Science, the Scientific Method and Biology



Science, the Scientific Method and Biology

Science is the mechanism by which humans strive to understand the world around us. The practice usually entails a combination of two distinct approaches: discovery driven and hypothesis driven inquiry techniques or methods, to ultimately find the natural causes for natural phenomena in our “world”. The scope is limited to the study of structures and processes that are either directly or indirectly observable. The foundation of “discovery science” is the observation and measurement of phenomena, that is verifiable, to draw conclusions best describing a particular observation. This process is based on inductive reasoning: that is the generalization or conclusion is based on summarization of many concurrent observations.

The aforementioned approach is the basis of the second approach to science: hypothesis driven science which utilizes the Scientific Method, which succinctly can be described as an organized rationale approach to problem solving. A key element of this approach is the use of deductive reasoning: use of general observations to produce specific conclusions .

The generalized procedure of the scientific method is to first make observations regarding a particular phenomenon (either directly or by using the knowledge of others). Subsequently, one can then make generalizations (hypotheses) to explain the generalization. A hypothesis (alternate) is a tentative explanation of the phenomenon. The hypothesis is the basis for organization of experimentation to see if results of experimentation are in agreement or disagreement with the hypothesis. In this case deductive reasoning is utilized. That is, we are extrapolating specific outcomes of experimentation if the hypothesis (premise) is correct. A null hypothesis is the opposite of the alternate hypothesis, that is the premise has no effect on the outcome of the experiment. Ultimately after much experimentation the object is elevate the hypothesis (if validates by experimentation) to a theory. This can only be accomplished if many different types of experiments and observations support the hypothesis and there is no valid contradictory information gathered during experimentation. In science theories are considered to be the best explanation for particular phenomena. However, if during experimentation evidence contradictory to the hypothesis or theories becomes available, new hypotheses and ultimately new theories must be formulated. When generalizations are strongly supported (theories) it is possible to make predictions about similar phenomena.

When asking questions using the scientific method experimentation has to be highly organized and controlled to have any value. While there are no specific rules to experimentation the guidelines should be followed:

First one should recognize there are two hypotheses:

The Null hypothesis, which says the experimental treatment, has no effect on the outcome of the experiment and secondly the Alternate hypothesis, which says the experimental treatment, has an effect on the out come of the experiment.

Since many things (known as variables) can affect the outcome of experimentation the experiment should be designed such that there is potentially only a single explanation for the results. The variable that is being tested (i.e. affects the outcome of the experiment –the alternate hypothesis) is known as the independent variable (that factor manipulated during the experiment). The outcome one measures as one varies the independent variable is called the dependent variable. . Every other factor or condition is referred to as a controlled variable and they must be maintained constant during experimentation. During experimentation one usually runs control and experimental procedures where is only difference is the experimental has a quantifiable manipulation of the independent variable.

Remember experimentation requires validation, thus the results of a single experiment are not valid. The experiment should be repeated (known as replication) several times and if possible the results analyzed statistically.

Notice the hypotheses only include the dependent and independent variables.

The purpose of science is our attempt to understand the world around us, what is it, how does it function and what are the controlling factors and may be ultimately gain some control of it. As a result it must be guided by natural law and must be empirically testable with conclusions usually being tentative.

1 Biology

Succinctly, Biology is the scientific study of Life. While life (or living things) is intuitively obvious it is often difficult to concisely describe. Life can be determined or defined by its characteristics. Despite life’s great diversity there are several generally accepted characteristics that separate living and non-living things:

i) it is a complex, highly and precisely organized structure consisting of organic molecules

ii) it is capable of growth and development

iii) has self regulated metabolism where materials and energy are acquired from the environment and converted to different forms

iv) is capable of movement

v) responds to stimuli

vi) Has the ability to maintain its complex structure and internal environment by a process called Homeostasis

vii) is capable of reproduction whether simple or complicated using DNA genetic information)

viii) adapts to environmental changes which results in evolution

Life is not described as the sum of its parts. It arises as a result of a complex ordered series of interactions among the parts known as Emergent Properties

In addition the characteristics or properties are dependent upon the following three major factors:

i) Evolution

ii) Transmission of Information

iii) Energy transformations

All of the above is the result of a phenomenon called the Central Dogma (DNA-> RNA-> protein). All life forms are controlled by the same chain of commands. The information that gives life its properties and capabilities are stored in genes which are parts of chromosomes. The macromolecule that contains the information is Deoxyribonucleic Acid. In order to utilize the information it must be converted to Ribonucleic acid. Ribonucleic Acid is then utilized to produce the enzymes (protein) which control the biochemical reactions resulting in the specific life forms attributes and capabilities.

