Principals De Bioo

Woo hoo. Bio (Created while listening to "mother" by Danzig)

*What is the format of this course?*

Studio format where we lecture for 15 minutes, go into lab and hands-on work for a while, and 15 minutes of wrap-up lecture at the end of class.

What is the test schedule and grading scheme, and what’s expected of students?

Grading is 11% quizzes, 11% capstone quizzes, and 78% exams. Students are expected to study for 8-12 hours outside of class.

What were the two different methods used to estimate the number of yeast cells?

First method was using __**spectrophotometer**__ which measures how much light is absorbed in a substance. If more light is absorbed, then more yeast is in the solution. The second method is using the __**microscope**__ and counting the number of yeast cells.

Which method is more efficient at counting yeast cells?

Spectrophotometer

Which method is more reliable?

Apparently microscope (You count with you’re eyes)

What are the interactions of science and why are some questions inappropriate for scientific investigation?

Science **interacts** with the natural world, and it requires __**evaluation**__ and __**replication**__ from others. Conclusions in science can also be proven wrong. Some questions are inappropriate because they’re limited by experimentation

What are the major parts of the scientific method and how do they relate to each other?

1. Making **observations**
2. Formulate a **hypothesis**
3. Perform an **experiment**
4. Gather **new data**
5. Come to a **conclusion**
6. If proven correct, turn hypothesis into **theory**

They all can interact back and forth, for example: if your new data proves your original hypothesis wrong then you must create a new hypothesis.

What are the unifying characteristics of living things and what’s a good definition of life?

Living things __**respond**__ to their environment. __**Take in**__ and __**use**__ energy from their environment. They maintain a constant internal environment through __**homeostasis.**__ At an organism level they __**reproduce**__, and at a population level they can __**evolve**__. Living things are also __**made of cells**__, and compared to their environment are __**organized**__.

Why may it be hard to define life?

It’s impossible to define life because of how **diverse** it is. It’s difficult to encompass everything in one definition when not all living things meet every characteristic. 

What is the hierarchy of organizational levels?

The biological hierarchy is a range of biology from the smallest **atom** to the entire **biosphere**. The hierarchy: (A.M.C.T.O.O.O.P.C.E.B)

**A**__llen__ **M**__ade__ **C**__upcakes,__ **T**__he__ **O**__range__ **O**__ctopus (of)__ **O**__regon__ **P**__ut__ **C**__arrots (in)__ **E**__very__ **B**__atter__

Atoms

Molecules

Cells

Tissue

Organs

Organ Systems

Organisms

Populations

Community

Ecosystems

Biosphere

What is the importance of **repeatability** in investigations?

Repeatability is very important in experiments because it gives other scientists the opportunity to prove, or even disprove, your theory or results. A single observation will hold no credibility in the scientific world, but if something can be repeated then it’ll be accepted. It can allow for scientists to gather new data from changing small aspects of an experiment as well.

What is the importance of gathering appropriate sample sizes in investigations?

Gathering an appropriate sample size is important to help reduce the amount of error that can be made. If a scientist takes a poll from 5 people, then it won’t be very accurate, however a poll from 5,000 people can give much better results.

What is a scientific hypothesis?

A scientific hypothesis is a **testable** and **falsifiable** guess based on previous experience or data. A scientific hypothesis can be changed or if proven correct lead to the creation of a theory.

What is the difference between observational and experimental scientific investigations?

Observational investigations are made purely by observing and require no manipulation of the system in which you’re working with. An experimental investigation requires the observer to make changes to the subjects they’re studying or the conditions in the experiment.

What is biological evolution?

Biological evolution is the idea of **descent with modification**; a change in the genetic makeup of a population over time.

How is biological evolution a unifying principle of biology?

This is a unifying principle because without the idea of evolution nothing would make sense. Biology explains much if not all the diversity of life on Earth.

What is natural selection and what role does it play in evolution?

Natural selection is the engine that runs Evolution and allows for the organisms with the best traits to survive. If not for Natural Selection, then there’d be nothing actually executing the concept of Evolution. Natural selection forces the individuals that are less fit to survive to die, and allows for the individuals better equipped with more adaptive traits to live on and pass down those better traits. 

How does selection act on individual organisms?

Natural selection will kill off the individuals with traits that are less fit to help them survive, and allow the individuals with better adapted traits live on in their environment and pass down those traits.

How can natural selection result in evolution of a population?

This can create a change over time in the population by forcing those worse traits out through the death of the individuals with the traits, and let the individuals with the better traits reproduce more and live on.

What are the three conditions needed for natural selection to occur?

1. __**Heritable variation**__ must happen among individuals. This means through the expression of different versions of genes, we can see different traits in individuals which will allow variation to be passed down.
2. __**The number of offspring that CAN be produced, is greater than the that which IS produced.**__ Not every individual will survive or reproduce. There are forces that kill off many individuals in a species and this just further allows natural selection to occur by killing off the less adaptive individuals.
3. **Not all individuals in population are** __**equally**__ **successful at survival or reproduction.** This condition simply requires that Heritable variation have an effect on the survival and reproductive rates. If there were random effects on the survival rates then it would lead to no true evolution and would basically be a mess of genes, however, with Heritable variation being a factor towards the survival rates this allows it to pass on the traits that are found in those who are better fit to survive.

