Chapter 1.

SCIENTIFIC METHOD

 Evolution - overarching theme of biology. Evolution accounts for the unity and
diversity of life.
 Emergent properties - Characteristics that emerge as you ascend the biological
organizational chain.
(e.g. Photosynthesis can only occur when the molecules are arranged in a specific
way inside a complete chloroplast. Parang kapag gumawa ka ng bike, hindi mo
pwedeng ihagis lang sa cart yung wheels, chains, handle, frame, seat, at brakes
tapos tawaging bicycle yun. Each component has a different property but when
combined together they create another characteristic unique to the combined item
but logically relevant to its parts.)
 Reductionism - reduction of complex systems into simpler parts. Used in biology to
understand life processes.

Levels of Organization
Molecule < Organelle < Cell < Tissue < Organ < Organ Systems < Organism <
Population < Community < Ecosystem < Biosphere

 Population – 1 kind of species in 1 area at the same time (e.g. a pride of lions
living in the Sahara)
 Community – all organisms that are interacting in 1 area at the same time
(e.g. hyenas, trees, bacteria, zebras, giraffes, etc. living in the Sahara)
 Ecosystem – all organisms and all abiotic factors in an area that functions as
one unit. (e.g. Trees, rocks, winds, monkeys, ants in the Sahara)
Ecosystem Dynamics
1. Nutrient Cycling - nutrients that can be found in an ecosystem are
continuously recycled (e.g. Tree grows -> uses nutrients -> dies ->
decomposed by decomposers -> another tree uses the fertilizer -> Tree grows
-> repeat)
2. One-way flow of sunlight (energy) - sunlight -> producers -> consumers
 Biosphere - all regions of Earth that sustain life (e.g. Rainforest, Tundra,
Tokyo, Underground Caves etc)

 Systems Biology - study of complex biological systems through construction of

dynamic models.
 Why is it used? Successful models will show how the alteration of one or more factors
will affect other components or the entire system.
(e.g. How does the gradual increase of atmospheric carbon dioxide alter ecosystems
and the entire biosphere?)
 Systems Biology at the level of Cells and Molecules
o A cell of a fruit fly was observed. They created a model that mapped out the
interactions of proteins in that cell.

o How they applied systems biology:

1)Inventory as many parts as possible (all known genes and proteins in a cell).
 2)Investigate how they behave in relation to others in a working system.
3)Pool all the data using software.

 3 Important Contributors to Systems Biology:

1. "High-throughput" technology - tools that are capable of processing and analyzing

high volumes of data (e.g. Automatic DNA sequencing machines)
2. Bioinformatics - the use of computational tools to store, organize and analyze data
gathered by "high-throughout" technology
3. Interdisciplinary Research Teams

Themes in Biology

1. Organisms interact with their environments, exchanging matter and energy.

 In any ecosystem, it is observed that the organisms actively and continuously
interact with its environment. Ecosystem dynamics explains that all nutrients,
minerals and energy will cycle through the organisms and the environment
through interaction (grass eaten by sheep, sheep eaten by wolf, wolf dies of
old age, fertilizes the soil, feeds the scavengers, decomposers and producers,
methane dissipates from the decomposing body into the air).
 The exchange of energy necessary for these interactions involve the
transformation of one energy to another and these transformations generate
heat.
 Energy enters an ecosystem as light and exits as heat.

2. Structure and function are correlated at all levels of biological organization.

 This theme focuses on this one phrase: "Form fits function"
 Analyzing a biological structure by observing its form can tell us what it does
and how it works. For example, a leaf is shaped flat and thin to maximize the
amount of sunlight that can be captured by its chloroplasts. Conversely, one
can also deduce the form of a structure by knowing its function. (e.g. Xylem
transports water and nutrients from roots to leaves thus we can assume that it
is long and pipe-like.)

3. Cells are an organism's basic unit of structure and function.

 Cells determine structure and function in all organisms
 All cells share these characteristics:
o Enclosed in a membrane that regulates the passage of materials
between the cell and its surroundings
o Uses DNA as its genetic information
 2 types of Cells
1. Eukaryotic - has nucleus, membrane-enclosed organelles
2. Prokaryotic – lacks nucleus, membrane-enclosed organelles

4. The continuity of life is based of heritable information in the form of DNA.

  DNA (deoxyribonucleic acid) – made up of two long chains called strands, in
double helix; contains genes; is made up of nucleotides (A,C,T,G); Its molecular
structure allows it to store information.
 Genomics - investigation of whole sets of genes/ study of multiple sets of genes
 Proteomics - study of whole sets of proteins (Proteome - entire set of proteins
expressed by a given cell, tissue or organ)
 Gene expression - information in a gene directs the manufacture of a cellular
product
Transcription -> Translation -> Replication
 Enzymes - catalyzes processes
 Genome - entire "library" of generic information

5. Feedback mechanisms regulate biological systems.

 Feedback- a mechanism of most biological processes to self-regulate
 Negative fb - end product slows down the biological process; most common form of
feedback
 Positive fb - end product speeds up
 CORE THEME: Evolution
o Taxonomy - branch of biology that deals with naming and classification
o Organizing the Diversity of Life:
- Species - (Smallest group)
- Genus
- Family
- Order
- Class
- Phylum
- Kingdom
- Domain
o 3 domains of life:
- Bacteria - prokaryotes
- Archaea - prokaryotes
- Eukarya - eukaryotes
o Unity of Life
Even though organisms are diverse in type and structure, it is still possible to find
some similarities between organisms that are classified into different domains.
(e.g. Cilia of paramecium and cilia of human windpipe cells. These very different
organisms share the same architecture of their cilia.)

Charles Darwin and the Theory of Natural Selection

 Charles Robert Darwin - wrote a book entitled On the Origin of Species by Means
of Natural Selection published on November 1858
 2 main points of the book:
1. "Descent with modification" - species arose from a succession of ancestors

2. Natural Selection - evolutionary mechanism which states that organisms with

the traits most suited to the environment will be more likely to survive and
 reproduce than less fit individuals. Over time, individuals with the most
advantageous traits would populate the environment.
 He formed the theory of natural selection by using existing observations in the
scientific community which were: individuals in a population have varying traits,
populations create more offsprings than what can be supported by the environment
and species generally suit their environments.
 Darwin proposed that natural selection, by its cumulative effects over long periods of
time, could cause an ancestral species to give rise to two or more descendant
species.

*Kung may og na organism na nagreproduce tapos na-isolate yung mga populations na yun,
magsusurvive yung mga may traits na bagay sa environment kung saan sila na-isolate at
sila naman yung magrereproduce kaya magiging slightly different sila from the original kasi
mayroon silang traits na wala yung og organism. Pwede ito mangyari sa iba-ibang
environments kaya pwede magkaroon ng maraming derivatives ng og organism*

Scientific Inquiry
 Inquiry - scientists make and record observations (data)
 Hypothesis - a testable prediction
 Theory - broad in scope; able to create new, testable hypotheses; supported
by a large body of evidence. Not to be equated to a hypothesis
 Inductive Reasoning - analyze these observations to conclude a hypothesis
 Deductive Reasoning - If....Then; Used to test a hypothesis through
experimentation
 Experiment - a scientific test conducted under controlled conditions
 Controlled Experiment - designed to compare an experimental group with a
control group. Unwanted factors are cancelled out by using the control
groups.
 Variables - feature/quantity that varies in an experiment
o Independent variable - factor being manipulated
o Dependent variable - factor being measured
 Model Organism - easy to grow in the lab, lends itself particularly well to
questions being investigated.