2 Organization of Life

There are several methods or ways of looking at the organization of life, each of which are outlined in the following text. The first and most common, is to look at life’s organization from its basic sub units to its most complex. The smallest components of life are electrons, protons and neutrons. (Of these electrons are probably the most important as we shall see in chapter 2). These are the fundamental sub units of which the next level of organization, atoms, are comprised. An atom is the smallest unit of an element that still retains the properties of that element. It is the particular arrangement of electrons, protons and neutrons that define the specific properties of a given element. There are more than one hundred known elements varying in size and properties as a result of their subatomic composition. However, 99% of biological material is comprised of only six of these elements; carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur. All of these elements are relatively small and chemical unstable. All unstable atoms will naturally undergo chemical reactions to gain stability. These reactions require the formation of some kind of bond between the atoms that result in some type of association. The associated atoms form the next level of organization, molecules, where molecules are a unit of two or more atoms (of the same or different elements) bonded together. In biological systems hydrogen and oxygen bond to for water, which occupies approximately 70% of the mass of life forms. While water is the dominant molecule there are many other molecules of varying properties and sizes in biological systems. The next level of organization requires stable molecules to become unstable such that they interact by formation of bonds to produce specific macromolecules with definite properties. In biological systems there are four major macromolecules with unique properties: carbohydrates, proteins, nucleic acids and lipids. As we shall see later, the latter is not a true macromolecule. To produce a basic life form (called a cell) there is a requirement to associate macromolecules together in specific ratios and minimal quantities. A cell may be defined as the smallest living unit that may live independently or as a part of an organism. All cells have a membranous structure surrounding them to isolate them from their external environment and thus impart organization. Robert Hooke coined the term cell and was the first scientist to actually observe these structures as components of multi-celled organisms. Anton Van Leeuvenhoek is credited with being the first person to observe individual cells as single celled organisms. Notice all cells have the same hierarchy of organization, known as biochemical unity. Approximately 170 years after the first observation of cells, in the 1830’s, Schwan and Schlieden independently proposed a fundamental concept called Cell Theory-all living things are composed of cells and that all cells come from other cells. Cells have unique properties associated with life, they have genetic information that enables them to make exact copies of themselves, they are capable of biochemical reactions (Biosynthesis) for the formation of new biological material (protoplasm) and are all capable of Energy transformations. Biosynthesis and energy transformations in biochemistry are termed Anabolism and Catabolism respectively.

Actually at the cell level there are two fundamentally different cell types, Eukaryote and Prokaryote. There is a fundamental difference in their hierarchical organization. In eukaryotic cells certain macromolecules and biochemical reactions are isolated and thus separated from the rest of the cell in membrane bound structures called organelles. One can thus organize life forms very simplistically into one of two groups based on cell type. Organisms are either Prokaryotic or Eukaryotic. Prokaryotic organisms are always single celled, while eukaryotic can either be single or multi celled.

In many multi-celled organisms and thus eukaryotic organisms, but not all, one finds cells organized in masses called tissues. One can define tissues as a group of cells and intercellular substances functioning together in a specialized way. One can then organize one or more types of tissue into an interacting structural or functional unit known as an organ. Two or more organs whose separate functions are integrated in the performance of a specific task are termed an organ system. By specific aggregation of specialized independent cells arranged in tissues, organs and organ systems one can create a highly complex multi-celled organism that fundamentally has the same basic properties as a very simple single celled organism (independent existence and the capability of producing competitive offspring –Inclusive fitness).

Any organism prokaryotic or eukaryotic, single or multi –celled that has specific properties is termed a species. Currently there are approximately ?????? known species in the biological world. Many individuals of the same species occupying a given area are known as a population. In the world around us, many different populations nearly always coexist in some fashion in a given area. This level of organization in ecology is referred to as a community. Any community and the physical and chemical environment in which it exists is termed an Ecosystem. Many different types of ecosystems can be found on the planet earth, each having its own communities due to variations in the physical and chemical environment.

A biome usually contains many types of ecosystems that are determined by specific climatic and vegetation conditions and thus characteristic organisms adapted to the particular conditions. In essence a biome is a very large geographic ecosystem of which there are eight major terrestrial currently recognized. Ultimately one can group the biomes together. The regions of the earth’s surface (crust, waters and atmosphere) where live forms are found, that is the biomes are recognized as the Biosphere. In one sense, the biosphere may be considered one large complex living entity- the Gaia hypothesis.

Notice in this organizational scheme there is a similarity up to the cell level, variation or diversity only occurs at the cell level and above.

Also associated with this organization is the idea of Emergent properties- that is the number of properties exhibited at any given level is greater than the number of properties exhibited at the previous level (i.e. the sub components 2+2 = ................
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