Welcome to Emergence of Life

Overview

In this module, you will become familiar with the course, your instructor, your classmates, and
our learning environment.

Time
This orientation should take approximately 2 hours to complete.

Goals and Objectives

The goal of the orientation module is to familiarize you with the course structure and the online
learning environment. The orientation also helps you obtain the technical skills required for the
course.

After this module, you should be able to:

 Recall important information about this course.

 Get to know your classmates.

 Be familiar with how discussion forums operate in the course.

Instructional Activities
Below is a list of the activities and assignments you must complete in this module. Click on the
name of each activity for more detailed instructions.

Estimated
Activity Time
Required

Watch the Course

5 minutes
Introduction Video

Read and review the 30 minutes

Syllabus and About
the Discussion
 Forums pages

Complete the
15 minutes
Orientation Quiz

Update your
Coursera Profile and
15 minutes
check out the Social
Media Page

Introduce yourself to
your fellow 30 minutes
classmates

Syllabus

Course Description

How did life emerge on Earth? How have life and Earth co-evolved through geological time? Is
life elsewhere in the universe? This course reevaluates these questions and the 4 billion-year
history of life on Earth through the lens of the most up-to-date concepts of the "Tree of Life." The
course fundamentally reconsiders what early life and evolution looked like before the root of the
Tree of Life, the overall succession of life that has inhabited our planet, and the search for life in
the cosmos.

Course Goals and Objectives

By the end of this course, you will:

 Summarize the fundamentals of molecular phylogeny and the essence of the Tree of
Life.

 Name the major extinctions and radiations punctuated by meteor impacts through
geological time.

 Compare the fossil record throughout the Phanerozoic.

 Examine controversial questions in evolutionary biology and astrobiology.

 Apply scientific inquiry to new observations and ideas not encountered before.

 Conduct a basic analysis of a scientific research paper.

Textbook
There is no required textbook for this course. Supplementary reading materials listed in the
weekly overview page are from the following textbook, available for purchase here.

Bruce W. Fouke and Tom Murphy, The Art of Yellowstone Science: Mammoth Hot Springs as a
Window on the Universe (Livingston: Crystal Creek Press, 2016)

Course Outline
The course consists of eight weekly modules.

Week 1: Geological Time and the Nature of Science

 The week begins with a discussion of the historical and philosophical approaches
that have been developed for (and are now actively applied to) the completion of
scientific research. If done well, scientific research is both reproducible and predictive
in nature. The work of Professor Carl Woese is evaluated as an example. The basic
tools required for this type of scientific reasoning and the ability to overcome the
challenging concepts of scale and complexity are then presented. We'll see how
NASA utilized these approaches to send a message into space. Next, we'll explore
the dynamic formation of the Earth itself with respect to the environmental
conditions present on the earliest and most ancient version of planet Earth.

Week 2: The Tree of Life and Early Earth Environments

 The advent of life on Earth came about as a result of a remarkable confluence of

physical, chemical and biological processes, all of which were intrinsically linked to
rapidly changing early Earth environments. Within this context, cutting-edge
approaches in molecular phylogeny have revealed new understandings of the series
of events associated with the emergence of life and the possible distribution of Life
within the cosmos. In this process, early assemblages of biochemical components
(called the progenote) then transitioned into individual living cells. These cells then
evolved to form the Tree of Life (Bacteria, Archaea, and Eucarya). From this time
forward, Earth environments directly controlled life, but in turn life rose to directly
control Earth environments. A key example was the evolution of photosynthesis by
the Bacteria to oxygenate the atmosphere 2.5 billion years before present, which
then triggered microbial mat growth on the ancient seafloor. The end of this
Precambrian time period was associated with extreme global climate change.
Week 3: Fossilization and Precambrian Life-Earth Interaction

 The accurate interpretation of ancient fossilized life requires the extreme

development of crime scene investigative approaches. This version of ancient
forensic science yields remarkably detailed and complete reconstructions of the
lifestyles of ancient organisms that have been deceased for hundreds, thousands,
millions, and even billions of years. These reconstructions, when conducted within
the context of ancient environmental conditions, provide valuable information
regarding the evolutionary success of organism morphology and lifestyle. Therefore,
“survival of the fittest” becomes “survival of those fit best.” The first great natural
experiment in this respect, run by the lineage of the Eucarya, was the Ediacaran
fauna at the end of the Precambrian.

