Engineering and Biology

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Circuit Simulation of Genetic Networks

(A) Circuit diagram of a

hypothetical genetic network. Bold
line indicates the RNAP path on the
DNA after binding at PA. Promoter
PC is ON when protein signal A is
ON; that is, at effective
concentration at its site of action.
Switch T, which is usually open but
closes to permit RNAP passage in
the presence of the protein signal
C, models terminator site function.
(B) Timing diagram of signals A, B,
and C. Time lags depend on the
gene spacing on the DNA,
transcription rates, the time
required for accumulation of an
effective signal concentration, and
protein decay rate constants.

McAdams and Shapiro (1995) Science 269:650-656

Biology is in your
BLOOD
Structural changes in Heme
Estimated time line of global evolution and spread of HIV types, groups, and subtypes
Enlarged parts of map show the main disease epicentres. The time line indicates the key events in the evolution of HIV-1
groups M, N, and O and of HIV-2. CRF=circulating recombinant form.
Tebit and Arts (2011), The Lancet Infectious Diseases 11:45-56
 Climate Change

The new NASA global data set combines historical measurements with data from
climate simulations using the best available computer models to provide forecasts of
how global temperature (shown here) and precipitation might change up to 2100 under
different greenhouse gas emissions scenarios.
Credits: NASA
Rising World Population
 Why a Study of Biology is
Important

 To be an informed citizen
 An understanding of biology is important to
address a number of social issues today.
– DNA testing
– Birth control
– Global warming
– AIDS

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 Chapter 1

1-10
The word Biology comes from two Greek words:

1. BIOS meaning LIFE,

and
2. LOGOS meaning A STUDY

So Biology could mean A study of life

The study of living organisms, divided into

many specialized fields that cover their
morphology, physiology, anatomy, behavior,
origin, and distribution.
Biology has many different areas
of study
 Anatomy
 Biochemistry
 Botany
 Ecology
 Genetics
 Microbiology
 Physiology
 Zoology

1-12
 So then, what is biology?

 Biology is the science that deals with life.

 What is science?
– A process used to solve problems and
understand natural events
– Involves the scientific method

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
The Scientific Method in Action
 Observation
John watches his
grandmother bake
bread. He asks his
grandmother what
makes the bread rise.
She explains that yeast
releases a gas as it
feeds on sugar.
 Problem/Question

John wonders if the

amount of sugar used
in the recipe will affect
the size of the bread
loaf?
Formulate a Hypothesis
After talking with his
teacher and
conducting further
research, he comes
up with a hypothesis.
“If more sugar is added,
then the bread will rise
higher.”
 Hypothesis

The hypothesis is an educated

guess about the relationship
between the independent and
dependent variables.
The Scientific Method in Action
 Size of Baked Bread (LxWxH) cm3

Size of Bread Loaf (cm3)

Trials
Amt. of Average
1 2 3
Sugar (g.) Size (cm3)

25 768 744 761 758

50 1296 1188 1296 1260

Control group

100 1188 1080 1080 1116

250 672 576 588 612

500 432 504 360 432

 Size of Baked Bread (LxWxH) cm3

Size of Bread Loaf (cm3)

Trials
Amt. of Average
1 2 3
Sugar (g.) Size (cm3)

50 1296 1440 1296 1344

Control group

60 1404 1296 1440 1380

70 1638 1638 1560 1612

80 1404 1296 1296 1332

90 1080 1200 972 1084

 Conclusion

John finds that 70g.

of sugar produces
the largest loaf.
His hypothesis is
accepted.
 Communicate the Results

John tells his

grandmother about
his findings and
prepares to present
his project in
Science class.
 The Scientific Method

 A way of gaining information about the world

that involves
– forming possible solutions to questions.
– rigorous testing to determine if the solutions are
supported.
– continual checking and rechecking to make sure
that previous conclusions are still supported.
– modification of unsupported conclusions.

