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Chapter 1

Lecture Outline

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Zombie Parasites

• The study of life reveals fascinating characteristics of living species

• Biology also leads to the development of medicines and research tools that benefit the lives of people

• Example: Neuroparasitology - the study of how parasites control the nervous systems of their hosts.

Examples of Zombie Parasites

Table 1.1 Examples of Zombie Parasites

Host Parasite Description

House cricket (Acheta domesticus)

Horsehair worm (Paragordius varius)

A horsehair worm larva infects a cricket and grows inside it. The cricket is terrestrial, but the adult stage of the horsehair worm is aquatic. When the larva matures into an adult, it alters the behavior of the cricket, causing it to jump into the nearest body of water! As the cricket drowns, an adult horsehair worm emerges.

Spider (Plesiometa argyra)

Wasp (Hymenoepimecis argyraphaga)

A female wasp glues an egg onto a spider’s body. After the egg develops into a larva, the larva pokes a few holes in the spider’s abdomen, which allows it to suck the spider’s blood and also to transfer chemicals into the spider, which control its behavior. The spider stops building its normal orb-shaped web and starts building a web whose geometry is strikingly different: The new web is designed to suspend the larva’s cocoon in the air, where it will be protected from predators.

Various vertebrates, including mice and rats

Protozoan (Toxoplasma gondii)

Toxoplasma gondii is a parasite whose life cycle involves more than one vertebrate host. The definitive host is the cat, which is where T. gondii becomes mature and reproduces sexually. An intermediate host can be any of a variety of vertebrates, including mice and rats, which can ingest the parasite from cat feces. In the intermediate host, the parasite develops and reproduces asexually. To escape an intermediate host, such as a mouse or rat, and move to the definitive host, T. gondii dramatically alters the host's behavior. The infected animal becomes attracted to the smell of cat urine! This makes it more likely to be eaten by a cat and thereby allows T. gondii to enter its definitive host and mature.

Chapter 1

An Introduction to Biology

Key Concepts:

• Levels of Biology

• Core Concepts of Biology

• Biological Evolution

• Classification of Living Things

• Biology as a Scientific Discipline

• Core Skills of Biology

Levels of Biological Organization

• Atoms

• Molecules

• Cells

• Tissues

• Organs

• Organism

• Population

• Community

• Ecosystem

• Biosphere

Figure 1.3: Levels of Biological Organization

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Core Concepts of Biology

• Evolution

• Structure and function

• Information flow, exchange, and storage

• Pathways and transformations of energy and matter

• Systems

Biological Evolution Unity

• All life displays a common set of characteristics

• United by a shared evolutionary history

Diversity

• Life has a diversity of form in diverse environments

Evolutionary History 1

• Life began on Earth as primitive cells between 3.5 to 4 billion years ago (bya)

• Those primitive cells underwent evolutionary changes to give rise to the species of today

• Evolutionary history helps us understand the structure and function of an organism

Evolutionary History 2

• Evolutionary change involves modifications of pre-existing characteristics

• Structures may be modified to serve new purposes

• Example:

Walking limbs were modified into a dolphin’s flipper or a bat’s wing

Figure 1.5: Modification as a Result of Evolution

Two mechanisms of evolutionary change 1

Vertical descent with mutation

• Progression of changes in a lineage

• New species evolve from pre-existing species by the accumulation of mutations

• Natural selection takes advantage of beneficial mutations

Figure 1.6: Vertical Evolution Example

Two mechanisms of evolutionary change 2

Horizontal gene transfer

• Genetic exchange between different species

• Relatively rare

• Genes that confer antibiotic resistance are sometimes transferred between different bacteria species

Figure 1.7: Horizontal Gene Transfer

Bacterial species such as Escherichia coli

Bacterial species such as Streptococcus pneumoniae

Tree or web of life?

• Horizontal gene transfer was an important part of the process that gave rise to modern species

• Tree of life focuses on vertical evolution

• Web of life includes the contribution of horizontal gene transfer

Figure 1.8: The Web of Life

Genomes and Proteomes 1

Genome

The complete genetic makeup of an organism

Genomics

• Techniques used to analyze DNA sequences • Comparison of genomes of different species

Proteome

The complete complement of proteins of an organism

Proteomics

• Techniques used to analyze the proteins of a species • Comparison of proteomes of different species

Genomes and Proteomes 2

The genome carries the information to make the proteome.

Genomic and proteome analysis illuminate the evolutionary history and relatedness of all living organisms.