Week 4: Paleozoic Life After the Advent of Skeletons

 A watershed event in the evolution of life on Earth was the development of external
hard skeleton components, called the Cambrian Explosion, at 542 million years
before present. The initial successes of the invertebrates were shortly followed by the
appearance of vertebrates with internal skeletons. Life then utilized these new-found
evolutionary capabilities, beginning distinct cycles of radiation, diversification, and
extinction, which define the three great Eucarya faunas of the Phanerozoic. A
benchmark event in this process was the evolution of jaws and its ensuing influence
on predation.

Week 5: Paleozoic Plants, Reptiles, and the Transition to Land

 In the early Paleozoic, plants evolved to leave the water and invade the terrestrial
landscape. The shift meant an abundant food source was readily available on land
and was followed by the transition of vertebrates into land-based ecosystems.
Global increases in CO2 and associated greenhouse warming in the Pennsylvanian
further propelled the success of both prevascular and vascular plants and the related
terrestrial radiation of the three lineages of the reptiles (Anapsids, Synapsids, and
Diapsids). While Synapsid predators dominated the late Paleozoic, a massive meteor
impact and later environmental changes reset the ecological and evolutionary stage,
opening the door to the rise of the Diapsids.

Week 6: Mesozoic Reign of the Dinosaurs and the Development of Flight

 More than 80% of life was extinguished during the Permian-Triassic meteoric impact
event, opening vast swaths of ecological opportunity for radiation and diversification
of life during the Mesozoic. Symbiosis, the mutually beneficial association of two
living organisms, was widely utilized during this time period. A fascinating lineage of
Diapsid reptiles rose to replace the Synapsid predators of the late Paleozoic,
evolving multiple distinct types of reptiles. Flight evolved in the process, allowing
Pterosaurs to have a global reach in their annual migrations. Radiation and
diversification continued, with the emergence of the lineage of the Dinosaurs,
 Archaeopteryx, and eventually the birds. The end of the Mesozoic was ushered in by
another catastrophic meteor impact, driving the dinosaurs to extinction and opening
the evolutionary stage for the Cenozoic.

Week 7: Cenozoic Mammals and Global Environmental Change

 With the demise of the Dinosaurs, Mammals rapidly radiated and diversified during
the Cenozoic. The combination of abundant food sources and significant
fluctuations in global climate fostered extreme variations in morphology, body size,
and interaction with the environment. One distinct advantage that mammals had
over previous groups was the increase in brain size within respect to body size,
evidenced by fossilized mammal skulls. Multiple theories on primate and hominoid
evolution are visited, focusing on recent evidence that sheds new light on
intermediate transitional forms in the lineage. This is contextualized with an overview
of the extreme changes in global climate that have taken place throughout the
Cenozoic and into the modern day Earth.

Week 8: Astrobiology and the Search for Life in the Cosmos

 All people ask the same fundamental questions: Where are we from? Where are we
going? Is there life elsewhere in the universe? The National Aeronautical and Space
Administration (NASA) is dedicated to searching for answers to these questions. The
NASA Astrobiology Roadmap describes our current state of knowledge regarding
the origins, evolution, distribution, and future of life in throughout the universe.
These fundamental concepts of life and habitable environments, established upon
the modern synthesis of the Tree of Life, will direct us in recognizing biospheres that
might be quite different from our own. Previous, current, and future NASA missions
continue to fundamentally reset and enhance our ability to scientifically answer
these vexing questions.

