Important
words and concepts from Chapter 1, Campbell & Reece, 2002 (1/14/2005):
by Stephen T. Abedon (abedon.1@osu.edu)
for Biology 113 at the Ohio State University
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Course-external links are
in brackets Click [index] to access site index Click here to access
text’s website Vocabulary
words
are found below |
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(1)
Chapter title: Introduction: Themes in the Study of Life
(a)
Throughout this course (i.e., these notes) I will be doing my best to
supply you with links to supplemental material found on the World Wide Web
(b)
If you have additional interest in presented material or need
additional exposure to concepts, consider following these links (on line, of
course)
(c)
If you know of any links that you think ought to be included in this site,
please send the URL, along with where in
this site you think the link belongs, to abedon.1@osu.edu
(d)
I will regularly include Google searches
that may be followed for abundant additional information on material—however,
always keep in mind that your first, best reference will usually be your text
book
(e)
There also exists an index to this site called BioPort that is found at http://www.phage.org/biology.htm or by pressing
[index] throughout these notes
(f)
Note that by and large within these notes you will be held more responsible
for information that is found outside of parentheses (other than the vocabulary
words found to the right of section headings) and not indicated as a
“supplemental discussion;” that material [found within brackets] or indicated
as a “supplemental discussion” is for your (and my) benefit but will not be
found on exams; don’t forget, however, that there is more to learning biology
than just memorizing material not found within parentheses or brackets!
(g)
Note that I will additionally be including “FAQs” in these notes, which
stands for “Frequently Asked Questions;” These are answers to actual questions
that students have supplied me by e-mail over the years; I include them to help
you with your studies, rather than as a burden; If you have a question and a
computer is handy, PLEASE DO NOT HESITATE TO SEND ME AN E-MAIL!!!!!!!!
My e-mail address is abedon.1@osu.edu
(h)
[themes in the study of life
(Google Search)]
[index]
HOW TO SURVIVE THIS COURSE
(SUPPLEMENT)
(2) Studying tips:
(a)
Biology can be a difficult subject to become familiar with then to
learn then to effectively do; below I list a number of tips that might be
helpful to you as you as a guide towards the implementation of your limited
biology-studying resources
(i)
Read your text before lectures over the material
·
Read your text well so that, minimally, you have made an attempt at
understanding the presented concepts
(ii)
Read over the supplied lecture notes (i.e., these)
·
Read lecture notes well so that you have made an attempt at
understanding the presented concepts
·
Make an effort to memorize the supplied vocabulary
(iii)
Come to class prepared to ask questions
(iv)
After class, organize the material, integrating the notes that you take
during class
(v)
Study for the first exam in this course harder than you have ever
studied for an exam before
·
Triage the material you will be studying such that you don’t waste your
time studying the material you already know/understand
·
Make sure that you have extensively been through the material and have
organized it before you begin to study
·
Don’t put off your studying to the last minute
·
Don’t count organizing and learning your material as exam study
time—studying for an exam involves making sure that you have memorized and can
lucidly regurgitate the material, not simply becoming familiar with it
·
Simply reading over notes again and again is not necessarily equivalent
to doing the hard work of learning
(vi)
Don’t forget that labs are worth a good chunk of your grade
·
Don’t blow off labs
·
Read labs before you come to laboratories and as you are doing them
·
Read your lab schedule also for tips on how to do labs
·
Labs are much (much, much) easier to do when you are familiar with
them; I will be able to tell when you are unfamiliar with labs; I will
reserve the right to quiz on lab preparation if I get the impression that
students are coming to laboratories unprepared
·
Answer questions and make notes while the material is still fresh in
your mind
(b)
For numerous additional tips on how to study for biology, see: [biology and "study
