What is Life?How is it Organized?

How do we Classify it?What is Knowledge?How do we obtain it?

• Get out a piece of paper and a pen.• Watch this video• 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

Nature appears to have order. There is an underlying organization to it.How do we know this?

It is a basic human instinct to seek order in things. There is an, underlying premise to the way in which we examine things.

How we learn:

Authority (“Look both ways before crossing the street!”)

Experience (I should have looked both ways before crossing the street…)

Intuition (“If I’ve seen cars driving by fast, then when I get to the corner, I should probably look both ways before crossing the street”)

Science (90% of people that cross the street but do not look both ways before moving cost upwards of 1.2 million dollars a year in public health costs. According to these statistics, we strongly recommend those crossing streets to look both ways)*

*I made that up.

A B

The Dumbbell Nebula A Cancer Cell Nucleus

A B

Cateye Nebual Actin Filaments &PML Bodies

• 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 our emotions and subjectiveness, yielding the most accurate information to the best of our ability.

General IdeaSpecific Knowledge

“My back is killing me” “Sitting for long periods of timeCan hurt my back”Induces you to think

Inductive Reasoning

Deductive Reasoning

General Idea Specific Knowledge

“Old Milk Curdles” “My milk might taste bad.”You deduce that

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.

• Gather into groups of 3-4. Designate a group leader.• As a group, write a list of 5-10 biological objects. They can be anything

(reasonable). Keep It clean!• As a group, discuss and pick two.

– Link them together in a creative way to describe some kind of phenomenon, from which you will form a hypothesis using inductive reasoning.

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

• Each group will read their hypothesis out loud.• Each group will then come up with a Prediction for that hypothesis by

deductive reasoning.• From that prediction, each group will design a simple experiment to test

the prediction, and include appropriate controls.– Each group will briefly describe their experiment and controls.– We will try to go over each experiment’s strengths and weaknesses.

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

Atoms make up molecules …which make up macromolecules …which make up cellular structures …which make up cells…which make up cell systems …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

EmergenceEach 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

Emergence• Elementary particles (electrons, proteins, neutrons)

do not have color. But together, they form particle systems (atoms), which can

absorb specific wavelengths of electromagnetic radiation. Therefore, Color is an emergent property of elementary

particles• Surface 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.

1

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

This work includes a vast amount of different processes…maintaining homeostasis (pH, salts, 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 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)

2

Ensures survival.Running away from a bear, fire, or gun-wielding

crazy person; Getting closer to the fire on a cold night

Moths to a flame… so it’s not always a good thing.

Plants bend towards light. This is an example of tropism, in this case, phototropism. What other kinds of tropisms are there?

3

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.

It is important to understand that offspring are NOT identical to parents. There are many processes at work that cause a continual variation between generations.

4

“If you can’t beat it, join it.”Brown Fat: instead of making ATP, the cells simply give off extra

heat.Webbed feet of a duckNatural Selection: The principle that organisms with beneficial

traits with respect to the environment, will, over time, produce more offspring.

Descent with modification: All living being share the same basic characteristics (particularly at the molecular level); this suggests there was a single common ancestor (LUCA)

We will discuss this at more length when we cover the Principles of Evolution.

5

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 evolutionary connections with each other

Taxonomy: 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.

• 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.

» Recently: 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?

» Concept: Life as an emergent property of complex systems.

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

• Also 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.

– This type of

• 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)

• We used to classify things by morphology (how things looks), shared characteristics (bony fishes vs. cartilaginous fishes; warm-blooded vs. cold-blooded), etc. This is the field of taxonomy.

• With the advent of genetic research, things have changed. We are now beginning to shuffle around the way in which things are classified depending upon their evolutionary relationship to one another.– Ultimate goal: The Tree of Life, where every organism is

linked to every other through a continuous chain of lineages.

DomainKingdom

Class

Family

Order

Genus

Species

Phylum

Currently AcceptedTaxons

Taxons vary inBotanyZoologyVirology

Bacteria EukaryaArchae

Domain3

Protista Plantae Fungi Animalia

DomainKingdom

Bacteria EukaryaArchae

Kingdoms in progress….

4

Protists are the “pot-luck” kingdom.

There are:

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

38 animal11 plant 6 fungi16 bacteria

2-3 Archae

DomainKingdom

PhylumOver 70

Protista Plantae Fungi Animalia

Bacteria EukaryaArchae

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.

http://en.wikipedia.org/wiki/Image:Gray_Wolf_in_Grand_Teton_NP-NPS.jpg

• 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.