Elements of This Course

The course is comprised of the following elements:

 Lecture videos. Each week your instructor will teach you the concepts you need to
know through a collection of short video lectures. You may either stream these
videos for playback within the browser by clicking on their titles, or you can
download each video for later offline playback by clicking the download icon.

 In-lecture questions. Each lecture has questions associated with it to help verify
your understanding of the topics. These questions will automatically appear while
watching the video if you stream the video through your browser. The questions are
available as a separate downloadable text file for those who prefer to download the
videos. These questions do not contribute toward your final score in the class.
  Quizzes. Each week will include two for-credit quizzes, a Quiz A and Quiz B. You will
be allowed three attempts at each quiz every eight hours.

 Discussions. There will be one discussion activity in each week in which you will
have a choice of questions to answer. During Weeks 2–7, you will have an
opportunity to submit your discussion samples for peer review in order to receive
credit.

 Optional Scientific papers. There will be three optional paper assignments during
the course. For each assignment, you will read a few short papers and then write a
short paper of your own, which will be evaluated by your peers. The purpose of this
is to teach you how to understand and approach scientific papers.

Week 1 - Geological Time and the Nature of Science

Overview
The week begins with a discussion of the historical and philosophical approaches that have been
developed for (and are now actively applied to) the completion of scientific research. If done well,
scientific research is both reproducible and predictive in nature. The work of Professor Carl
Woese is evaluated as an example. The basic tools required for this type of scientific reasoning
and the ability to overcome the challenging concepts of scale and complexity are then presented.
We'll see how NASA utilized these approaches to send a message into space. Next, we'll explore
the dynamic formation of the Earth itself with respect to the environmental conditions present on
the earliest and most ancient version of planet Earth.

Time
This module should take approximately 6 hours of dedicated time to complete, with its videos
and assignments.

Activities
The activities for this module are listed below (with assignments in bold):

Activity Estimated Time

 Required

Week 1 Video
2 hours
Lectures

Week 1 Quiz
1 hour
A

Week 1 Quiz
30 minutes
B

Week 1
2 hours
Discussion

Goals and Objectives

Upon successful completion of this module, you will be able to:

 Identify the major events and dates that provide the structure for geologic time on
Earth.

 Discuss the major philosophical and experimental tools used when practicing good
science.

 Name the steps that resulted in the formation of the Universe, the Solar System, and
the Earth.

 Analyze the differences between reductionist and holistic approaches to science.

 Understand, in part, the nature of evolution and conditions on Earth that may have
allowed the emergence of life (covered in more detail in Week 2).

 Debate both sides of controversial questions in science, supporting their arguments

with citations and sources.

Guiding Questions
Develop your answers to the following guiding questions while completing the readings and
working on assignments throughout the week.

 What is the structure of geological time, and what were the major events in Earth's
history that demarcate the divisions of time?

 What are the major dates and names of the eons and eras?
  What are the names of the periods in each era of the Phanerozoic Eon?

 Who were the major developers of scientific philosophy?

 What is the difference between scientific method and scientific inquiry? Which
model provides a better template for a rigorous scientific endeavor and why?

 What is the difference between reductionism and holism? Evaluate the effectiveness
of each approach.

 How and when did the universe form?

 What is the structure of the solar system?

 What were the environmental conditions on Early Earth?

 What is the definition of evolution?

 What were the major theories regarding the emergence of life, and what is the
evidence supporting those theories? (This will be covered in more detail in Week 2.)

Additional Readings and Resources

 The Art of Yellowstone Science: Mammoth Hot Springs as a Window on the Universe -
Chapters 1, 2, and 5

Key Phrases and Concepts

Keep your eyes open for the following key terms or phrases as you complete the readings and
interact with the lectures. These topics will help you better understand the content in this module.