Classification of Living Things

Taxonomy is the grouping of species based on common ancestry

Three domains of life

• Bacteria- unicellular prokaryote

• Archaea- unicellular prokaryote

• Eukarya- unicellular and multicellular eukaryotes

• Complex cells with a nucleus

• Four kingdoms: • Protista, Plantae, Fungi, and Animalia

Domain Bacteria: Mostly unicellular prokaryotes that inhabit many diverse environments on Earth.

a) Domain Bacteria: Mostly unicellular prokaryotes that inhabit many diverse environments on Earth.

©BSIP/age fotostock

Domain Archaea: Unicellular prokaryotes that often live in extreme environments, such as hot springs.

b) Domain Archaea: Unicellular prokaryotes that often live in extreme environments, such as hot springs.

©Eye of Science/Science Source

Domain Eukarya: Unicellular and multicellular organisms having cells with internal compartments that serve various functions.

c) Domain Eukarya: Unicellular and multicellular organisms having cells with internal compartments that serve various functions.

Protists: Unicellular and small multicellular organisms that are now subdivided into seven broad groups based on their evolutionary relationships.

Plants: Multicellular organisms that can carry out photosynthesis.

Fungi: Unicellular and multicellular organisms that have a cell wall but cannot carry out photosynthesis. Fungi usually survive on decaying organic material.

Animals: Multicellular organisms that usually have a nervous system and are capable of locomotion. They must eat other organisms or the products of other organisms to live.

(protists): ©Jan Hinsch/Getty lmages;(plants): ©Kent Foster/Science Source; (fungi): ©Carl Schmidt-Luchs/Science Source; c(animals): ©Ingram Publishing/age fotostock

How Organisms are Classified

A species is placed into progressively smaller groups that are more closely related

Emphasizes the unity and diversity of different species

Example:

• Clownfish (Amphiprion ocellaris)

Figure 1.11: Taxonomic classification of the ocellaris clownfish

Taxonomic group

The ocellaris clownfish is found in

Approximate time when the common ancestor for this group arose

Approximate number of modern species in this group

Examples

Domain Eukarya 2,000 million years ago

> 5,000,000

Supergroup Opisthokonta 2,000 million years ago

> 1,000,000

Kingdom Animalia 600 million years ago

> 1,000,000

Phylum Chordata 525 million years ago

50,000

Class Actinopterygii 420 million years ago

30,000

Order Perciformes 80 million years ago

7,000

Family Pomacentridae Approximately 40 million years ago

360

Genus Amphiprion Approximately 9 million years ago

Species ocellaris < 3 million years ago

Classification

Binomial nomenclature

• Each species has a unique scientific name

• Genus name capitalized

• Species descriptor is not capitalized

• Both names are italicized

Amphiprion ocellaris = Ocellaris clownfish

Biology as a Scientific Discipline

Science is the observation, identification, experimental investigation, and theoretical explanation of natural phenomena

The Scientific Method is used to test theories

Some scientists also gather information

• “Fact-finding mission”

Biologists investigate life at different levels

Different branches of biology study life at different levels using a variety of tools.

• Ecology, anatomy, physiology, cell biology, molecular biology, etc.

As new tools become available, they allow scientists to ask new questions

Systems biology aims to understand how emergent properties arise, at any level

Figure 1.13 a and b: Biological Investigation at Different Levels

a) Ecology—population/ community/ecosystem levels

b) Anatomy and physiology— tissue/organ/organism levels

a: ©Diane Nelson; b: ©Purestock/SuperStock;

Figure 1.14 c and d: Biological Investigation at the Cell and Molecular Levels

c) Cell biology—cellular levels d) Molecular biology— atomic/molecular levels

c: ©Erik Isakson/Blend Images; d: ©Northwestern, Shu-Ling Z hou/AP Images

Figure 1.13 e: Biological Investigation at the Systems Level

e) Systems biology—all levels, shown here at the molecular level

Systems biologists may study groups of molecules. The microarray shown in the inset determines the expression of many genes simultaneously.

