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7/28/2019 BI6101 L01 Overview
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Overview of the
Life Sciences
About Life, The Life Sciences, and theBiologists Way of Life!
BI6101 Introductory Biology
MSc Bioinformatics, AY2012/2013, July Semester
Lecture 1 - Timothy Tan
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Map of the HumanGenome?
You are here
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Map of the HumanGenome?
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Source: Newsweek, August 2001
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What are the Life Sciences?
Life sciences refer to scientific study of the living world as awhole, a new synthesis of several traditional scientificdisciplines including biology, zoology, and botany, andnewer, more specialised areas of study such as biophysics,sociobiology, biotechnology, biopharmaceuticals, tissueengineering, biostatistics, bioinformatics, etc.
This approach has led to many new ideas and discoveriesas well as to an emphasis on ecology, the study of livingorganisms in their natural environments.
Broadly speaking, life sciences include any study orresearch discipline that contributes to the understanding oflife processes.
From Singapore Science Centre Q&Ahttp://www.science.edu.sg/ssc/detailed.jsp?artid=79&type=6&root=4&parent=4&cat=39
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Word Cloud generated by wordle.net from text on http://en.wikipedia.org/wiki/Life_sciences
Life Sciences = Biology ?
WhataretheLifeSciences?
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Taking an IntegrativeApproach to the Teaching of
Life SciencesWhataretheLifeSciences?
L01-7
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www.sciencecartoonsplus.com
WhataretheLifeSciences?
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ScienceSilo Mentality vs.an Integrated Approach?
http://www.flickr.com/photos/tim_best_1972/2925719953/
L01-9
WhataretheLifeSciences?
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BI6101
BI6101 - Foundations
Only selected key topics will be covered:
Molecular Biology, Biotechnology
Cell Biology, Reproduction, Cellular Energetics
Classical Genetics, Population Genetics
Developmental Biology
Ecology, Biodiversity
Evolution, Molecular Evolution
Some classical biology (botany, zoology)
(Human Physiology)
Hidden curriculum
Ethical, Legal & Social Issues (ELSI)
Self-directed learning, critical evaluation of information
L01-10
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BI6101 Course Structure
Molecular
Building Blocks
Molecular Genetics
Cell
Structure & Function Mitosis & Meiosis (Cell Cycle)
Cellular Energetics (Biochemistry)
Systems
Classical Genetics Developmental Biology
Ecology & EvolutionL01-11
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Biology
Studying the basics - and the basis -of life
L01-12
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Biology as a Science
Biologists tend to:
Classify
Compare
Ask Why? and How?
Formulate theories based on observations to explainnatural phenomena
Adopt a hypothesis-driven methodologyL01-13
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Biologyas
aScience
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http://home.comcast.net/~fsteiger/theory.htm
Biologyas
aScience
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http://www.cs.msstate.edu/~hualin/acss.htmlhttp://ink.primate.wisc.edu/~assay/bioassay.html http://bbu.uwcm.ac.uk/html/research/bioinfo.htm
in vivoin life - studies in living organism
in vitroin glass - studies on living cells orbiological processes in the lab
in silicoin silicon - computational studies,simulations, ie. bioinformatics
Biologyas
aScience
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Bio-XandX-omics
Genomics
DNA: molecular genetics
Whats hidden in junk DNA ?
Transcriptomics
RNA: messenger, ribozyme, riboswitch, antisense
Proteomics
Study of Proteins
Metabolomics
Protein-Protein interactions, cellular function
Epigenetics
Non-inheritable interactions between Proteins, DNAand RNA. Source of complexity and individuality?
Et cetera
L01-18
Biologyas
aScience
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BI6101 aims to provide framework to understandthe Bio in Bioinformatics and other Bio-X fields
L01-19
Word Cloud generated by wordle.net from text on http://en.wikipedia.org/wiki/Bioinformatics
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http://www.lsi.us.es/~isanepo/research.html
Scope of Bioinformatics?
Bioinformatics (BI) is all aboutcollecting, integrating and processingbiologically-derived data,to generate
useful and understandableinformation
Whats in a name?
bioinformatics biological informatics
computational biology
in silico biology
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Molecular BI /Sequence BI
L01-21
atgcatgt
agctgatg
catgcatg
ctagctgtgtatgtct
aatctatta
gcgcggc
gctatcgt
Wikimedia Commons; nexomics.com; semanticlifescience.wordpress.com
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Structural BI
L01-22
http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb2_2.html
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http://abeautifulwww.com/2008/05/29/network-visualization-for-systems-biology/
Systems Biology
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Biomedical Informatics
L01-24
Bioscience
Medicine
Informatics
BioinformaticsBiomedical
Science
Biomedical
Informatics
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So what i s Life?
L01-25
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Defining Life
How do we know this is a living thing?