 Archaea

 Asteroid

 Asteroid belt

 Bacteria

 Big Bang

 Comet

 Eukarya

 Evolution

 Extinction

 Holism

 Hypothesis

 Meteor

 Meteorite
  Nebula

 Paradigm-shift (Kuhn)

 Photosynthesis

 Planetesimal

 Powers of 10

 Prebiotic molecular theory of evolution

 Reductionism

 Scientific inquiry

 Scientific method

 Socratic method

Tips for Success

To do well this week, we recommend that you do the following:

 Review the video lectures a number of times to gain a solid understanding of the key
questions and concepts introduced this week.

 When possible, provide tips and suggestions to your peers in this class. As a learning
community, we can help each other learn and grow. One way of doing this is by
helping to address the questions that your peers pose. By engaging with each other,
we’ll all learn better.

 It’s always a good idea to refer to the video lectures and chapter readings we've read
during this week and reference them in your responses. When appropriate, critique
the information presented.

 Take notes while you read the materials and watch the lectures for this week. By
taking notes, you are interacting with the material and will find that it is easier to
remember and to understand. With your notes, you’ll also find that it’s easier to
complete your assignments. So, go ahead, do yourself a favor; take some notes!

Getting and Giving Help

You can get/give help via the following means:

 Use the Learner Help Center to find information regarding specific technical
problems. For example, technical problems would include error messages, difficulty
submitting assignments, or problems with video playback. If you cannot find an
answer in the documentation, you can also report your problem to the Coursera staff
by clicking on the Contact Us! link available on each topic's page within the Learner
Help Center.
  Use the Content Issues forum to report errors in lecture video content, assignment
questions and answers, assignment grading, text and links on course pages, or the
content of other course materials. University of Illinois staff and community TAs will
monitor this forum and respond to issues

1. Emergence of Life

2. Week 1

3. Welcome to the Emergence of Life!

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Play video starting at :: and follow transcript0:00

[SOUND] 

[MUSIC]

Play video starting at ::17 and follow transcript0:17

I'm Bruce Fouke. 

In the departments of geology, microbiology, and the institute for 

genomic biology at the University of Illinois Urbana-Champaign.

Play video starting at ::26 and follow transcript0:26

One of the things that every human being on this planet shares is a thirst and 

a desire to understand, where have we come from?

Play video starting at ::37 and follow transcript0:37

How did we end up here? 

How did we get here? 

And where are we going? 

And this fundamental quest to understand, why we are here and where we came from? 

That's driven so much of human endeavor, and indeed, 

it's a great inspiration for us. 

And the thing that is really fascinating 

about that is that the answers are slow in coming. 

It takes a long time, a lot of work to understand where are we from, 

what's the origin of our lives? 

And where is life on this planet going? 

So I'm a geologist and I've had significant training over the last decade 

to also add microbiology to the kind of work that I do and 

one of the reasons I've done this from the very beginning is because I am really 

interested in using science to answer this question, where we come from and 

what's the origin of life as we see it on planet Earth? 

And that endeavor has been going on ever since the dawn of mankind, but 

especially over the last 150 years, 

when Darwin initiated the first concept of origin of species and 

the idea that some organisms then evolve and change through geological time and 

that organisms on this planet are related to each other somehow. 

And that if you look deep back and pull back the draperies of geological time, 

if you have tools to do that then you can start to answer this question about 

the origin of life on our planet.

Play video starting at :2:4 and follow transcript2:04

So welcome to the Emergence of Life. 

A course where we want to catch up now with the last 150 

years of the quest to answer the question, what is the origin of life on this planet. 

[COUGH] And how did life come to be what it is now, with its immense and 

breathtaking diversity. 

It's distribution in environments that go from mountain tops 

to the deepest parts of the ocean, and, indeed, into the deep sub-surface crust. 

And, also, have the ability to look for life on other planets.

Play video starting at :2:34 and follow transcript2:34

Now, in this last 150 years there's been many benchmark events. 

Technology within science has changed, and keeps changing drastically. 

With each advent of new technology, 

we also have the advent of the development of new concepts and theories within 
science that help explain the emergence of life and the origin of life. 

