and so be sure that it will occur. Such a control is called positive. We can also remove one of the preconditions for the phenomenon and so be sure that it will not occur. Such a control is called negative. An experiment can be done with a positive control, with a negative control or with both controls (the more the better). Then results from the experimental and control samples are compared. From all "technical details" of the scientific method, the use of controls is maybe the most important, because they provide a standard for objective comparison.
An example of studies using a negative control are the clinical trials testing new drugs (it is clear that a positive control cannot be used here). Patients participating in the study are randomly assigned into a test group receiving the drug and a control group receiving an ineffectual substance called placebo. Patients and researchers assessing their condition must not know who is test and who is control ("double blind" setting). This way, if there is a difference between the two groups, it can be concluded that it is due to the action of the drug. Without the control group, even if some improvement is observed, it would be impossible to say whether is is due to the drug. It must be kept in mind that human organism has a potential for spontaneous recovery and also a tendency to imagine improvement after the application of placebo.
The good control must be identical with the test sample in everything except one key parameter. For example, if we study effects of thymectomy (thymus removal) in mice, we could use as negative controls intact mice. However, they are not good controls, because we cannot know whether the deterioration observed in operated mice is due to the loss of thymus or to the invasive surgery itself. So we must perform on control mice "sham thymectomy", i.e. open and then close the chest cavity, leaving the thymus in place.
2.5. The scientific work
Every scientific study after being completed is published in a peer-reviewed scientific journal, or at least is presented at a scientific forum. An unpublished result is, for all intents and purposes, a non-existent result.
Every scientific study addresses a problem. It can be about finding new facts and comparing them to current theories, or about known facts contradicting current theories. The article which describes the study begins by summarizing available data and current theories. Previous relevant studies are cited in a References section. Then, the problem is stated. So-called review articles stop here. For original articles, this is the Introduction section.
Next, the authors describe how they approached the stated problem: what observations and/or experiments they carried out, and how. This is described in the Materials and methods section. Description must be elaborate enough to allow others to reproduce the study. All procedures must be carefully designed and carried out. Bad materials and methods invalidate everything that follows.
What is found after the experiment (or, in observational studies, after spontaneous course of events), is described in the Results section. The new evidence is presented using photos, graphics, tables etc. If relevant, statistical methods are applied to prove that the difference found between test and control samples is statistically significant, i.e. highly unlikely to be due to mere chance. In this section, the authors do not state any ideas. Their findings must speak for them.
WNext, a Discussion section follows where the authors analyze and explain their results and compare them to previous published studies. Conclusions from the study are made, sometimes in a short separate section. The authors explicitly state the new contribution(s) of their study. It is not quaranteed that the analysis will be correct. However, if the results are original and accurate, they are valid anyway.
Villee C.A., V.G. Dethier. Biological Principles and Processes. W.B. Saunders Co., Philadelphia, 1971.
Markov G. The secrets of the cell [in Bulgarian]. 3rd revised edition. Narodna Prosveta, Sofia, 1984.
Popper K.R. Unended Quest: An Intellectual Autobiography. Open Court, La Salle, Illinois, 1982.
Weisz P.B. The science of biology. 3. edn. McGraw-Hill Inc., USA, 1967.
The citation about how science is taught:Prometheus (2005). If you want to drive the bus... [Online] http://photoninthedarkness.blogspot.com/2005/07/if-you-want-to-drive-bus.html
The photo from Mars:Robert Nemiroff, Jerry Bonnell (1996). Astronomy Picture of the Day: If You Could Stand on Mars. Credit: NASA, Viking 1, USGS. [Online] http://zuserver2.star.ucl.ac.uk/~apod/apod/ap960207.html
Published in 2006
At this URL since 2016
Last updated 2016
Copyright © Maya Markova