CHAPTER 1

Life & Science

Unit 1 Week 1 Week 2 Week 3Th Tu Th Tu Th Tu Th

22-Jan 27-Jan 29-Jan 3-Feb 5-Feb 10-Feb 12-FebLecture Ch1, 2 Lab 1 Ch 2,3 Ch 3 Ch 4 Ch 4,5

Quiz/Test Q 1 Q 2 Test 1Homework Due HW1,2 Reading1 HW3 Reading2

Your First Classwork.

The Inner Life of a Cell.Please take out out a piece of paper and a pen.

Write down anything that you recognize, or any thoughts that come to your mind as you watch.

Within the electron cloudScale: 10-12 meters = 1 pm = 1 picometerThe inner electron cloudScale: 10-11 meters = 10 pm = 10 picometers

Carbon's outer electron shellScale: 10-10 meters = 100 pm = 100 picometers The molecules of DNA Scale: 10-9 meters = 1 nm = 1 nanometer

DNA within a virus Scale: 10-8 meters = 10 nm = 10 nanometers A virus Scale: 10-7 meters = 100 nm = 100 nanometers

Virus on a bacteriumScale: 10-6 meters = 1 µm = 1 micrometer Bacteria Scale: 10-5 meters = 10 µm = 10 micrometers

Pollen Scale: 10-4 meters = 100 µm = 100 micrometers A bee's eye Scale: 10-3 meters = 1 mm = 1 millimeter

A bee's headScale: 10-2 meters = 1 cm = 1 centimeterA lily and a bee Scale: 10-1 meters = 10 cm = 10 centimeters

The one-meter square Scale: 100 meters = 1 meterA pond with lily pads Scale: 101 meter = 10 meters

Japanese Tea Garden Scale: 102 meters = 100 meters Golden Gate ParkScale: 103 meters = 1 km = 1 kilometer

San Francisco Scale: 104 meters = 10 km = 10 kilometers The San Francisco Bay AreaScale: 105 meters = 100 km = 100 kilometers

CaliforniaScale: 106 meters = 1 Mm = 1 megameter North and Central America Scale: 107 meters = 10 Mm = 10 megameters

Earth Scale: 108 meters = 100 Mm = 100 megameters Earth and Moon Scale: 109 meters = 1 Gm = 1 gigameter

Four days in July Scale: 1010 meters = 10 Gm = 10 gigametersVenus, Earth, and MarsScale: 1011 meters = 100 Gm = 100 gigameters

The orbit of Jupiter Scale: 1012 meters = 1 Tm = 1 terameter The Solar System Scale: 1013 meters = 10 Tm = 10 terameters:

Sol Scale: 1014 meters = 100 Tm = 100 terameters Sol Scale: 1015 meters = 1 Pm = 1 petameter Sol Scale: 1016 meters = 10 Pm = 10 petameters (1ly)

Stars within 50 light yearsScale: 1018 meters = 1 Em = 1 exameter (~100 light years)The nearest stars Scale: 1017 meters = 10 Pm = 100 petameters (~10 light years)

Quarks Scale: 10-16 meters = 100 am = 100 attometers Within the proton Scale: 10-15 meters = 1 fm = 1 femtometer

The carbon nucleusScale: 10-14 meters = 10 fm = 10 femtometersThe nucleusScale: 10-13 meters = 100 fm = 100 femtometers

Scale: 1019 meters = 10 Em = 10 exameters (~1 000 light years) The stars within the armScale: 1020 meters = 100 Em = 100 exameters (~10 000 light years) Our spiral armScale: 1021 meters = 1 Zm = 1 zettameter (~100 000 light years) The Milky Way Scale: 1022 meters = 10 Zm = 10 zettameters (~1 million light years) The local groupScale: 1023 meters = 100 Zm = 100 zettameters (~10 million light years) The Virgo ClusterScale: 1024 meters = 1 Ym = 1 yottameter (~100 million light years) Galactic ClustersScale: 1025 meters = 10 Ym = 10 yottameters (~1 thousand million light years) The limit of our knowledge

KNOWLEDGE & LEARNING

How do you “know” something?

Can you really “know” anything?

The processes that give rise to knowledge:

Authority.Experience.Intuition.Science.

• Our mind comprehends reality by categorizing and dividing things up into chunks

• Science is the methodological way in which we go about this. While it is of course prone to error (we’re only human), when attempted faithfully, it removes human emotion and subjectivity, yielding the most accurate information to the best of our ability.

The Scientific MethodIt starts with a phenomenon. Something that piques our curiosity. We take note of an

observation.

Then, drawing on ….current knowledgepast experiencesIntuitiondiscussions with othersCreativity

… we reason our way through our thoughts, and come up with an idea. A “tentative statement”. Not a question, a statement.