tips" (Google Search)]
[index]
(a)
The basic recipe for success in biology is to learn how to work
effectively, and then to work long, hard, and preemptively at mastering the
material
(b)
Note the word “effectively” in the above sentence (or phrase if you are
a stickler for periods); your goal always should be to effectively learn the
material—quantity time is a poor (and inefficient) substitute for quality time
(c)
I will do my best to gear this course towards unambiguously presenting
you with the material that I expect you to learn—your job is to put in the
effort necessary to learn that material… no excuses, just do it
(d)
What I am hoping that you do is
(i)
To take the time to read assigned chapters before the material is
covered in class (and to read them well—not skimmed or with the difficult parts
skipped over, but with a devotion to the subject)
(ii)
To take the time to read assigned lectures (ditto)
(iii)
To organize your notes after lectures so that you have an outline of
material that is in you own words (or, at least, notes to go with lecture
outlines, though to some extent I do you a disservice by making it so tempting
for you to avoid taking the time to organize the material for yourself)
(iv)
To make sure that you understand (and have memorized) all of the
required material well in advance (days) of an exam
(v)
Don’t forget that it is learning the material that is your goal,
not simply studying the material; learning takes time, organization, and
effort as well as an understanding of background material; studying only takes
time and is not necessarily equivalent to doing the hard work of learning;
also, memorization, though important, is not equivalent to understanding
(vi)
Get on top of this course early and stay on top; try studying twice as
hard as you can possibly imagine your needing to study for a course—the worst
that can happen with a strategy like that is that you might consider studying
less after you take the first exam
(vii)
Don’t devote the first weekend of the term to blowing off biology
class!
(viii)
To take care of yourself the night before (sleep, quoi?) and day of an
exam so that you are relaxed and in top intellectual form when you take the
exam (rather than a burned-out wreck unable to think coherently much less
answer challenging exam questions)
(ix)
Don’t give yourself a hard time; it is far easier to work with and
enjoy your environment than it is to fight against the daily grind
(e)
For more on how to succeed in this course (and other science courses)
see:
(ii)
Introduction to Majors’ Biology
(iii)
Biology FAQs
(f)
Here are my only-slightly-tongue-in-cheek Majors’ Biology FAQs
(click on questions for answers):
(iii)
Why doesn't my success in
chemistry translate directly into success in majors’ biology?
(v)
Biology in high school was
easy. Why isn't majors’ biology similarly easy?
(vi)
I'll bet majors’ biology in
Columbus is a lot easier than this. Why do you make biology so hard?
(viii)
I'm pre-med. I've just got to
do well in this class. Why are you ruining my GPA?
(ix)
On an essay question, what
exactly do you mean by "be as thorough and as detailed as you can
be"?
(g)
See additionally my discussion of what it takes to succeed in a majors introductory
biology course as presented in this course’s syllabus
(h)
Note that you will only
start to experience the difficulty of this course as we reach chapters
5, 6, and 7 of your text
which together have over 150 terms and concepts that you will be held
responsible for (compared to chapters 2, 3, and 4
which together have barely 60)
(i)
For numerous additional tips on how to study for biology, see: [biology and "strategies
for success" (Google Search)] [index]
(4) Additional considerations
(a)
First Law of Biology 113: You can study anything you like in this course, but
ultimately the information in the handed-out lecture notes is what you need to
know for exams. Study these notes daily. Memorize them. Understand them.
THE MOST IMPORTANT THING FOR YOU TO UNDERSTAND IF YOU INTEND TO DO WELL IN THIS
COURSE IS THAT YOU MUST LEARN THE MATERIAL!
(b)
Second Law of Biology 113: To do well, most of you should be studying
biology five or six days/week, with a minimum of about 20 hours per week
devoted to this class. You need to learn the material well in advance of
studying for the first exam. You must take the time to learn and
understand material before we (rapidly) move on to the next topic.