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 Components of the Scientific Method

 Observation
 Questioning and exploration
 Forming and testing hypotheses
 Evaluation of new information
 Review by peers

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 Observation, Questioning and
Exploration

 An observation is a thoughtful and careful

recognition of an event or a fact.
 The careful observation of a phenomenon
leads to a question.
– How does this happen?
– What causes it to occur?
 The question must be testable.
 Scientists then explore scientific publications
to find any information that has been gathered
about the question.

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 Constructing Hypotheses

 Once the question is asked, scientists

propose answers.
 These answers are hypotheses.
 Hypotheses must:
– be logical
– account for all current information
– be testable
– make the least possible assumptions

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 Testing Hypotheses

 Hypotheses need to be tested to see if they

are supported or disproved.
– Disproved hypotheses are rejected.
– Hypotheses can be supported but not proven.
 There are several ways to test a hypothesis:
– Gathering relevant historical information
– Make additional observations from the natural
world.
– Experimentation

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 Experimentation

 An experiment is a re-creation of an
occurrence.
– It tests whether or not the hypothesis can be
supported or rejected.

 Experiments must be controlled.

– This means that all aspects except for one variable
must be kept constant.
– They usually include any two groups.
 Experimental group: variable is altered
 Control group: variable is not altered

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 Experimental Design

 The variable that is altered is called the independent

variable.
– Experiments should have only one independent variable.
 The variables that change in response to the
independent variable are called dependent variables.
– Changes in the dependent variables are documented as
data.
 Data from the experiment is analyzed and
hypotheses are rejected and revised or supported.

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 Experimental Data
 Experiments must:
– use large numbers of subjects or must be
repeated several times (replication).
– be independently reproducible.
–

 The validity of experimental results must:

– be tested statistically.
– be scrutinized by other scientists.

 If the hypothesis is supported by ample

experimental data, it leads to a theory.
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The Scientific Method in Action
 A Sample Experiment
 Hypothesis: Male sex hormones produced by the
testes stimulate male birds to sing.
 Experimental group: Male birds with testes removed
at birth.
 Control group: Male birds subjected to a similar
surgery that were allowed to develop normally with
testes.
 Independent variable: presence or absence of
testes.
 Dependent variable: presence of singing behavior.
 Data: Male songbirds without testes do not exhibit
singing behavior.
 Conclusion: Hypothesis is supported.
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 Theory

 A theory may be defined as a widely accepted,

plausible general statement about a
fundamental concept in science.

– The germ theory states that infectious diseases are

caused by microorganisms.
 Many diseases are not caused by microorganisms, so we
must be careful not to generalize theories too broadly.

– Theories continue to be tested.

 Exceptions identified
 Modifications made

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 A Scientific Law

 A scientific law is a uniform and constant fact of nature

that describes what happens in nature.
– An example: All living things come from pre-existing living things.

 Scientific laws promote the process of generalization.

– Inductive reasoning
– Since every bird that has been studied lays eggs, we can generalize
that all birds lay eggs.

 Once a theory becomes established, it can be used to

predict specific facts.
– Deductive reasoning
– We can predict that a newly discovered bird species will lay eggs.

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 Scientific Communication

 Data is shared with the scientific

community through research
articles published in scientific
journals.
– These articles are usually
scrutinized by other scientists
before they are published.

 Scientists present preliminary

data at conferences.

 Scientists collaborate directly by

phone and e-mail.

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 Fundamental Attitudes in Science

 Scientists must distinguish between opinions and

scientific facts.
– Scientists’ opinions may become facts if supported by data.

 A good scientist must

– be skeptical.
– not be biased.
– be honest in analyzing and reporting data.

 The critical difference between science and non-science

is that in science, one can test the
principle. In non-science, one may not be able to.

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Theoretical vs. Applied Science
 Theoretical vs. Applied Science

 Initially, some scientific data seems to be purely

informational and not very practical.

 Practical applications usually follow the

discoveries of basic science.