(This is Inductive Reasoning)

The idea we call a hypothesis “the basis of an argument” hypo, under, thesis, proposition.

We sometimes refer to the hypothesis as a “model”.

We then make a prediction based on our idea, using Deductive Reasoning, which follows “if, then” logic.

The Scientific MethodOur prediction leads us to an experimental design that gives us the opportunity to falsify our prediction. Note prove it. Disprove it.

FALSIFIABILITY is the underlying concept here. It’s not science if it can’t be disproven.

We plan our experiment. We design our controls so that ANY data we get can be properly interpreted (positive, negative, or somewhere in between). Controls give us a comparison, or benchmark for our unknown.

We obtain data, and analyze, and make conclusions.

We ask the key question: does it fit the hypothesis? Is it consistent with our idea?

If it is, we aren’t done. We do another experiment, attacking our idea from a different angle.

Hypotheses / Models are ALWAYS being investigated and thought about, even when we think we have it down (gravity theory is a good example).

If it DOESN’T support our hypothesis, we change our idea to support the new data.

In this way, the idea becomes more and more refined, until, to the best of our ability, we can be confident that it is probably correct.

“prove” is a very strong word in science, and is rarely used. “Support”, “consistent with”, are the way we normally talk about data and hypotheses.

If you read anything that discusses scientific topics, and read “this proves x”, take that with a very large grain of salt.

Scientists don’t claim to know everything. And the true scientist has no ego. They are happy when their hypotheses turn out to be wrong – it means there’s something out there to discover.

Definitions• Inductive Reasoning: Bottom-Up; moving from something

specific to something general. (“induce” brings something from nothing – induce change, etc. It brings something new into being.)

• Deductive Reasoning: Top-Down; moving from the general to the more specific. (“Deduce” is subtracting – deduct a sum of money from an account, etc. Take away the layers and uncover what’s underneath.– In the case of the science, you dig through the data and uncover a

conclusion.

Scientific Method - Summary

ExperimentControls

PhenomenonSomething Interesting

HypothesisInductive Reasoning

DataAnalysis

ObservationSenses / Instruments

PredictionFalsifiable

ConclusionDoes it fit the hypothesis?

Principle / Law

A theory that has been around long enough without being refuted.

Theory

A hypothesis that is continually

supported by experimental data over time, with no

direct contradictions

Cell TheoryAtomic Theory

Evolution TheoryGravitational Theory

Etc.

ACTIVITYGather into groups of 3-4. Designate a group leader. Name your group.

As a group, write a list of 5-20 nouns. They can be anything (reasonable). Keep It clean! Don’t use any outside source, besides your mind.

As a group, discuss and pick two or three, and link them together to form some kind of observation.

Develop an idea that explains your observation – why is your observation true?You’ll be using inductive reasoning here.

Raise your hand for help.Group leaders make final decisions if there are any disagreements.

Now come up with a Prediction that you can test. Remember it needs to be FALSIFIABLE. You’ll be using deductive reasoning.

Now design a simple experiment to test the prediction, and include appropriate controls.

FIVE HALLMARKS OF LIFE ON EARTH

1. Organized2. Acquires material & energy 3. Respond to its environment4. Reproduce & Develop5. Has adaptations to its environment

LIFE IS ORGANIZEDAtoms make up molecules …which make up macromolecules …which make up cellular structures …which make up cells…which make up cell systems (tissues) …which make up organs …which make up organ systems …which make up organisms …which make up populations …which make up communities, …which, together with the environment, make up ecosystems…which make up the biosphere.

1

Important DefinitionsPopulation: a group of organisms of the same species.Community: a group of organisms of different species (look at

this as groups of populations).Ecosystem: A community + its surrounding environmentBiosphere: A system of interconnected ecosystems.

organism

organism

organism

population

community

environment

Ecosystem

Biosphere

Emergence

Each new level of organization leads to new properties of the system that the individual components do not have (e.g. cells can’t see, but as a system, the eye can)

Therefore, new properties emerge from the system as it becomes more complicated.

These new traits are called emergent properties.

Can you think of other emergent properties?

1

EmergenceSurface tension of water emerges as a result of the hydrogen

bonding of water molecules

Emergent structures of groups of organisms: flocks of birds, ant colonies, schools of fish.

Feet don’t run, leg’s do.

cells don’t see, eyes do.

A nucleus isn’t alive… but a cell is. Life can be viewed as an emergent property of complex systems.

1

LIFE ACQUIRES MATERIAL & ENERGY

Things that are alive extract energy from their environment, and use it to perform work.

