The Scientific Method and

Taxonomic Classification
BI 103 Marine Biology
Lab 01
 I. The Scientific Method
 What is science?
 Science is special knowledge derived by a
prescribed set of activities known as the
scientific method.
 Therefore, the scientific method is the
procedure of science.
 The method insures that all scientists follow
the same fundamental steps in reaching their
results.
 Procedures in the scientific method
 Observation
 all science begins with observation; anything that
cannot be observed cannot be investigated by
science
 to be valid, scientific observations must be

repeatable, actually or potentially

 correct observation is a most difficult task,

acquired only after long experience and many

errors
 the difficulty of observation lies largely in
unsuspected biases of the scientist, i.e., people
tend to see what they want to see or what they
think they should see
 for example, what do you see below?
 added to the difficulty of making objective
observations is the objective description of what is
observed
 some obstacles to good observation
 past experience
 subconscious prejudice
 “common knowledge” or “common sense”
 teachers!
 for these reasons, and more, a scientific
observation is not taken at face value until several
scientists have repeated the observation
independently and have obtained the same results
 a scientist does not collect observations because
her job requires it
 scientists collect observations, because they think

the observations are relevant and will help solve a

problem, confirm or refute a theory, or contribute
to a new theory
 scientists may use two ways of thinking!
 scientists do not always agree on the best way to
approach scientific study
 some scientists think that the only truly scientific
form of thinking is induction or inductive
reasoning, in which the scientist begins with a
number of separate observations and then arrives
at general principles
 other scientists think that the purest form of
scientific thinking is deduction or deductive
reasoning, in which the scientist begins with
general principles to reach specific conclusions
 Problem
 in defining the problem, the scientist asks
questions about the observation
 most questions deal with cause and effect for some
observation, not with teleology [the attribution of
purpose to natural phenomena, i.e., asking why]
 good questions, like good observations, are
difficult to formulate
 to be valuable scientifically, a question must be
 relevant
 testable
 the difficulty for many scientists is that it is very
hard, or even impossible, to tell in advance
whether a question is relevant or irrelevant,
testable or untestable
 Hypothesis
 hypothesis formulation involves the seemingly
unscientific procedure of guessing, but the guess
is based on pertinent observations
 a hypothesis is a tentative explanation that

accounts for observed phenomena

 whether the hypothesis is or is not correct is

determined in the next step

 Experimentation
 scientists are never content to simply make
hypotheses about their observations; they are
obsessed with testing the explanations to
determine if they are true or false
 experimentation is by far the most difficult part of

the scientific method

 there are few rules to follow, and
 each experiment is a case unto itself
 knowledge and experience usually help technically,
but to design the experiment and to decide on the
means by which a hypothesis might best be tested
are what separate the scientist from the layman
 it is the function of every experiment to test the

validity of a scientific hypothesis

 experimentation must include
 controlled variables
 replication
 results of experimentation should support or refute
the hypothesis
 objectivity in interpreting the results is maintained
through the use of statistical analysis of data
 if experimentation indicates that the hypothesis is

