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.
<Example cell theory: The observation of cells in all organisms leads to the conclusion: all organisms are
made of cells>

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 <since all organisms are made of cells then any specific entity
if an organism must be composed of cells>.

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. <Fig.1.18Essential Biology>

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. <Ex. Fertilizer and growth in plants>. 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.

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 <explain>
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.

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 = <4)
Biosphere
(Those regions of the earth in which organisms are present)

Biome
(A combination of ecosystems in a given geographical or climatic region)

Ecosystem
( A community and its chemical and physical environment)

Community
(many population of different species living in conjunction)

Population
(Group of individuals of the same species)

Species
( an organism with specific properties/characteristics)

Organism/*Multicelled organism
(life form either * **single or *multicelled)
(macrobial organisms composed of specialized, independent cells organised into tissues,organs and organ
systems)

*Organ System
(two or more organs whose separate functions are integrated to perform a specific task)

*Organ
( one or more tissues interacting as a structural , functional unit)

*Tissue
( a group of cells functioning together in a specialized manner)

Eukaryotic*
Cell
**Prokaryotic (always single celled)
(smallest living unit capable of independent existance as an organism or part of an organism)

Organelle*
(membrane bound structure in a eukaryotic cell containing macromolecules with specific functions isolated
from the rest of the cell)

Macromolecule (4)
(large molecules with specific functions)

Molecule
(two or more atoms of the same or different elements bonded together)

Element
( aprticular combination of protons, neutrons, & electrons with specific properties)

Atom
(Smallest unitof an element that retains the properties of that element)

Sub Atomic Particle

(Electrons, protons, & neutrons-particles of which atom comprised)
We have previously inferred a second type of organization of the biological world based simply on cell type
(i.e. Prokaryotic versus eukayotic). It is also possible to organize life forms into the Microbial versus the
Macrobial World. This is frequently referred to as Lower versus Higher organism organization. The
terminologies higher and lower should not be used since they imply some kind of superiority and inferiority
among life forms based on their complexity. While the terms imply the classification is based on size (small
Vs large) and while relative sizes may be relevant the basis for organization is cell type, cell number and
cell organization primarily.

In the microbial world the following types of organisms are found:

i) single celled prokaryotes
ii) single celled eukaryotes
iii) multicelled eukaryotes where all the cell are similar and independent
iv) multicelled eukaryotes where the cells are dissimilar and independent
The single celled prokaryotes are generally small (usually not visible to the naked eye, whereas the multi-
celled eukaryotic variants can be small but are usually clearly visible and may easily be one meter in size.
Multi-cellularity in cases iii) and iv) does not technically include tissue, organ and organ system
development. In the macrobial world organisms are comprised of many eukaryotic cells. The cells by
definition are dissimilar however; they are dependent up on each other because they are organized into
tissues, organs and organ systems that aggregate to form the organism. This cell type and organization is
specific to macroorganisms and as a consequence usually dictates a large and more complicated organism
relative to microorganisms.

Figure:
Prokaryotic (always singled celled organisms)
Cell
Eukaryotic Single celled organism
Multicelled organism i) similar independent cells
ii)dissimilar independent cells
iii)dissimilar dependant *

*macrobial world,

Systematics and Taxonomy

Systematics is the science of showing evolutionary phylogenetic relationships between organismsand its
classification. It employs Taxonomy ( the naming of organisms or groups of organisms to arrange
organisms) to reflect phylogeny.

Implicit in this organization is the naming of organisms using two names, Genus and species (Binomial
Nomenclature) as devised by Linnneaus. Organisms once named are then organized into a hierarchy of
broader taxonomic categories (Taxa) – family, order, class, phyla, and kingdom.

Initial classification schemes used motility and mode of nutrition to assign organisms into on of two
kingdoms – Animalia- motile, heterotrophs
Plantae - nonmotile, autotrophs

The discovery of “the microbial world” led to problems that Haekel addressed by creating a new kingdom,
the Protista

Further problems (the protista contained fundamentally different prokaryotic and eukaryotic cells) were
resolved by Whittaker. Using cell type and mode of nutrition (saprophitic), the protista were subdivided
into:- Protista- eukayotes
Fungi- eukaryotes, saprophitic
Monera- prokaryotes
The macrobial world kingdoms Plantae and Animalia were retained
More recently this five kingdom classification scheme has been modified using molecular level attributes
of cells. In this classification scheme Woese includes a new taxonomic level above Kingdoms- Domain.

There are fundamental differences in the size of ribosomes (primarily responsible for translation of
proteins) between Eukaryotes (80S) and prokaryotes (70S). On analysis of a specific ribosomal RNA
component of the ribosomes Woese found all Eukaryotes to be similar and thus grouped all eukaryotic
kingdoms into a single domain – Eukaryae.
However prokaryotic cells had two different rRNA structures and thus he divided the monera into two
Domains – Archae and Eubacteria . Each domain possessing one kingdom Archaebacteria and Eubacteria
respectively. Thus in this classification there are 3 domains.
Eukaryae divided into 4 kingdoms , animalia, plantae, protista, and fungi.
Archae, kingdom Archaebacteria
Eubacteria, kingdom Eubacteria

Cell size and multi cellularity.

