Pan Lab for Jesus

Laboratory of Transporter Biology, Department of Life Science,

Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Chapter 1
Invitation to Biology

BIOLOGY: Today and Tomorrow, 4e

5e
starr evers starr
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

1.1 The Secret Life of Earth

▪ Biology
▪ The scientific study of life

▪ We have found only a fraction of the organisms on Earth

▪ Scientists constantly discover new species
▪ Extinction rates are accelerating, (1,000x than normal rate)

▪ Example: New Guinea’s Foja Mountains

“Pinocchio Frog”
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

1.2 Life Is More Than the Sum of Its Parts

▪ The building blocks (Atoms) that make up all living things are
the same ones that make up all nonliving things

▪ The unique properties of life emerge as certain kinds of

molecules become organized into cells
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Life’s Levels of Organization

▪ Atom Levels of Organization
▪ Fundamental building block of all matter
in Nature
▪ Molecule
▪ An association of two or more atoms

▪ Cell
▪ Smallest unit of life
▪ ? Organs, Organ systems…
▪ Organism
▪ An individual; consists of one or more cells

▪ Population
▪ Group of individuals of a species in a given area

▪ Community
▪ All populations of all species in a given area

▪ Ecosystem
▪ A community interacting with its environment

▪ Biosphere
▪ All regions of Earth that hold life
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

1.3 How Living Things Are Alike vs different

▪ All living things have similar characteristics

▪ Require energy and nutrients
▪ Sense and respond to change
▪ Reproduce with the help of DNA
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Organisms Require Energy and Nutrients

▪ One-way flow of energy through the biosphere and
cycling of nutrients among organisms sustain life’s organization

▪ Energy
▪ The capacity to do work

▪ Nutrient
▪ Substance that is necessary for survival, but that an
organism cannot make for itself
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Organisms and Energy Sources

▪ Producers
▪ Organisms that make their own food using energy and
simple raw materials from the environment
▪ Example: photosynthesis in plants

▪ Consumers
▪ Organisms that get energy and carbon by feeding on
tissues, wastes, or remains of other organisms
▪ Example: animals
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Energy Flow and Material Cycling

 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Organisms Sense and Respond to Change

▪ Organisms keep conditions in their internal environment
within a range that favors cell survival

▪ Homeostasis (恆定作用)
▪ Set of processes by which an organism keeps its internal
conditions within tolerable ranges by sensing and
responding to change
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Response to Stimulation
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Organisms Grow and Reproduce

▪ Organisms grow, develop, and reproduce based on

information encoded in DNA, which they inherit from parents

▪ Growth
▪ Increase in size, volume, and number of cells in
multicelled species

▪ Development
▪ Multistep process by which the first cell of a new individual
becomes a multicelled adult
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Organisms Grow and Reproduce

▪ Reproduction
▪ Process by which parents produce offspring

▪ Inheritance
▪ Transmission of DNA from parents to offspring

▪ DNA (Deoxyribonucleic acid)

▪ Carries hereditary information that guides development
and functioning
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

1.4 How Living Things Differ

▪ Living things differ in observable characteristics, or traits

▪ Classification schemes help us organize what we understand

about Earth’s biodiversity

▪ Biodiversity (生物歧異度)
▪ Scope of variation among living organisms
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Classification Systems 因為不同 所以要分類

▪ Organisms can be grouped based on whether they have a

nucleus

▪ Nucleus (核仁)
▪ Sac with two membranes that encloses a cell’s DNA

▪ One system sorts all organisms into one of three domains:

Bacteria (細菌) , Archaea (古生菌), and Eukarya (真核生物)
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Prokaryotes (原核生物)

▪ Single celled organisms in which DNA is not contained in

a nucleus

▪ Bacterium
▪ A member of the prokaryotic domain Bacteria

▪ Archaeon
▪ A member of the prokaryotic domain Archaea
▪ More closely related to eukaryotes than to bacteria
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Bacteria and Archaea

A) Bacteria are the most numerous B) Archaea may resemble bacteria,

organisms on Earth. Left, a but they are more closely
bacterium with a row of iron crystals related to eukaryotes. These
that acts like a tiny compass; right, are two types of archaea from a
spiral cyanobacteria. hydrothermal vent on the
seafloor.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Eukaryotes (真核生物)

Organisms whose cells typically have a nucleus

▪ Fungus (真菌類)
▪ Eukaryotic consumer that obtains nutrients by digestion
and absorption outside the body
▪ Protists (原生生物)
▪ Eukaryotes that are not plants, animals, or fungi
▪ Plants
▪ Typically a multicelled, photosynthetic producer
▪ Animals
▪ Multicelled consumer that develops through a series of
embryonic stages and moves about during all or part of
the life cycle
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Some Eukaryotes
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

1.5 What is a “Species?”

▪ Taxonomy is the science of naming and classifying species
▪ A species (種名) is a unique kind of organism
▪ A genus (屬名) is a group of species that share unique traits