(c)
Third Law of Biology 113: Get on top of this course early in the quarter
(e.g., by the end of the first weekend). Ten weeks goes by very quickly. IF YOU
WAIT THREE, TWO, OR EVEN ONE WEEK TO REALIZE THAT YOU ARE GOING TO HAVE TO
STUDY VERY HARD IN THIS COURSE, THEN IT MAY ALREADY BE TOO LATE FOR YOU TO
CATCH UP!
(d)
Fourth Law of Biology 113: Study for the first exam as hard and as well
as you have ever studied for an exam THE BEST TIME TO BEGINNING STUDYING FOR
THAT EXAM IS TODAY!
(e)
Some of you will take this course without a reasonable background in
biology and may be better off taking Biology 101 before taking Biology 113
(i)
Don't make the mistake of derailing your biology goals and interests by
attempting Biology 113 without the necessary commitment and preparation!
(f)
Some you will have already taken Biology 101 but will underestimate
what it will take to do well in Biology 113
(i)
Don’t assume that having taken Biology 101 that doing well in Biology
113 will take the same level of commitment—Biology 113 is more difficult than
Biology 101 even if you have already taken the latter
(g)
Some of you will be coming from chemistry 121 but will not be prepared
for how learning biology differs from learning chemistry
(h)
Some of you are capable of doing well in Biology 113 but are unprepared
to devote the time to the course necessary for you to do well
(i)
This may be your first exposure to a major’s science course and you may
have no idea of the level of commitment and understanding that will be expected
of you
(j)
ABOVE ALL, EVERY YEAR ABOUT 50% OF MY BIOLOGY 113 CLASS DOES NOT EARN A
GRADE OF A C- OR HIGHER—PLEASE DO YOURSELF THE FAVOR OF EITHER PUTTING FORTH
THE EFFORT NECESSARY TO SUCCEED IN THIS COURSE, TO SELF IDENTIFY AS AN
INDIVIDUAL WHO IS NOT YET READY TO TAKE BIOLOGY 113, OR WHO IS PREPARED TO TAKE
THIS COURSE FOR REASONS OTHER THAN OBTAINING A GOOD GRADE
(i)
People who do not do well on daily quizzes typically do not do well in
this course
(ii)
People who do not do well on their first exam typically do not do well
on their subsequent exams
(iii)
If you do not have time to learn the material prior to moving on to
subsequent material, or prior to the first exam, then when will you have time
to learn the material?
THE BIOLOGY 113-114 SEQUENCE
(5)
Your text book (Campbell, Reece, and Mitchell, 1999)
(a)
These on-line notes are based on the introductory biology text, Biology, Fifth Edition, 1999, by Neil A.
Campbell, Jane B. Reece, and Lawrence G. Mitchell (Addison Wesley Longman,
Inc., Menlo Park, California), a most-excellent majors’ biology text
(b)
The following are the table of contents of Campbell et al., 1999, with links to the
associated on-line notes (no link implies notes do not exist):
(i)
Chapter 1: Introduction: Themes in the Study of Life (remember to read this
introductory chapter)
(ii)
The Chemistry of Life (covered in Biology 113)
·
Chapter 2: The Chemical Context of Life
·
Chapter 3: Water and the Fitness of the Environment
·
Chapter 4: Carbon and the Molecular Diversity of Life
·
Chapter 5: The Structure and Function of Macromolecules
·
Chapter 6:An Introduction to Metabolism
(iii)
The Cell (covered in Biology 113)
·
Chapter 7: A Tour of the Cell
·
Chapter 8: Membrane Structure and Function
·
Chapter 9: Cellular Respiration: Harvesting Chemical Energy
·
Chapter 11: Cell Communication
(iv)
Genetics (covered in Biology 113)
·
Chapter 13: Meiosis and Sexual Life Cycles
·
Chapter 14: Mendel and the Gene Idea
·
Chapter 15: The Chromosomal Basis of Inheritance
·
Chapter 16: The Molecular Basis of Inheritance
·
Chapter 17: From Gene to Protein
·
Chapter 18: Microbial Models: The Genetics of Viruses and Bacteria
·
Chapter 19: The Organization and Control of Eukaryotic Genomes
·
Chapter 21: The Genetic Basis of Development
(v)
Mechanisms of Evolution (covered in Biology 114)
·
Chapter 22: Descent with Modification: A Darwinian View of Life