©Andrew Brookes/Corbis/Getty Images; (inset): ©Alfred Pasieka/Science Source

Hypothesis or Theory? 1

Hypothesis

• A proposed explanation for a natural phenomenon

• Based on previous observations or experiments

• Hypotheses must make predictions that can be shown to be correct or incorrect (must be testable)

• Additional observations or experiments can support or reject a hypothesis, but a hypothesis is never really proven

Example:

• “Maple trees drop their leaves in autumn because of shortened hours of sunlight”

Hypothesis or Theory? 2 Theory

• Broad explanation of some aspect of the natural world that is substantiated by a large body of evidence

• Allows us to make many predictions

• Also can never be proved true, but due to overwhelming evidence, may be very likely to be true

Two key attributes of a theory:

• Consistent with a vast amount of known data

• Able to make many correct predictions

Example

• “DNA is the genetic material”

• Overwhelming body of evidence supports this theory

Understanding biology

Curiosity is the key

No rigid set of steps

Two general approaches

• Discovery-based science

• Hypothesis testing

Discovery-based science

Collection and analysis of data without the need for a preconceived hypothesis

Goal is to gather information

• Test drugs to look for action against disease

• Sequence genomes and proteomes

Often leads to hypothesis testing

Hypothesis Testing

Five stages

• Observations are made regarding natural phenomena.

• These observations lead to a testable hypothesis that tries to explain the phenomena.

• Experiments are conducted to determine if the predictions are correct.

• The data are analyzed.

• The hypothesis is accepted or rejected.

These steps comprise the Scientific Method

Figure 1.14: Steps of the Scientific Method

1. OBSERVATIONS The leaves on maple trees fall in autumn when the days get colder and shorter.

2. HYPOTHESIS The shorter amount of daylight causes the leaves to fall.

3. EXPERIMENTATION Small maple trees are grown in 2 greenhouses where the only variable is the length of light.

Control group: Amount of daily light remains constant for 180 days.

Experimental group: Amount of daily light becomes progressively shorter for 180 days.

4. THE DATA

A statistical analysis can determine if the control and the experimental data are significantly different. In this case, they are.

5. CONCLUSION The hypothesis cannot be rejected.

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Common features Data are often collected in parallel

• Control and experimental groups

• Differ by only a single variable

Data analysis

• Apply statistical analysis to determine if the control and experimental groups are different because of the single variable that is different

• Are differences statistically significant? • If the two sets are found not to be significantly

different, we must reject our hypothesis. • If the two sets of data are significantly different, we

accept our hypothesis (though it is not proven)

Example: Cystic Fibrosis 1

• Affects about 1 in every 3,500 Americans

• Persons with CF produce abnormally thick and sticky mucus that obstructs the lungs and pancreas

• Average lifespan for people with CF is currently in their mid- to late 30s

Example: Cystic Fibrosis 2

• In 1945, Dorothy Anderson determined that cystic fibrosis is a genetic disorder

• In 1989, research groups headed by Lap-Chi Tsui, Francis Collins, and John Riordan identified the CF gene

• Discovery-based science, not hypothesis-testing, found the CF gene

Hypothesis for function of CF gene 1

Hypothesis: The CF gene encodes a protein that transports chloride ions  Cl across the membrane of cells

Led to experiments to test normal cells and cells from CF patients for ability to transport Cl

• CF cells were found defective in chloride transport • Transferring a normal CF gene into cells in the lab

corrects this defect

Chloride transport hypothesis is accepted

Figure 1.15: CFTR Gene and Hypothesis Testing

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Hypothesis for function of CF gene 2 • Results supported the hypothesis that the CF gene

encodes a protein that transports Cl  across the plasma

membrane

• A mutation in this gene causes it to encode a defective

transporter protein, leading to a salt imbalance

• This imbalance affects water levels outside the cell,

which explains the thick and sticky mucus in CF patients

• In this example, hypothesis testing has provided a way

to accept or reject an idea regarding how a disease is

caused by a genetic change

Biology is a Social Discipline

• Within a lab, students, postdocs, technicians, and the PI work together

• Different labs often collaborate

• At meetings, scientists discuss new data – and debate!

• You can discuss science without having “all the answers”

• Science is a never-ending series of questions

Figure 1.16: The Social Aspects of Science

Core Skills of Biology

• Ability to apply the process of science

• Ability to use quantitative reasoning

• Ability to use models and simulation

• Ability to tap into the interdisciplinary nature of science

• Ability to communicate and collaborate with professionals in other disciplines

• Ability to understand the relationship between science and society

Features of This Textbook • Feature Investigations allow you to apply the

process of science.

• BioTIPS help you refine and apply your problem solving skills.

• Quantitative reasoning is a key component of the Feature Investigations and many questions.

• Modeling Challenges allow you to interpret a given model or propose your own model based on a scenario or data.

• “Connections” and “Science and Society” highlight the interdisciplinary nature of science

Model-Based Learning

Scientific model

• is a conceptual, mathematical, or physical depiction of a real-world phenomenon.

• In biology, models are testable ideas that are usually derived from observations and experiments.

Model-based learning allows students to evaluate or generate models to enhance understanding and improve critical thinking skills.

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