The size of an organism, the number of cells that make up the organism and the specific organization of the
cells as previously discussed, is not arbitrary. There are limits to the size of cells and thus these limits
will dictate the sizes of organisms and the number of cells and organization required to form a given
organism.
Generally, single cells and thus single celled organisms are no smaller than 1.0 (1/1000000M) in diameter.
One might ask why? The rationale is quite simple in reality. Remember cells have very specific properties
as a result of the four macromolecules of which they are comprised. Specific quantities of each
macromolecule are required to provide these properties that define life. Since macromolecules are
ultimately comprised of a given number of atoms and each atom has a specific size dictated by its
subatomic parts, one can theoretically calculate the minimum size of a cell simply by multiplication of
the sizes of the atoms by the number required to produce the minimum number of macromolecules
that result in the properties defining life. When this multiplication is performed the approximate size is
1.0. In this regard viruses are considered a-cellular because they are smaller than 1.0 and thus have
insufficient volume in which to place all the macromolecules required to define life. In fact most viruses
only have two of the four major macromolecules associated with them (nucleic acids and proteins).

The maximum size that a cell (and thus a single celled organism) can attain (approximately 100.) is
a function of the surface area to volume ratio. Prior to the discussion why? It is necessary to review
some simple geometry of three-dimensional shapes. The simplest case to review for conceptual purposes is
a cube. The surface area is simply calculated by multiplication of the length of a side by itself (L x L) to
obtain the surface area of a single side, this is then multiplied by six since there are six sides to a cube. If
one were calculating the surface area of a sphere (the approximate shape of most cells) the equivalent
calculation is 4  r2. To calculate the volume of a cube, the following formulation is used: L x L x L. Again
the equivalent calculation for a sphere for surface area is 4/3  r3..

The ratio of surface area to volume for a sphere thus is (6 x L x L) / (L x Lx L), or 6/L, whereas for a cube
the ratio is (4  r2) / (4/3  r3), or 3/ r. As can be seen in the following example, as one increase the value
of either L or r (as one does when the size of the object is increased) that while both the surface area and
volume increase, the volume increase proportionately more because the former is a square function and the
latter a cube function, thus decreasing the surface area to volume ratio. Consequently when the diameter of
a spherical cell is approximately 100 the surface area to volume ratio becomes limiting. Organisms larger
than this become multi-celled in order to overcome the limitation as we shall see. In addition the larger the
organism becomes the more complicated the organization of the cells that comprise the organism becomes.
There are exceptions to this general rule. If cells are elongated (the equivalent of cylinders) there is
technically no limitation to the absolute size (only diameter) because of different geometrical principles.
For cylinders the surface area is calculated in the following manner 2rL, where r is the radius of the
cylinder and L is its length. Volume is calculated according to the following formula,  r2 L. The ratio of
surface area :volume is thus 2rL /  r2 L. On solution the surface area : volume ratio is thus a function of
2/r. Consequently, cells can be of great length as long as they have a diameter no larger than 100 ., which
is generally the case. Exceptions to this rule require dead space with the cell to increase the ratio (as in the
case of plants).

The importance of the above is in relation to food uptake vs. food requirements. The volume represents the
food requirement of the cell. The larger the cell the more food required. One must recognize a volume
specific minimum requirement that needs to be provided to sustain life. Uptake through the surface area
provides this requirement. The more surface area the more uptake. However, there is an area specific
maximum uptake. Total minimal requirements can be determined by multiplication of the total volume of
the cell by the volume specific minimum requirement. Total uptake can be determined by multiplication of
the total surface area by the area specific maximum uptake. At approximately 100 cell diameter, the two
are equal, thus sufficient food can be acquired, however, above 100 cell diameter, uptake is less than that
required and the cell cannot sustain itself.

If organisms are larger than 100 then they are multicelled in order to overcome the surface area:volume
limitations. As they become very large there is a requirement for the evolution of differentiation of cells
into tissues organs etc. to take advantage of the surface area created (evolution of the microbial world).

History of Life

The processes leading to life are thought to have begun some 4 billion years ago when random chemical
reaction occurred that ultimately led to the formation of the four major macromolecules required for life.
The first single celled life form appeared as a result of these processes some 3.8 billion years ago and
presumably was a prokaryotic cell. Remember this is not necessarily true (urkaryote). The theory purported
to explain this is Spontaneous Generation. This first life form is now considered to be the common
ancestor to all organisms that exist today according to Buffon. Virchow proposed all organisms arose by
reproduction from this common ancestor. The initial organisms were metabolically relatively simple using
inorganic molecules as sources of nutrients ie Autotrophs.

It is thought that the autotrophic process of Photosynthesis evolved some 2 billion years ago. Initially this
was associated with prokaryotic organisms. The consequences of the evolution of this process are that
i organisms were now capable of migration from aquatic to terrestrial ecosystems
ii it enabled increased metabolic diversity- Heterotrophy (respiration & fermentation)

Between 1 amd 2 billion years ago Endosymbiosis occurred leading to single celled Eukaryotes. One
billion years ago the first multicelled Eukaryote evolved utlimately leading to the evolution of the
macrobial world somewhere between 1.billion years ago and now.