Bio 121: General Biology

Dr. Ippolito

Sections MC & SD

SC Room 309

Agenda0:00

Opening RemarksAttendanceRound Circle IntroductionContact Information

0:30 Syllabus Handout & overviewQuestion to the Class: What are your technology expectations?Break (10 minutes)

1:10 Lecture & Discussion: From Introduction & Parts of Topic 1 of the Syllabus

Knowledge, learning, and order; Hallmarks of Life; Organizing & Naming Life; The Scientific Method

2:15 Break into Groups of 3-4Activity: Scientific Method

3:05 Meeting Adjourned

Thoughts on Taking Good Notes What worked for me:

Materials: a spiral notebook, folder, 3-Ring Binder with Sections for every class lots of 3-ring punched, college-ruled paper A set of pens & pencils, etc.

Workflow: Lecture notes taken in the spiral notebook. Handouts in the folder. Same day of lecture (or day after): rewrite lecture notes (includes organizing it neatly) on fresh paper;

keep a separate page for questions I have; add this to my 3-ring binder section for the class. Chapter reading: Add notes to my rewritten lecture notes; attempt to answer all confusing points and

questions from lecture. End Product: EASY studying for tests. And I would actually remember the material for a

long time.

Research shows clearly that spreading out your work over time – not doing work ‘last minute’, or pulling all-nighters – is the BEST way to learn and retain information.

This is Less important for peripheral classes. ESSENTIAL for “core” classes are the backbone of the rest of your education!

Recall HS Spanish; freshmen year chemistry (and then organic and physical)

Other Tips & Tactics Read the chapter summary FIRST.

Our brains work best when we see the big picture and dig in, as opposed to the opposite (study on maps and remembering)

Keep a vocabulary list. Make Flash Cards Don’t just memorize. Understand the concept. Form a study group today! Everyone learns differently, having strengths and weaknesses in the following ways:

Auditory (hear) (lectures) Visual (see) (reading the book; handouts, etc.) Tactile (do) (activities, lab reports, rewriting notes & diagrams yourself)

Doing all of these is best. Survey the room to get a feel for the types of learners we have.

STAY ORGANIZED. Have a folder for handouts and returned graded material. Keep up regularly with your course work. Make it a priority.

TIME MANAGEMENT: Rule of thumb for doing college work: For every hour in the classroom, devote 2 hours outside of it. Some courses require even more; some less. CREATE A WEEKLY SCHEDULE AND SET GOALS.

Ideal: .5 to 1 hour of work a day (every day) if you can. Some days break this into two or more sessions. Some days it might be 2 hours with short breaks. Do what works for you.

Lecture 1

What is life?

How do we classify it?

What is knowledge?

How do we obtain it?

Knowledge, Learning, and Order 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.

Our book mentions 4 distinct paradigms of ordering the world Religion Esthetics Ethics Science

How we learn:

Authority Experience “Intuition” Science

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.

Five Hallmarks of Life on Earth

1. Organized

2. Acquires material & energy

3. Respond to its environment

4. Reproduce & Develop

5. Adapt to its environment

Five Hallmarks of Life on Earth

Organized

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

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

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

Five Hallmarks of Life on Earth

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 (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

Homeostasis Homos, 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

Five Hallmarks of Life on Earth

Respond to its environment

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

Five Hallmarks of Life on Earth

Reproduce & Develop

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.

4

Five Hallmarks of Life on Earth

Adapt to its environment Brown Fat: instead of making ATP, the cells simply give

off extra heat. Webbed feet of a duck We will discuss this at more length when we cover the

Principles of Evolution. Natural 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)5

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 evolutionary 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.

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)

Phylogenetics 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.

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

Generally 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.

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.

The Scientific Method It starts with a phenomenon. Something that piques our curiosity. We take note of an observation. Then, drawing on ….

current knowledge past experiences Intuition discussions with others Creativity

… we reason our way through our thoughts, and come up with an idea.

This kind of reasoning is Inductive. The idea we call a hypothesis “the basis of an argument” hypo, under,

thesis, proposition. We then make a prediction based on our idea. We make this prediction

using “deductive reasoning”.

The Scientific Method It starts with a phenomenon. Something that piques our

curiosity. We take note of an observation. Drawing on

current knowledge past experiences Intuition discussions with others Creativity

we reason our way through our thoughts, and come up with an idea.

This process of reasoning is called Inductive reasoning

General IdeaSpecific Knowledge

“My back is killing me”“Sitting for long periods of time

Can hurt one’s back”Induces you to think

Inductive Reasoning

Deductive Reasoning

General Idea Specific Knowledge

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

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.