And so what we want to do in this course is to be able to systematically put 

together that historical reference, that historical guidebook if you will, 

of how the science has emerged to our current understanding? 

And our most recent understanding or the origins of life and 

the emergence of life on the planet. 

Many of those deep seated understandings are very, very recent. 

And in fact, they're so recent, that a lot of what we're going to cover in this 

course, is still not necessarily in the normal, everyday language of 

either normal households, or in the language of everyday scientists. 

And so we want to go right to the cutting edge of the origin of life. 

And understand what the modern day concept is of evolution? 

And to do that we're going to be looking strongly at the work 

of professor Carl Woese, who was a professor here in microbiology at 

the University of Illinois Urbana-Champaign. 

And what Professor Woese was able to do was to bring to the table new technologies 

in analyzing some of the components of life, like DNA and RNA. 

That then allowed us to go back and utilize the work that Darwin and 

others had put together of looking at the shape, form, size, 

color, all the attributes of life, combining those together 

to come up with a brand new synthesis of what we call the Tree of Life. 

And so, going from the origination of early life 

all the way up through the diversity of life that we know now, 

that grand synthesis is the goal of the Emergence of Life course. 

And so in doing them were going to be looking at the sequential history 

through geological time through these changes of life on our planet. 

How their connected, how all life goals go back to some early rootstocks of life and 

uses as a way to look froward to guide are exploration of life in other 

parts of the universe. 

[MUSIC]

In the departments of geology, microbiology, and the institute for: Added to Selection. Press
[CTRL + S] to save as a note

1.1. Scientific World View

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In order to fully understand how evolutionary biology has linked with 

the history of the Earth and 

resulted in this amazing complexity we have on the planet, a very useful 

approach is to consider how a scientist views the earth in which they live. 

And how the scientific mindset is actually structured to move forward, 

to deal with the amazing complexity that we're surrounded with on a daily basis. 

One of the first thoughts is that as you look around and see nature and 

see your surroundings, see society, that a scientist would say, first of all, 

that it's understandable. 

At some fundamental level, no matter how complex it gets or 

unpredictable it seems, we can understand it to some level. 

So, I like to say to that scientists are actually quite optimistic people instead 

of pessimistic because they do see possibility even in what some 

people would call the impossible.

Play video starting at :1:14 and follow transcript1:14

Another scientific view of the world is that the ideas of your world, 

of how you view it and evaluate it are going to change. 

So there's not a definitive truth that will be anchored once it's established and 

stand the test of time. 

It will stand the test of time in terms of being evaluated, but it won't be the end 

answer because science will always be moving forward and finding new frontiers.

Play video starting at :1:38 and follow transcript1:38

This whole idea that scientific endeavor then once you apply it to these complex 

surroundings you're in, it's the idea that the work that is done, 

even though it will change that specific body of work is durable, or 

it's something that can withstand the test of scrutiny. 

And that's an important idea here, 

because a scientist would want their work to be absolutely excellent and rigorous.

Play video starting at :2: and follow transcript2:00

But there's also a knowledge is that as technology advances and 

concepts advance that the field will move forward. 

But whatever you do accomplish can always be gone back to and be defended and 

argued as relevant and real. 

Another thing that a scientist would have deeply implanted is the idea that 

you can't have complete answers to everything. 

You can get partial answers. 

And you can get very well established responses to 

questions that you put together via experimentation or observation. 

But you will never have every single answer. 

And that's something that society doesn't like. 

Society likes to have lots of answers.

Play video starting at :2:41 and follow transcript2:41

Fundamentally, science has to be both reproducible. 

In other words no matter when and where and who does the work, 

if the same approach is done that it will reproduce the same results. 

So science has to be reproducible. 

But also another litmus test of 

the efficacy of science is that it has to be predictable. 

In other words, you have to be able to make predictions in the future of what 

might be happening in natural or social, or environmental phenomenon. 

There must be reproducibility and there must be predictability. 

And if those aren't engaged, then the scientific result is inadequate. 