wrong, then the scientist must discard the

unsupported explanation and formulate a new
hypothesis that once again must be tested for
validity by performing new experiments
 Proof
 scientists rarely use the term, because it conveys the
certainty of the mathematical concept of proof
 Theory
 a theory may be proposed when
 a hypothesis has been supported by a substantial body
of evidence obtained in many different laboratories and
by many independent researchers, and
 the total accumulated evidence is reliable within carefully
specified limits (usually statistically within 95%
confidence levels, or greater)
 every good theory has predictive value, i.e., it
does not necessarily say that something will
happen, but only that something is likely to
happen with a stated degree of probability
 thus, the aim of science is to produce new
knowledge by making and using theories to
explain natural phenomena, NOT to make
value judgments or moral decisions
 Let’s follow the scientific method for a
class exercise
 Where does all scientific investigation begin?
 With an observation!
 Let’s start with a few simple observations.
 Observation
 The limpet Patelloida chamorrorum is a
common intertidal gastropod on rocky
shores in Guam
 Observation
 Each limpet occupies a depression in the
limestone that fits the outline of its shell
 The depression is called a “home scar.”
 Observation
 Limpets are herbivores, and they leave their
home scars to graze on algae during rising
and falling tides.
 The depression is called a home scar, because
the limpet returns to the same scar following
each feeding foray
 It is thought that the limpet can reduce its
risk of predation and desiccation by clamping
its shell to the home scar during high and low
tides.
 Problem
 Next step?
 Define the problem by asking question(s)
about the observation.
 N.B.: questions should deal with cause and effect
for some observation
 Problem: How do these limpets find their
own home scar among the thousands in the
rocky intertidal?
 Hypothesis
 Next step?
 Formulate a hypothesis.
 N.B.: To be valid, the hypothesis must be relevant
and testable.
 Null Hypothesis (Ho):
 Limpets locate their home scars by randomly
searching until they find them.
 Hypothesis
 Hypothesis (H1):
 Limpets relocate their home scars by following
the scent of the trail they made as they
crawled away to graze.
 Experiment
 Next step?
 Design an experiment to test the hypotheses.
 How do we remove the trail?
 Scrub the trail away with a brush and
detergent.
 Scrub the trail away with a brush and an
organic solvent.
 Result: Limpets returned directly to their
home scars.
 Hypothesis
 Therefore, we reject H1 and H0
 Now what?
 Either abandon the investigation, or develop a
new hypothesis.
 Hypothesis (H2):
 Limpets relocate their home scars by
navigating the micro-landscape from memory.
 Experiment
 How can we test the navigation
hypothesis?
 Use epoxy to produce an exact replica of the
area around the home scar
 Result:
 Limpets will not cross over the gap between
the limestone and the epoxy.
 However, limpets that are placed on the
epoxy do occupy their scar and will return to
it after that cross the gap the first time.
 We need to refine the method of implanting
the false scar before our results can be
accepted.
 II. Taxonomic Classification
 Taxonomy
 Taxonomy is the branch of biology devoted to
naming and describing organisms
 Any particular group of organisms is called a
taxon
 For example, all snails belong to the taxon known

as the Class Gastropoda

 Need for Classification
 Scientists need to communicate the
results of their research
 They must be sure that everyone
understands exactly which species
was studied in their research
 There are more than 1 million
species of animals described and
about 250,000 plant species
described
 A L L O R G A N IS M S : TO TA L S PEC IE S 1,413,000

Insects
751,000

Other
Anim als
281,000

Higher
Plants Viruses
248,000 1,000

Prokaryotes
Protozoa (Eubacteria &
30,800 Algae Archaebacteria)
26,900 4,800
Fungi
69,000
 The number of undescribed species
may be as many as 99 million
 Therefore, scientists must be able to
arrange life forms into a workable
classification scheme
 History of Classification
 Over the centuries, several
classification schemes have been
proposed
 All are hierarchical—reflecting
different degrees of similarity among
organisms, i.e., similar organisms are
placed together in the same taxon
 In the early years, similarity in
appearance was believed to be a result
of common ancestry, but there were
some exceptions
 Modern classification dates from mid-
eighteenth century
 Carolus Linnaeus (1707–1778) is considered the
Father of Modern Taxonomic Classification
 Linnaeus was a Swedish medical student studying in
Belgium
 His real name was Carl Ingemarsson

 To help pay his tuition costs, Linnaeus was contracted by

wealthy Dutch patrons to catalog all species in their curio
cabinets
 Linnaeus adopted a system of binomial
nomenclature
 He assigned a unique, two-part scientific name derived
from Latin or Greek to each kind of organism
 Therefore, each organism is called by its Genus and
species names
 Conventions of Linnaean taxonomy:
 A scientific name is always italicized or underlined
 A genus name begins with UPPERCASE, while a species
name is lower case, e.g., Homo sapiens or Boa
constrictor
 The genus is a noun, and the specific epithet is an
adjective that must agree with its noun in both number
and gender
 When a binomial designation has been published,
then it cannot be used for any other species
 Why?
 Binomials are unique to eliminate confusion that
often arises from regional differences in common
names
  For example, what is a skipjack?
 In Guam, a skipjack is a young trevally
 In Hawaii, a skipjack is a tuna