·
Chapter 23: The Evolution of Populations
·
Chapter 24: The Origin of Species
·
Chapter 25: Tracing Phylogeny
(vi)
The Evolutionary History of Biological Diversity (covered in Biology 114)
·
Chapter 26: Early Earth and the Origin of Life
·
Chapter 27: Prokaryotes and the Origins of Metabolic Diversity
·
Chapter 28: The Origins of Eukaryotic Diversity
·
Chapter 29: Plant Diversity I: The Colonization of Land
·
Chapter 30: Plant Diversity II: The Evolution of Seed Plants
·
Chapter 32: Introduction to Animal Evolution
·
Chapter 34: Vertebrate Evolution and Diversity
(vii)
Plant Form and Function (not covered—those interested in agriculture,
horticulture, how ecosystems function, or the merely intellectually curious
should consider reading these chapters)
·
Chapter 35: Plant Structure and Growth
·
Chapter 36: Transport in Plants
·
Chapter 37: Plant Nutrition
·
Chapter 38: Plant Reproduction and Development
·
Chapter 39: Control Systems in Plants
(viii)
Animal Form and Function (not covered—those interested in agriculture,
medicine, veterinary medicine, how ecosystems function, or the merely
intellectually curious should consider reading chapters)
·
Chapter 40: An Introduction to Animal Structure and Function
·
Chapter 41: Animal Nutrition
·
Chapter 42: Circulation and Gas Exchange
·
Chapter 43: The Body’s Defenses
·
Chapter 44: Controlling the Internal Environment
·
Chapter 45: Chemical Signals in Animals
·
Chapter 46: Animal Reproduction
·
Chapter 47: Animal Development
·
Chapter 48: Nervous System
·
Chapter 49: Sensory and Motor Mechanisms
(ix)
Ecology (covered in Biology 114)
·
Chapter 50: An Introduction to Ecology and the Biosphere
·
Chapter 51: Behavioral Biology
·
Chapter 52: Population Ecology
·
Chapter 53: Community Ecology
·
Chapter 55: Conservation Biology
(6) What is Biology 113?
(a)
Biology 113 considers how living things work at or below the level of
the cell plus includes a significant chunk of genetics plus a smidgen of
developmental biology
(b)
The prerequisites for Biology 113 are Chemistry 101 or 121. However, it
has been my experience that students who struggle through their chemistry
courses will also struggle through Biology 113, perhaps more so. It cannot be
stated strongly enough that individuals who are interested in biology should
take their chemistry studies very, very seriously. Don't make the mistake of derailing your biology goals and interests
by attempting Biology 113 without the necessary commitment and preparation!
If you have never had a college-level biology course or equivalent (e.g.,
biology in high schools the way college-preparatory courses ought to be taught,
but usually are not when teachers are uncomfortable with teaching chemistry-,
math-, or evolution-based biology), then please strongly consider taking
Biology 101 before attempting Biology 113.
(c)
Biology 113 is a typical introductory biology course for majors with an
approximately average level of rigor/difficulty. Academically strong students
will find Biology 113 challenging but not overwhelming. Students who are not
used to rigorous college-level science courses, however, may find Biology 113 extremely
difficult. Basically in ten weeks we go through the first 20 chapters of our
text, covering most of three units called "The Chemistry of Life,"
"The Cell,", and "Genetics." About half of the course is
chemistry!!!! Another sixth or fifth is math!!! You can see all of
the material you will be held responsible for at http://www.phage.org/bio_113_schedule.htm. Be prepared to devote a minimum of about 20 hours/week to this
class. Typically 50% of the class present on day 1 will receive a grade of D+
or less. If you are not prepared
to seriously dedicate yourself to learning biology, then don't sign up for
this course. See http://www.phage.org/bio_113_warning.htm for more information on what it takes to succeed
in this course.