What is “Work”? _________________________This work includes a vast amount of different

processes…maintaining homeostasis (temperature, pH, salt

concentrations, etc.)Constantly repairing DNA against external insults

every cell in your body has about 20,000 DNA damage events a DAY… and you have ~3 trillion cells

2

HomeostasisHomos, same, stasis, standing still.Maintaining a stable, constant set of parameters.You sweat when you’re hot, shiver when you’re cold, hunger

when you’re low on energy, and thirsty when fluids get low. You breath heavily when you run so you can maintain the same level of oxygen in your system as it uses it faster.

There’s a ‘zone’ for each characteristic. Think of a standard blood test – there is a range in which things can fall. The farther you move out of the zone, the more uncomfortable you feel… pain and discomfort are necessary survival traits.

2

Metabolism

Metabole, “change”

The total sum of all chemical reactions taking place inside an organism. These include those responsible for breaking down the raw materials (from food usually) and building what they need to make their parts (e.g. fix a damaged gene, patch a hole in the membrane, etc.) and products (e.g. hormones)

Look at the map on the wall (or hallway)

2

LIFE RESPONDS TO ITS ENVIRONMENT

Ensures survival.

Running away from a predator. Getting closer to the fire on a cold night

Plants bend towards light. This is an example of tropism, in this case, phototropism.

3

LIFE REPRODUCES & DEVELOPS

Modern Life only comes from other modern life.Question: “What came first, the chicken or the egg?” Answer: “There is no beginning or end to a circle”

Development: What decides that an embryo develops into a human or a mouse?Our Genes. We’re 85% genetically identical to mice and

99.98% (or so) identical to chimps.

NOTE: Offspring are NOT identical to parents. There are always variations introduced in each generation. Without this, a species would go extinct.

4

LIFE HAS ADAPTATIONS TO ITS ENVIRONMENT

“If you can’t beat it, join it.”While ALL of life contains a core set of identical components,

individual species have unique differences that enable them to survive and thrive in their unique environment.

The bones in our arm are the same bones in a bat wing, a whale fin, a bird’s wing, a horse’s leg. They are simply shaped differently, matched for the use they have in their environment.

5

WHAT IS THE ORIGIN OF LIFE?

So if life only comes from life, where did life start?Evolution theory does NOT address this question.

It simply addresses the diversity of life, not its origin.

This question falls within the theory of abiogenesis (or how life began from inanimate matter).

Short answer: We don’t know, yet, but much work has been done.

Aside

1. exploringorigins.org2. Scientific American article on reconstructing f

irst living cell3. The origin of life video4. The origin of life research project of Drs. Russ

ell & Hall

FURTHER READING

Natural Selection: a primerWe’ll cover this in more detail at the end of the semester.

The basics of evolution theory :– 1: individuals within a population have variations– 2: not all offspring survive. There are limited resources.– 3: some offspring will survive better than others because of their natural variations.– 4: those that survive will pass on their successful variations, while those that don’t, perish.– 5: this cycle repeats itself for very long spans of time.

Evolution Theory is to Biology as Atomic Theory is to Chemistry, and Quantum Theory is to Physics. Without it, the observations and data biologists generate would not make sense. The predictions derived from evolution theory have always been consistent with all data, past and present.

Are there any questions you have regarding evolution theory?

Break

How we Organize Life

Invented for ourOwn understanding

Existing relationships we uncover through

research

Binomial Nomenclature

Taxonomy

Phylogenetics

We work to name all living things.

We work to categorize all living things based on their

similarity to each other.

We discover each living thing’s connections with each other

The National Center for Biological Information Infrastructure : http://www.nbii.gov/

How Life is Currently Classified

Systematics: Taxonomy + Phylogenetics

Taxonomy: organizing life based on physical similaritiesPhylogenetics: organizing life based on evolutionary relationships

From greek taxis or tasso, meaning “arrangement”Nomia, “method”, “usage”, “law”

The swedish ‘natural philosopher’, Charles Linnæus, is considered the father of modern scientific classification.

TaxonomyA made-up system (by humans) that attempts to neatly fit

everything alive into a category.

A human contrivance that attempts to pigeonhole every living thing on earth, both extinct and extant, into a single category.

Problems: • Things don’t always fit within the system (Platypus, anyone?)• There is still MUCH to learn and discover.

– There are still huge realms of “undiscovered country” in the realm of life science, and new surprises are happening on a regular basis.

» Largest virus discovered, found to be on par with bacteria – and possess much – but not all – of what a cell is thought to have. How do we classify it??

» Plasma in outer space is shown to actually develop organized structure. This clearly does not fit within the paradigm of carbon-based life. Are there other paradigms of life?