Caranx melampygus Kasuwonus pelamis

 Linnaeus began his work on zoological
classification with publication of the first edition of
Systema Naturae in 1735 (at age 28!)
 He subsequently published twelve editions of the
Systema in all, but modern zoological taxonomy dates
from the 10th edition, published in 1758
 Botanical classification dates from Linnaeus’
Species Plantarum published in 1753
 Linnaeus was such a proponent of his binomial
system that he Latinized his own name, changing
Carl to Carolus and adopting a new last name
based on a huge linden tree that grew near his
father’s home
 Learning scientific names
 Learning scientific names is not difficult, and
can even be amusing
 In fact, you already know some scientific
names
 Homo sapiens is sapient (wise or aware) man
 But, what is Cocos nucifera?
 the coconut tree
nuc = nut + fera = carrying
 What about Streptococcus pneumoniae?
 This is the bacteria that causes serious throat and lung
infections, e.g., strep throat and pneumonia
 What is Vibrio cholerae?
 This is the bacteria that causes cholera
 Linnaeus had some fun with the binomials
that he published [N.B., he was a medical
student]
 Tibia fusus
 He named this species Distorsio anus
 He named this species Crepidula fornicata, based
on its unusual life history and sex reversal
 Other anatomical parts, some ribald, were used as
well
 He named the butterfly pea Clitoria ternatea because of
its resemblance to human female anatomy
 Male anatomy was not ignored, either
 He named the stinkhorn mushroom Phallus impudicus
 Other scientists have revealed a sense of humor
 Surprisingly, the author of a new genus of clams that he
called Abra did not describe the first species as Abra
cadabra, but another scientist did later
 Alan Solem enjoyed a good pun
 He wanted to name the species that came first when

all species were listed in alphabetical order, so he

described Aaadonta (to precede Aardvark), but he as
been displaced by the genus Aa
 He also wanted to name the last species in

alphabetical order, so he described Zyzzyxdonta,

which interesting enough is the extreme opposite in
shell characters as Aaadonta
  Solem also described a new species of land snail that he
found near the village of Ba in Fiji
 The new species did not belong to a recognized

genus, so Solem described a new genus, Ba, as well

 The new species? Ba humbugi

 Professor Emeritus Lucius Eldredge named a new

tunicate after his favorite drink, Didemnum gintonicum
 Not all taxonomy is frivolous, and there are rules
governing the naming of new species
 Rules are established by international bodies, e.g., the
International Commission on Zoological Nomenclature
and the International Commission on Botanical
Nomenclature
 Higher-Level Classification
 Linnaeus also categorized the natural world
into higher taxa of kingdoms and classes
 He recognized three kingdoms: plants, animals,
and minerals
 Within the animal kingdom, he recognized six

classes: mammals, birds, amphibians, fish, insects,

and worms
 The number of higher taxa has increased to
reflect the complexity of living organisms
 Higher systematics include the following taxa in order
of increasing similarity and common ancestry

Kingdom
Phylum [Bot. = Division]
Class
Order
Family
Genus
Species
 There may be intermediate taxa between
these major categories, e.g., Superclass or
Suborder or Infraorder
 The hierarchy is designed to reflect
phylogenetic relationships
 Higher taxa include many organisms that share
certain common characteristics & presumably a
common ancestor
 Higher taxa share fewer similarities but include

more organisms
 Lower taxa share greater similarities but include

fewer organisms
 Modern Taxonomy
 Modern taxonomists strive to classify
organisms based on phylogeny rather than
just similar in appearance
 Phylogeny describes the evolutionary relationships
of organisms
 Therefore, modern classification reflects
commonality of descent
 Therefore, all taxa in any given group have a
common ancestral origin, which is usually depicted
in a phylogenetic tree
 Taxonomists try to determine phylogeny by
analyzing as many characters or character
states as possible
 Characters and character states may include a
diversity of factors, including morphology,
anatomy, life history, biogeography, habitat,
behavior, protein structure, chromosome structure,
gene structure
 Character states may be shared because:
 1) organisms are related
 Homologous structures have common origin
 e.g., foreleg of mammal and wing of bird