Feeds
GrowsBreathes
Reproduces
Excretes
Moves
Responds
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Characteristics of Living Things
Growth and development
Reproduction
Respond to Stimuli
Interactions with others and environment Adaptation (Evolution)
Made up of cells
Have nucleic acids as genetic material Acquisition and conversion of energy
Have structure and organisation
But
L01-27
De
finingLife
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http://post.queensu.ca/~forsdyke/prions.htm
Prions
Fred Murphy, CDCSARS Virus
Made up of cells
Have nucleic acids
De
finingLife
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Themodynamics
Entropy generaltendency towardsdisorder / randomness Resulting in lower energy state (energy is released)
things fall apart
ENERGY is needed to create and maintainstructure
Living things are able to use energy to maintainor decrease/reverse entropy
Building biomass (more complex molecules fromsimpler molecules)
L01-29
http://www.sciencecartoonsplus.com/
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... life feeds on negative entropy
the essence of life isthe information in genes
Erwin Schrdinger, What is Life?(1944)
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Information Theory of Life
Encoding of Information
Complexity, not chaos
Confers characteristics
Information Structure Function
Transmission ofInformation
Characteristics can beinherited (Heredity)L0
1-31
Jane Ades, NHGRI
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Life Support
The Prerequisites for Life to Exist
Liquid water (and its peculiar properties!)
Energy (heat)
Organic molecules
contain carbon, hydrogen and oxygen atoms
Other factors that support life
pH (acid, neutral, alkaline)
salinity (concentration of various ions/salts) temperature
redox conditions (reduction-oxidation)
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Some Essential
Biological Concepts
L01-33
www.sciencecartoonsplus.com
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atoms
molecules
macromolecules
cells
tissues
organs
organisms
populations
communitiesecosystems
Hierarchy of Life
organelles
BIOSPHERE
Levels of Biological Organisation
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The Tree of Life
All life is inter-related and descended from acommon ancestor
ie. life begets life, life comes from life
Therefore, there is inherent unity in thediversity of life
The ancestry of all living things can be traced
How?
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Dynamic Tree of Life -http://www.discoverlife.org/mp/20m?tree=Life&flags=all:
L01-36
http://genetics.nbii.gov/systematics.html
http://www.discoverlife.org/mp/20m?tree=Life&flags=all:http://www.discoverlife.org/mp/20m?tree=Life&flags=all:7/28/2019 BI6101 L01 Overview
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Traditional Lineage
Purves et al., Life: The Science of Biology
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A Newer Lineage
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Five Kingdom Classification
KINGDOM STRUCTURAL ORGANISATIONTYPES OF
ORGANISMS
NAMED
SPECIES
ESTIMATED
TOTAL
SPECIES
Monera small, simple single prokaryotic cell(nucleoid is not enclosed by amembrane); some form chains or mats
bacteria, blue-greenalgae, and spirochetes
4,000 1,000,000
Protista large, single eukaryotic cell (nucleus isenclosed by a membrane); some formchains or colonies
protozoans and algaeof various types
80,000 600,000
Fungi Unicellular, multicellular filamentous formwith specialisedeukaryotic cells
fungi, molds,mushrooms, yeasts,mildews, and smuts
72,000 1,500,000
Plantae multicellular form with specialisedeukaryotic cells; do not have their ownmeans of locomotion
mosses, ferns, woodyand non-woodyflowering plants
270,000 320,000
Animalia multicellular form with specialisedeukaryotic cells; have their own meansof locomotion
sponges, worms,insects, fish,amphibians, reptiles,birds, and mammals
1,326,239 9,812,298
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Monera
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/science/scimeth3.htm
http://www.hhs.gov/asphep/presentation/images/bacteria.jpg
Unicellular bacteria and archaea
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Protists
Unicellular organismsplant-like,
animal-like
fungus-like
L01-41
http://megasun.bch.umontreal.ca/protists/gallery.html
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Fungi
Unicellular, Multicellular
Consumers that digest food externally
L01-42
http://www.ndsu.nodak.edu/instruct/mcclean/plsc431/science/scimeth3.htmhttp://elib.cs.berkeley.edu/photos/fungi/
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Plants
Multicellular
Producers (Photosynthesis)
L01-43
http://elib.cs.berkeley.edu/photos/flora/
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Animals
Multicellular, Move about
Consumers that ingest food
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Prokaryotes and Eukaryotes
Prokaryotes Bacteria and Archaea (Monera)
Latin: Pro before; karyo cell nucleus
Does not have a true nucleus
DNA lies within nucleoid region
Eukaryotes
Everything else!
Latin: Eu true; karyo cell nucleus Has a membrane-bound nucleus
DNA is kept entirely within the nucleusL01-45
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http://www.phschool.com/science/biology_place/biocoach/cells/common.html
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Learning Resources
Dolan DNA Learning Center http://www.dnalc.org/
DNA From the Beginning
http://www.dnaftb.org/
DNA Interactive http://www.dnai.org/
Genetic Science Learning Center
http://gslc.genetics.utah.edu/
National Centre for Biotechnology Education http://www.ncbe.rdg.ac.uk/
Online Biology Book http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.html
L01-47
http://www.dnalc.org/http://www.dnaftb.org/http://www.dnai.org/http://gslc.genetics.utah.edu/http://www.ncbe.rdg.ac.uk/http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.htmlhttp://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookTOC.htmlhttp://www.ncbe.rdg.ac.uk/http://gslc.genetics.utah.edu/http://www.dnai.org/http://www.dnaftb.org/http://www.dnalc.org/