Another thing that's really important, 

people think of scientists as automatons almost. 

And people who are shedding every part of their humanity to be a scientist. 
And I would argue that it's actually the opposite. 

Science depends on people who are imaginative and clever, daring, 

willing to do things that people haven't done before. 

All the aspects of human nature that I think are some of 

the most beautiful to capture, all need embodied in a scientific endeavor. 

So far from being robotic, science needs to bring forth the best in people, 

and it is a truly human endeavor in that way. 

And because science is completed by humans, 

then of course along with the strengths of humanity, like I said, courage and 

vision, there's also all the weaknesses of being human. 

There's bias, there's inconsistency, there's tiredness, there's frustration. 

And so all these factors come into play to describe and 

constrain the way that a scientist would want to approach what they're doing. 

Now this is probably best expressed in a simple look at what 

are some of the end members, or some of the spectrum of scientific approach. 

The list I just gave, it sounds good, but then how is it actually coming out 

in terms of the application and the end result of scientific endeavors? 

And so, one of the ways we look at this is that one end member we call reductionism, 

one end member we call holism, 

and there's actually a third variability that runs right down the middle. 

So let me just explain to you. 

Reductionism has been practiced in science really since its founding, and 

it's the idea that well, if you use your powers of observation and 

use the latest technology, 

you can identify what the individual pieces are of something that's complex. 
So if you had a car that didn't work, and let's say that the carburetor was bad, and 

you went to a garage that said Reductionist Garage on the top, then 

the mechanic in that garage would have you bring in the car, ask you what was wrong. 

And then that mechanic would say, okay, well to understand your problem, 

I'm going to take your carburetor out and I'm going to take all 3,746 pieces and 

lay them on the table. 

And then once I lay them all on the table, 

I hope I'll see something that gives me an idea how to put it back together. 

Well, that's a valuable approach and it gives a lot of information, but 

I think that all of us might be a little wary of spending a lot of money for 

someone who is going to have 3,700 plus parts sitting on a table and may or 

may not know how they fit together. 

The other extreme is called holism. 

And the holistic aspect is that someone would say, well, bring your car here, and 

I'm going to look at all the parts. 

I'm going to start at the bumper and the fender and the hood, and 

then I'll get to the carburetor. 

And I'll have every single part kind of understood and 

put together in a very generalized sense, but 

I'm not sure always that we're going to know what all the individual pieces are. 

That would make me equally nervous, right? 

I think to be really good at fixing an exhaust system is 

a different set of tools than fixing the carburetor. 

So I'm not sure I would want to go the Holism Garage as well. 

But there is one repair shop that I like to plug into on a regular basis, and 
I think this is the one that gives a lot of strength 

to the approach of studying evolutionary biology. 

And that's the middle path between the two. 

There's a mantra or a statement that somewhat encapsulates this, and 

it's that the whole is greater than the sum of the parts. 

So, in other words, the best way to move forward now is to use a blend of 

reductionist and holistic approaches. 

And the way to do that is you'd want to carefully pick the few detailed parts of 

the system that you know will have relevance and 

importance in terms of how the system works. 

But you're not going to describe and analyze every single part. 

And at the same time, 

you want to understand how that part fits into the whole. 

And so, you won't want to have just the carburetor but 

maybe there's some kind of back pressure coming from the exhaust system that's 

preventing efficient firing in the cylinder. 

So you do need to have some idea how the system works and 

this idea of system sciences is very important now and it's moving forward. 

So the middle path is what we're after in this kind of scientific endeavor to 

truly understand the manifestation of evolutionary biology in the context of 

the history of the earth. 

[MUSIC]
1.2. Philosophical Benchmarks in Science

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I want us to discuss the basic understanding of how we do science. 

How did science originate? 

What brought us to the moment of applying science in a way that we can ask very 

complicated, but very meaningful questions about the history of life, 

evolutionary biology, and how the Earth came to be. 