(d)
Presentation of Biology 113 includes both a lecture and a lab component
with lots of encouragement of student participation/responsibility for the
material. Lack of student participation (and preparation) will seriously hamper
the learning experience. No assignments will be handed in or graded. Your lab
efforts will be graded using one or two lab exams. These will be open book
exams, but students who blow off labs or attend but don't care will tend to
fail these lab exams. I will assume and expect that students will not only keep
up with text reading but that they will keep up with the material on a daily
basis. Some can pass and even do well in this course without putting forth a
serious effort. Most can't.
(7) What is Biology 114?
(a)
The second half of the Biology 113-114 sequence, Biology 114, considers
how living things work at or above the level of the individual organism,
including evolutionary biology, ecology, and an overview of the diversity of
life
(b)
Learning the material presented in Biology 114 is an almost completely
difference experience from that presented in Biology 113
CHAPTER 1
(a)
What is Biology?
(b)
Biology is the science that studies life
(a)
What is life?
(b)
Life is the manifestation of how organisms
live (and why)
(a)
What is an organism?
(b)
Organisms (those found on this planet, at
least) are complex organic machines that take in energy (and various
chemicals), modifying these things that they take in order to
(i)
Obtain additional energy and nutrients
(ii)
Grow
(iii)
Protect themselves
(iv)
Repair themselves
(v)
Compete with other organisms
(vi)
Reproduce
(c)
See Figure 1.3, Some properties of life,
for a additional ways of looking at what life is all about
(11) Hierarchy of biological order
(a)
The hierarchy of biological order is a recurring theme in your text so
it is worthwhile to take a little time to consider just what this phrase means
(b)
See Figure 1.1, The
hierarchy of biological order
(c)
The hierarchy of biological order is a fancy way of saying that living
things can be viewed at numerous, nested levels
(d)
These levels start with the physical; progress through the chemical
(this chapter); enter into the realm of the biochemical (chapters 3,
4,
5,
6,
9,
10,
11
and 26); then sub-cellular organelles (chapters 7,
8,
9,
and 10); cells (chapter 7); tissues
(which are collections of cells); organs; collections of organs into systems;
collections of organs, tissues and systems of organs into organisms (chapters 27,
28,
29,
30,
31,
32,
33,
and 34); collections of organisms into populations (chapters 22,
23,
24,
25,
51,
52);
collections of populations into communities (chapter 53); collections of
communities into ecosystems (chapter 54), and collection
of ecosystems into the biosphere (chapter 50)
(e)
In addition to all of the above is genetics, the movement of
chemically-coded information from organism to organism, e.g., from parent to
offspring, which is covered throughout your text, though in particular by the
middle chapters 13, 14, 15,
16,
17,
18,
19,
20,
21,
22,
23,
24,
and 25
(f)
In the first half of this biology sequence (biology 113) we will be concerned mostly with biological order
at and below the level of the cell (chapters 1-6, 7-12)
plus genetics (chapters 13-21)
(g)
In the second half of this biology sequence (biology 114) we will be concerned particularly with biological
order at and above the level of the organism (chapters 22-25 =
evolutionary biology, chapters 26-34 = biodiversity, and chapters
50-55 = ecology)
(h)
If you are interested in the middle ranges of the hierarchy of
biological order, ranging from tissues to organ systems, then you are
interested in anatomy and physiology which is covered by a variety of courses,
but also by your text over 15 excellent chapters: chapters 35-39
(plants—this section of chapters should be of considerable interest to those
intending careers in agriculture) and chapters 40-49 (animals—this section of
chapters should be of considerable interest to those intending careers in human
and veterinary medicine)
(i)
By the way, do yourself a favor and read Chapter 1 of your
text before you start in on this chapter (chapter 2); Chapter
1 provides a reasonably good overview of the subject of biology, plus serves as
an obvious place to start reading a text (duh); if there is one thing that I’ve
learned over the years, it is that in biology there is no good that comes from