 2) they are convergent

 Analogous structures have similar function but do not
have common origin
 e.g., wing of insect and wing of bird

Homologous bones have same shading, from left to right:

horse, man, whale,
Analogous crocodile,
structures: wingand bird.
of an (Patterson
insect, 1997)
bird bat
and pterosaur
 Convergence is a major difficulty in
constructing phylogeny
 Convergent evolution describes the similarity
between two organisms (or proteins or DNA
molecules) because of independent evolution
along similar lines, rather than because of a
common ancestor
 Convergence usually occurs when organisms
inhabit very similar habitats
 Therefore, natural selection favors similar
adaptations
 e.g., fins of fishes and whales
 e.g., shells of sand-dwelling species like augers and
turritellas and ceriths
 Species Concept
 The most objective biological unit of
classification is the species, because it is not
an artificial construct
 A species consists of all the organisms that
can interbreed, thereby exchanging genetic
information, and producing viable offspring
 Important points in the definition of a species
 Species are genetically isolated from other species
 Even if different species attempt to mate, there may be
incompatibilities in structure of sex organs or in sperm-
egg interactions
 Species are self-perpetuating
 Species may or may not be morphologically distinct (e.g.,
sibling species)
 Sometimes closely related species may
overcome the barriers and attempt to mate
 If fertilization occurs, offspring are usually
inviable (i.e., they are not capable of living either
during embryonic stages or after birth)
 If viable offspring are produced, the hybrid (or

cross-bred) offspring are usually sterile

 e.g., mules
 Mules are sterile hybrids produced by mating male

donkey with a female horse

  e.g., ligers and tigons are hybrid offspring of captive
Pilot Whale
lions and tigers
 e.g., the “wholphin” at Sea Life Park in Hawaii is a cross
between a pilot whale and a dolphin Dolphin

“Baby” Wholphin

Liger
Tigon
 Subspecies are geographically isolated
populations of species
 They are capable of interbreeding, but they are
separated by geographic barriers such as oceans,
mountain ranges, etc
 Three Kingdoms
 Biologists have found that the Archaebacteria
are as different from the Eubacteria as they
are from all eukaryotes
 Thus, they suggest that there are three
kingdoms: Eubacteria, Archaea, and Eucarya
instead of the traditional five kingdoms
 (N.B.: Your textbook refers to these as Domains
rather than kingdoms)
 Kingdom Archaebacteria
 Archaebacteria inhabit extreme environments,
e.g., hot springs, anaerobic muds, saline ponds
 They are believed to be primitive bacteria, possibly

similar to life forms of early evolution

 This kingdom includes thermophilic bacteria,

halophilic bacteria, and methanogens

 Kingdom Eubacteria
 This kingdom includes advanced bacteria and
cyanobacteria (or blue-green algae)
 Kingdom Eukarya
 This kingdom includes both unicellular and
multicellular organisms that are nucleate and
possess complex internal membranes
 Organisms range from includes protists and green

plants to fungi and animals

 Eukarya may be autotrophic or heterotrophic
 Eucarya
Archaea A n im als 544 M a
G reen n onsu lfu r E n tam o eba e S lim e
Eubacteria ba cte ria E uryarchaeota
m old s
F un gi
C ren- M etha nosa rcina P lants
G ram - M etha no- H alo ph iles
po sitive s archaeota ba cte rium C ilia te s
P u rple b acteria M etha no- 1200--1000M a
T he rm oproteus coccus
C yano ba cteria T. cele r
P yro dictium 2800 M a F lag ella te s
F lavo bacteria
Trich om on ads
2100 M a
T he rm otoga les
2700 M a
2700 M a M on ospo ridia
D iplom on ads

T he U niversal Tree dep icts th e p hylo gen etic relatio nsh ips o f extan t o rg anism s, as inferred fro m sequ en ce
com pariso ns of rib oso m al R N A g enes. Th e b oxed dates in dicate the m in im u m ag e o f selected bran ches,
b ased o n paleo ntolo gical and bio geo ch em ical data. N ew b iog eoch em ical co nstrain ts repo rted b y B ro cks
et al. (1999) are sh ow n in red . [Adapted from K noll, 1999].