What are some examples of environmental factors that can be agents of natural selection?

**Abiotic** Factors (non-living things): weather, natural disasters

**Biotic** Factors (living things): predators and competition

What is “relative fitness”?

How fit an individual is at surviving and reproducing in their environment compared to the individuals around it. An example of this is if one of my dogs has a litter of 10 puppies while my other smaller dog has 3 puppies. The dog who is better at reproducing in its environment is relatively more fit for that environment than the other.

What role does relative fitness play in natural selection?

Relative fitness will allow the most fit to survive in their environment. This is a force of natural selection that kills off the relatively less fit individuals

How can the differences of reproductive output from individuals in a population lead to adaptive changes within the population in future populations?

Those individuals who are better adapted for their environment will reproduce more than those who aren't, which will help them pass on the better traits over time.

What are the simulations of cumulative and single-step evolutionary change?

\*Methinks it is like a Weasel\* A __single-step__ simulation represents a big change over one generation, while a __cumulative__ simulation represents one small change at a time

Why is the cumulative simulation a better model than the single step simulation for showing the process leading to evolutionary change?

The cumulative simulation shows how evolution is much more likely because it takes one small step at a time and doesn’t require huge change all at once.

How does natural selection explain the diversity of earth?

Natural selection forces individuals to have small changes over time, and after enough time passes this would result in so many different variations and unique changes or characteristics among individuals that can explain how diverse the world is. If we were to consider Natural Selection taking place since the beginning of life, then it would easily build to the diversity there is now over the billions of years.

What are the connections between taxonomy (classification of organisms into groups) and phylogeny (hypothesized evolutionary relationships)?

**Taxonomy** classifies animals based on a number of factors and names them by their species. Both Taxonomy and Phylogeny use relation to classify animals. In taxonomy, scientists group together individuals based on if they’re in the same Genus or species (the two most specific levels) which includes other individuals that share similar characteristics or traits. In **phylogeny** they classify similarly by making trees that separate as they find differences in individuals and end up with branches containing closely related organisms. However, with phylogeny it often uses the Most Common Recent Ancestor to show how exactly the individuals are related. Taxonomy uses much broader ways of grouping; once you leave the most specific levels you get broader levels of classifying organisms. Both processes of classification are hypotheses.

Classify all life using the hierarchical classification system (Kingdom, phylum, etc.)

**D**on’t **K**eep **P**ouring **C**oncrete **O**ver **F**rank’s **G**reen **S**hoes

Domain

Kingdom

Phyla

Classes

Order

Family

Genus

Species

What is the three-domain classification system?

The **“3-Domain” classification system** is the most widely accepted tree which divides all living things into 3 major domains. It divides life into **1.** Bacteria, **2.** Archaea, and **3.** Eukarya. This classification system proposed evolution from 1 being, believing that every living thing is related. Eukarya contains animals, fungi, and plants.

How do you find the M.R.C.A. (most recent common ancestor)? How do you know which organisms are most closely related?

The most common recent ancestor is the last point on a phylogenetic tree where 2 organisms connect. If two individuals share their most recent common ancestor, then they’re closely related. If you have to decide between 3 individuals about which one is closer related, you look to see which shares a most recent common ancestor and that would be closer related. 

What are “Cladistics”?

Cladistics is a way of classification that classifies the characteristics of an organism as either **Ancestral** or **Derived**

How do we use ancestral and derived characteristics to make a phylogenetic tree?

__Ancestral__ characteristics are inherited attributes that resemble an ancestor of the individual. __Derived__ characteristics are features that are different from those found in an Ancestor. We use __derived__ characteristics to separate individuals on a tree as points to know how to differentiate them, however we also use __ancestral__ characteristics as ways of connecting individuals. However, this can be misleading at times if a characteristic may look similar but is actually unrelated to an individual's ancestry. 

How do phylogenetic trees combine to form a “tree of life”?

Many phylogenetic trees can just continuously go back in time to connect to other trees again and again until eventually it will develop a huge tree displaying the evolutionary history of the world. We can see this on the **3-domain** tree which more broadly classifies life into 3 domains.

What do phylogenetic trees indicate about the evolutionary relationship of life on Earth?

The **3-domain tree** essentially points to the belief that all life on earth originated from the same point or basically that we all share a common ancestor. 

What is the difference between homologous and analogous structures?

__Homologous__ structures have similar locations in organisms and come from common ancestors, yet have **different functions.** An example is the forearm bones found in mammals, reptiles, and birds. Birds may have similar bones to a lizard's arm but a lizard can’t fly. __Analogous__ structures share the **same function** but don’t come from a structure found in a common ancestor. An example of this is wings in Bats and Butterflies; they both have the similar function of allowing them to fly yet the come from different structures. 

How can homologous and analogous structures be used to trace evolutionary history?

Homologous shows a true change over time and helps us trace the change and how the function changes while maintaining similar structures/ locations. Analogous shows how just because individuals share the same functions, doesn’t mean they have similar ancestors.