– The discovery of the structure of DNA has

led to new drug treatments for many
diseases.
– The discovery of microorganisms has led to
a dramatic decrease in infectious disease
and food preservation.
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 Non Science

Science
 Science vs. Nonscience

 Scientists continually challenge and test

principles to determine cause-and-effect
relationships.
– Biology, Physics, Chemistry, Astronomy

 Nonscientists cannot test their hypotheses

directly and often cannot establish cause-
and-effect relationships.
– History, Literature, Philosophy, Art, Sociology,
etc.

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 Pseudoscience
 A deceptive practice that
uses the language of
science to convince
people into thinking that
a claim has scientific
validity.
– Marketing claims of
nutritional supplements.
– Marketing claims of
organic foods.

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 Limitations of Science

 The scientific method can only

be applied to questions that have
a factual base.
 Questions of morality, values,
social issues and attitudes
cannot be tested scientifically.
 Science is limited by scientists.
– People are fallible.
– The sun orbits the earth.
 But, science is self-correcting.
– New data shapes new
hypotheses.
– The earth rotates on its axis, so
maybe the earth orbits the sun.

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 The Science of Biology

 Biology is the study of living things.

 Theoretical biology
– Evolutionary biology, animal behavior

 Applied biology
– Medicine, crop science, plant breeding, wildlife
management

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 What makes something alive?

 Living things can manipulate energy and

matter.

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 Characteristics of Living Things

 Metabolic processes
– Organisms gain and store energy in the
chemical bonds in the nutrients they take in.

 Generative processes
– Organisms grow by increasing the number
of cells.
– Organisms reproduce either sexually or
asexually.
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 Characteristics of Living Things

 Responsive processes
– Organisms react to changes in their
environment.
 Irritability:
the ability to recognize that
something in its surroundings has changed (a
stimulus) and respond to it quickly.
 Individual adaptation: a longer term response
to an environmental change.
 Evolution: changes in a population over time.

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 Characteristics of Living Things

 Control processes
– Enable organisms to carry out metabolic
processes in the right order.
 Coordination: Enzymes coordinate metabolic
reactions.
 Regulation: Enzymes are regulated in order to
maintain homeostasis.

 Unique structural organization

– Organisms are made of cells.

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 2 Ecosystems Zooming in
3 Communities
on life
4 Populations
1 5 Organisms
Biosphere

6 Organ
Systems
and
Organs
10 Molecules and Atoms

9 Organelles
Atom

Nucleus
8 Cells 7
Tissues
 Levels of Biological Organization

 Biosphere—the worldwide ecosystem.

 Ecosystem—communities that interact with
one another in a particular place.
 Communities—populations of different
organisms interacting with each other in a
particular place.
 Population—a group of individual organisms in
a particular place.
 Organism—an independent living unit.

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 Levels of Biological Organization

 Organ system—many organs that perform a particular

function.
 Organ—many tissues that perform a particular function.
 Tissue—many cells that perform a particular function.
 Cell—simplest unit that shows characteristics of life.
 Molecules—specific arrangements of atoms.
 Atoms—the fundamental units of matter.

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 The Significance of Biology in our
Lives
 Biology has significantly contributed to our
high standard of living.

 For example:
– Advanced food production
– Significant progress in health
– Advances in disease control
– Advances in plant and animal breeding
– Advances in biotechnology
– Progress in genome studies
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 Technology drivers of the
Bioscience revolution
 Gene sequencing
– sequencing of genomes of viruses and bacteria to help
fight against infection
 The development of molecular techniques
– gene chip arrays to determine gene activity
 Advances in imaging techniques
– fluorescence to observe genes/proteins in real time
 The IT revolution
– Bioinformatics
 Nanotechnology
– Nanobiosensors and drug delivery methods
 Hot growth potential sectors: new and
emerging areas

 Healthcare
 Biofuels and green/clean tech. energy
 Personalized medicine
 Telemedicine, mobile HC apps.
 Healthcare informatics (i.e. electronic health
records
 Bioinformatics (personalized medicine)
 Data management, bio-IT

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