So to do that, let's encapsulate that in a discourse about the nature of science. 

What does science provide for us? 

And how did science come to be? 

Now, again this is not a philosophy course. 

There are courses that will go into great detail about this. 

But, a short encapsulation I believe is very important for 

us to understand how we use the basic concepts throughout the class. 

So one of the things that I think we should start with is 

the idea of critical free thought.

Play video starting at :1:8 and follow transcript1:08

Now, there's many parts of our society that critical free thought thrives and 

it's actually the underpinning. 

There's other parts of our society that does everything possible to stop 

critical free thought. 

And this is not a new thing. 

Actually, society used to squash and 

try to destroy all forms of critical free thought. 

So let's start with society several thousand years ago, and 

then we're going to come up to the modern day. 

So, one of the great heroes of scientific endeavor is Socrates. 

And Socrates lived from about 470 BC to 399 BC. 

And he lived in the time period in Ancient Greece where society was 

very hierarchical, and that's truly what Socrates did for us. 

Socrates brought the idea, I describe it as society at that 

time in many ways was kind of a dark void within a large balloon. 

And Socrates came and brought a pinhole. 

Pricked the balloon. 

And brought a small pinhole of light into a dark morass. 

And, that dark morass was that society would tell people what to do and 

that was the end of the story because it was truth. 

Socrates brought to the table the idea that. 

Well, let's employ critical free thought. 

Let's use our mind. 

Let's use our reason. 

Let's use our senses, and let's discuss this. 

And that discussion process of abusing those techniques and 

then having an open free discourse. 

He called that the Dialectical Method. 

And that Socratic Dialectical Method is the idea that you freely, 

critically, evaluate and challenge. 

And you even go to one more step where the instructor, or the professor, or 

the politician, 

or who ever is guiding the discussion, takes the attitude of a devil's advocate. 

In other words, taking a stance that that person may or may not believe in. 

But using it as a leveraging tool to draw out from the participants what they really 

think and what their evidence is for that.

Play video starting at :3:2 and follow transcript3:02

So, the Socratic method, what was critical. 

But what's I think especially sobering 

is that the Socratic method was the step forward towards accuracy and truth. 

But it was also the death sentence for Socrates. 

Because eventually society responded very negatively to this. 

And society not only was unhappy, but they put Socrates to death. 

They put him in prison, and they forced him to drink hemlock.

Play video starting at :3:29 and follow transcript3:29

Now Aristotle, ended up being one of the first true paleontologists who 

thought about evolutionary biology. 

Now, it wasn't couched in those terms, but Aristotle, 

[COUGH] did a lot of hiking in the mountains, throughout Greece. 

And, when he was high up in the mountains he thought about and 

wrote about the idea that he saw fossils in rock that were lifted out of the ocean. 

And he saw that those fossils lived in the marine environment. 

And he deduced from that, that those rocks must have formed in the ocean and 

then been uplifted by some kind of force. 

He also saw that in those rocks, the fossils that are at the base of the rock, 

corals and brachiopods and clams and snails. 

They changed from the bottom of the rock to the top of the rock. 

And he further deduced that there must be a history of evolutionary biology change. 

Again, he didn't use these words but he observed that. 

So our first true paleontologist, evolutionary biologist was Aristotle. 

And then we've had a little bit of time in human history to move forward from that. 

Now some of the questions that Aristotle would want us to bring to the table for 

studying evolutionary biology. 

Are things like, what is your main point? 

Can you give me a good example of what you're talking about? 

Can you summarize for me what you just discussed?

Play video starting at :4:45 and follow transcript4:45

What are you assuming?

Play video starting at :4:48 and follow transcript4:48

What kinds of ideas do you know but not know? 

And then what are you assuming might be possible to support your assumption? 

What evidence do you have? 

That's always a good one, right? 

What real evidence do you have? 

Versus some kind of an emotional knee jerk response to something you feel 

strongly about. 

We as humans always trying to decipher those things and really calling out true, 

cold and hard fast evidence, from emotion or from assumption is really, really good. 