skipping over the basics, or anything else that might give you an edge towards
getting on top of the material
(j)
[hierarchy of biological order
(Google Search)] [index]
(a)
From the hierarchy of biological order
comes the concept of emergent properties
(b)
The idea here is that as one goes to higher levels in this hierarchy,
new properties emerge that are difficult to predict from properties at lower
levels
(c)
In other words, there exist properties of groups of things that are
difficult to predict if one studies individual things in more-or-less isolation
(d)
See Figure 1.2, The
hierarchy of biological organization
(e)
For example, in the next chapter we will discuss numerous
emergent properties of water that constitute bulk properties of water such as
the fact that ice floats or an important phenomenon
known as hydrophobic exclusion
(f)
We will be considering emergent properties all through this course
(though not always explicitly); in this chapter we consider chemistry so that
we may subsequently consider the biological properties (e.g., biochemical
properties) that emerge from the underlying chemistry of organisms
(g)
[Of course, the concept of emergent properties is also a statement of
our own ignorance of the connections between lower-level and higher-level
order. The following quote is how two quantum physicists have considered these
concepts (and also serves as an interesting indication of how physicists view
complicated things like biology): “Theories can be crudely organized in a
family tree where each might, at least in principle, be derived from more
fundamental ones above it [of course, it would have been preferable had they
placed the more fundamental stuff at the bottom but we’ll try to avoid being too
critical of these non-biologists]. Almost at the top of the tree lie general
relativity and quantum filed theory. The first level of descendants includes
special relativity and quantum mechanics, which in turn spawn electromagnetism,
classical mechanics, atomic physics, and so on. Disciplines such as computer
science, psychology and medicine appear far down in the lineage. ¶ All these
theories have two components: mathematical equations and words that explain how
the equations are connected to what is observed in experiments. Quantum
mechanics as usually presented in textbooks has both components: some equations
and three fundamental postulates written out in plain English. At each level in
the hierarchy of theories, new concepts (for example, protons, atoms, cells,
organisms, cultures) are introduced because they are convenient, capturing the
essence of what is going on without recourse to the theories above it [a
biologist, of course, would have preferred, “below it” and a tree that grows up
rather than down, but try to keep this from confusing you]. Crudely speaking,
the ratio of equations to words decreases as one moves down the tree, dropping
near zero for very applied fields such as medicine and sociology. In contrast,
theories near the top are highly mathematical, and physicists are still
struggling to comprehend the concepts that are encoded in the mathematics. ¶
The ultimate goal of physics is to find what is jocularly referred to as a
theory of everything, from which all else can be derived. If such a theory
exists, it would take the top spot in the family tree, indicating that both
general relativity and quantum filed theory could be derived from it.
Physicists know something is missing at the top of the tree, because we lack a
consistent theory that includes both gravity and quantum mechanics, yet the
universe contains both phenomena. ¶ A theory of everything would probably have
to contain no concepts at all. Otherwise one would very likely seek an
explanation of its concepts in terms of a still more fundamental theory, and so
on in an infinite regress. In other words, the theory would have to be purely
mathematical, with no explanations or postulates. Rather an infinitely
intelligent mathematician should be able to derive the entire theory tree from
the equations alone, by deriving the properties of the universe that they
describe and the properties of its inhabitants and their perceptions of the
world.” (emphasis mine) p. 75 of Max Tegmark and John Archibald Wheeler
(2001), 100 Years of Quantum Mysteries Scientific American February:
68-75]
(h)
[emergent properties
(Google Search)] [index]
(13)
Vocabulary [index]
(a)
Biology
(c)
Hierarchy of biological order
(d)
Life
(e)
Organism