Post on 25-Dec-2015
Your First Classwork.
• Get 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 …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.
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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?
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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.
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LIFE ACQUIRES MATERIAL & ENERGY
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 (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
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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.
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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)
Look at the map on the wall.
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LIFE RESPONDS TO ITS ENVIRONMENT
Ensures survival.Running away from a predator. Getting closer to
the fire on a cold nightPlants bend towards light. This is an example of
tropism, in this case, phototropism. What other kinds of tropisms are there?
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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.
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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.
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Natural Selection: a primer• We’ll cover this in more detail at the end of the semester.• Evolution Theory does NOT explain the origin of life. It explains its diversity.• Abiogenesis is a theory that addresses the origin of life.• The basics of evolution theory is pretty straightforward:
– 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?
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
How Life is Currently Classified
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.
Taxonomy• 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.
Nomenclature• 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.
• 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)
Phylogenetics• Taxonomy 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 Project
DomainKingdom
Class
Family
Order
Genus
Species
Phylum
Currently AcceptedTaxons
Taxons vary inBotanyZoologyVirology
Protista
Plantae
Fungi
Animalia
DomainKingdom
Bacteria
Eukarya
Archae
Kingdoms in progress….
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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
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.
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.
End Chapter 1
Next Week
TuesdayTextbooks, Labbooks & Notebooks are required.Chapter 1 and Chapter 2 Homeworks are due before class starts.Quiz on Chapter 1 & 2.Lecture: Chapter 2.Please email me over the weekend with any study questions you might have.
ThursdayLab 1: Important Biological Molecules. Read the lab beforehand. A very short lab quiz may be administered.
Forecast: Tuesday: Chapter 3 homework due, Chapter 3 lecture. Thursday: Test on Ch 1-3.