And then other things like what can you generalize from this? 

And how can you make predictions? 

Because fundamentally, science has to be reproducible and predictable. 

And if it doesn't fulfill both those, then it's really not rigorous, or 

useful science.

Play video starting at :5:36 and follow transcript5:36

Later on in history, people took these ideas and they changed the wording a bit. 

And the wording's a little bit complicated. 

But it's important I think to put on the table right now. 

The phrase is analogy identifies anomaly. 

So the concept of analogy is that we as humans have an experiential base that we 

bring to anything that we are a part of. 

And if we see something new, 

the first thing we do is compare it to something else we've seen or experienced. 

So that's the analogy. 

Now, in that experience if we see something that we, if through analogy, 

from our experiences that doesn't fit. 

It's something new. 

It's something unexplained. 

Then it's something that rises as something that's may be concerning, 

or startling, or interesting. 

And something that should be identified as a topic of further investigation. 

So that's anomaly. 

So analogy identifies anomaly is a really important toolkit we have. 

The next person we want to look at, and again this is a whirlwind tour. 

There's many others we could bring into play. 

But it's Rene Descartes, and he lived in 1596 to 1650 in France. 

He was a true Renaissance man, a philosopher, mathematician, writer. 

But he wrote a book in 1637 on the discourse on the method. 

And in other words, what Descartes did was to bring the concept of Socrates to 

the next level and say. 

If we have critical free thought, 

and we use our multiple senses in everything we do in our everyday life. 

That we can acquire knowledge, and have a genuine foundation of what is going on. 

But it also, it's encapsulated in this great statement of I think, 

therefore I am. 

And so, he gave an example called the wax model. 

And I think that kind of explains where Descarte was bringing us. 

The wax model is the following. 

If you have a candle that's cool with a wick in the middle. 

Let's say that some candle maker just made it. 

And you set the candle in a candle holder in front of you on the table, and 

you describe it. 

You say, well it has a certain temperature. 

It has a color. 
It has a waxiness. 

It has a beautiful white wick. 

It has all these characteristics. 

But then if you light the candle, and allow the candle to burn all the way down. 

You'll end up with something that's very different than what you've started with. 

But it's still a candle, right? 

And so let's say that you let the candle burn all the way down. 

You have this molten, gooey mass. 

If there's any wick left, it's black and it's carbon. 

And it doesn't have the same color. 

It has none of the same shapes. 

But it still is a candle. 

So therefore, the idea there is that we must utilize 

our multiple senses simultaneously all the time. 

But at those moments then, 

we have to understand the context of our observations. 

Another really important philosopher. 

And again, we're jumping through time here dramatically, is Tom Kuhn. 

He lived from 1922 to 1996. 

And Professor Kuhn was at Harvard and Berkeley and MIT. 

And did a lot of very influential, philosophical writings about science. 

But his most important, and I think profound work was the structure of 

scientific revolutions, which he published in 1962. 

And so, this bills upon what we've been talking about so far. 

But it has another important caveat, and that is that the nature of humanity. 
Scientist are humans. 

And we bring to the table all the baggage that humans all have. 

One of the natures of science is that it's done by humans. 

And therefore, change is almost universally resisted. 

And so what Kuhn puts forward is, a look at the historical development of science. 

And saying that some of the most important things we've ever had developed 

scientifically was a result of. 

A lot of pain, a lot of struggle, and a lot of rejection by society. 

And so, the scientific revolutions he talks about is the idea that people will 

methodically do scientific method or scientific inquiry. 

Conduct research, have hypothesis tested, move forward with data, 

synthesize it, try to make predictions. 

Try to put this in the process models. 

But often times, the most important developments of this process, 

is actually rejected by not only society, but other scientists. 

And then eventually, if the scientific work that's being rejected or 

shunned at some level. 

If it's strong, solid science, and based in reproducibility, and prediction. 

It finally prevails. 

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