▪ Every species is given a unique two-part scientific name

consisting of its genus and species
▪ Example: Panthera leo (The lion )

Carl Linnaeus
瑞典植物學者
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Taxa

▪ Each rank, or taxon is a group of organisms that share a

unique set of traits (經分類而成的同類)
▪ Morphological (structural) traits
▪ Biochemical traits
▪ Behavioral traits (response to stimuli)

▪ Each taxon consists of a group of the next lower taxon

▪ Species, genus, family, order, class, phylum, kingdom,
and domain (種、屬、科、目、綱、門、界、域)
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Taxonomic Classification

domain Eukarya Eukarya Eukarya Eukarya Eukarya

kingdom Plantae Plantae Plantae Plantae Plantae
phylum Magnoliophyta Magnoliophyta Magnoliophyta Magnoliophyta Magnoliophyta
class Magnoliopsida Magnoliopsida Magnoliopsida Magnoliopsida Magnoliopsida
order Apiales Rosales Rosales Rosales Rosales
family Apiaceae Cannabaceae Rosaceae Rosaceae Rosaceae
genus Daucus Cannabis Malus Rosa Rosa
species carota sativa domestica acicularis canina
common name wild carrot marijuana apple prickly rose dog rose
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

兩種分類系統:
Two Classification Systems 1. 六界 Six-kingdom
2. 三域 Three-domain

Bacteria Archaea Protists Plants Fungi Animals

A Six-kingdom classification system in which all eukaryotes

have been sorted into one of four kingdoms: protists, plants, fungi, and
animals. The protist kingdom includes the most ancient multi-celled and
all single-celled eukaryotes.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Two Classification Systems (續)

Bacteria Archaea Eukarya

B Three-domain system sorts all life into

three domains: Bacteria, Archaea, and Eukarya.
The Eukarya domain includes all eukaryotes.
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Identifying Species
▪ How do we decide if similar-looking organisms belong to
different species or not?

今昔不同

▪ Early naturalists classified species according to what they

looked like and where they lived

▪ Today’s biologists compare biochemical traits such as

DNA sequence
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Four butterflies, two species

Top row shows two forms of

Heliconius melpomene

Lower row shows two forms of

Heliconius erato
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Biological Species Concept

▪ “Biological species concept”

▪ Ernst Mayr defined a species as one or more groups of

individuals that potentially can interbreed, produce fertile
offspring, and do not interbreed with other groups

恩斯特·瓦爾特·邁爾，出生於德國巴伐利亞的肯普滕，
逝世於美國麻塞諸塞的貝德福德。
是20世紀最主要的演化生物學家之一
，也是一位分類學家、熱帶探險家、鳥類學家、博物學家與
科學史家。
•出生: 西元 1904 年 7 月 5 日, 肯普田
•逝世: 西元 2005 年 2 月 3 日 (享年100歲), Bedford
•獲獎紀錄: 達爾文-華萊士獎章, 美國國家科學獎章生物學獎
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

1.6 The Science of Nature

▪ Critical thinking
▪ Deliberate process of judging the quality of information
before deciding whether or not to accept it

▪ Science
▪ Systematic study of the observable world

▪ Hypothesis
▪ Testable explanation of a natural phenomenon.

▪ Scientific method
▪ Systematically making, testing, and evaluating hypotheses
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

The Scientific Method

 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

The Scientific Method

▪ Prediction
▪ Statement, based on a hypothesis, about a condition that
should exist if the hypothesis is correct

▪ Model
▪ Analogous system used for testing hypotheses

▪ Experiment
▪ Test designed to support or falsify a prediction
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

The Scientific Method

▪ Variable
▪ Characteristic that differs among individuals or over time

▪ Experimental group
▪ Group of individuals who are exposed to a variable

▪ Control group
▪ Group not exposed to the variable being tested.

▪ Data
▪ Factual information from experiments or surveys
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Biological Research
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

1.7 Analyzing Experimental Results

▪ Researchers experiment on subsets of a group, which may

result in sampling error

▪ Sampling error
▪ Difference between results derived from testing an entire
group of events or individuals, and results derived from
testing a subset of the group
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Probability
▪ Researchers try to design experiments carefully in order to
minimize sampling error

▪ Probability
▪ The measure, expressed as a percentage, of the chance
that a particular outcome will occur

▪ Statistically significant
▪ Refers to a result that is statistically unlikely to have
occurred by chance
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Bias in Interpreting Results

▪ Researchers risk interpreting their results in terms of what
they want to find out (bias)

▪ Science is a self-correcting process because scientists

continuously retest and recheck each other’s ideas
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

The Limits of Science

▪ Science is an objective way of describing the natural world

▪ Science does not address subjective questions; moral,

aesthetic, and philosophical standards; or the supernatural
 Pan Lab for Jesus
Laboratory of Transporter Biology, Department of Life Science,
Institute of Bioinformatics and Structural Biology, National Tsing Hua University

Q & A

Thank you very much for your attention.