• Bottom Line: We’re still working on it.

The Nomenclature of TaxonomyNomenclature: a system or set of terms or symbols especially in a particular science,

discipline, or art.– It’s purpose is to allow communication.

The nomenclature of taxonomy is a work in progress

There is a distinction between naming an organism or group of organisms, and grouping them.

– Whether I group you according to where your ancestors came from, or whether I group by your hair color, you are still homo sapiens and don’t change your name.

• This is important, because while we can readily identify two different species (and therefore give them unique names with confidence), because we are still trying to understand the deepest complexities of biology at the molecular level, our classifications schemes remain imperfect.

• This is where Phylogenetics comes into play. – This is the study of how related species are based on their evolutionary

relationships (particularly how their DNA sequences fit together, forming branched lineages.

A taxon (plural taxa) is just a group of organisms – or sometimes, just a species.

The current system underwent its last major revision in 1990, when the most inclusive taxon level (the kindgom) was replaced by an even MORE inclusive taxon called a “Domain”.

Have you ever played 20 questions and wondered why we start by saying “is it an animal, vegetable, or mineral”? Those were the original Three Kingdoms set up by Charles Linnaeus in his Systema Naturae (1735-1758, 10 editions overall)

PhylogeneticsTaxonomy classifies things by morphology (how things looks),

shared characteristics (bony fishes vs. cartilaginous fishes; warm-blooded vs. cold-blooded), etc.

Phylogenetics classifies things by their evolutionary relationships, uncovered within their genetic material.

The Ultimate Goal of classification is ambitious: The Tree of Life, where every organism is linked to every other through a continuous chain of lineages.

The Tree of Life Web ProjectExample Phylogenetic tree

DomainKingdom

Class

Family

Order

Genus

Species

Phylum

Currently AcceptedTaxons

Taxons vary inBotanyZoologyVirology

Knowledge

People

Can

Oppose

For

Good

Deliver

Bacteria

Eukarya

Archae

Domain3

prokaryotic

Protista

Plantae

Fungi

Animalia

DomainKingdom

Bacteria

Eukarya

Archae

Kingdoms in progress….

4

Protists are the “pot-luck” kingdom.

There are:

“Plant-Like” Protists“Animal-Like” Protists“Fungus-Like” Protists

38 animal

11 plant

6 fungi

16 bacteria

2-3 Archae

DomainKingdom

PhylumOver

70

Protista

Plantae

Fungi

Animalia

Bacteria

Eukarya

Archae

Kingdoms in progress….

From the greek Phyle, “tribe” or “clan” and phylon, “race” or “stock”.

Generally speaking, phylum (also known as ‘divisions’ sometimes, mostly by botanists) are arranged based on shared evolutionary traits and physical appearance (up until only a the last 2 decades have we been able to more accurately classify life based on gene sequences)

DomainKingdom

Phylum

Chordates: Have notocords. Includes both Vertebrates and Invertebrates.

(in higher vertrebrates the notocord is only present during development, and is eventually replaced by the spinal cord)

A ‘sub’ phylum includes the vertebrates. Here is an example in which the current taxonomy isn’t very orderly.

DomainKingdom

Class

Family

Order

Genus

Species

Phylum

Mammals

DomainKingdom

Class

Family

Order

Genus

Species

Phylum

Carnivores.

DomainKingdom

Class

Family

Order

Genus

Species

Phylum

Generally named for a type of genus.

Canidae (dogs, wolves, foxes, coyotes, dingoes, jackals, etc.)

DomainKingdom

Class

Family

Order

Genus

Species

Phylum

Also named for a type of genus.Canidae (dogs, wolves, foxes, coyotes, dingoes, jackals, etc.)

DomainKingdom

Class

Family

Order

Genus

Species

Phylum

Domestic Dogs are Canis Lupus. However, some classify them as a sub-species of Grey Wolf, Canis Lupus Familiaris.

So genetically speaking, there is VERY little difference between that little fluffy pocketbook dog and the huge mastiff.

www.despair.com

Summary

Classical Taxonomy (organizing life by similar characteristics) is still distinct from

Phylogenetics (connecting organisms by their evolutionary relationships, mostly through biochemical and genetic links)

It is still unclear how these two will merge.

Homework 1/27/09

Choose a news story from www.sciencedaily.com and write a 1-3 paragraph summary (no more than 1 page typed.)

Suggested stories– http://www.sciencedaily.com/releases/2009/01/090126203157.htm – http://www.sciencedaily.com/releases/2007/08/070809172213.htm – http://www.sciencedaily.com/releases/2009/01/090125142127.htm

This homework will be graded for content, grammar, and spelling, and worth a maximum of 5 points.