i. what is biology?. a. definition: webster’s new world dictionary: "the science that deals...

I. What is Biology?

I. What is Biology?A. Definition:Webster’s New World Dictionary: "the science that deals with the origin, history, physical characteristics, life processes, habits, etc. of plants and animals: it includes botany and zoology."


The scientific study of living systems.


The scientific study of living systems.

Begs two questions – “what is science?” and “What distinguishes living systems?”

II. What is Science?A. Definition:Webster’s: “systematized knowledge derived from observation, study, and experimentation carried on in order to determine the nature or principles of what is being studied. The systematized knowledge of nature and the physical world.”


B. Limitations:


B. Limitations: - What is studied: the physical world /universe



- How it is studied (Method): empiricism



- How it is studied (Method): empiricism

- Methodological Approaches:

-Methodological Approaches:1. REDUCTIONISM

Gaining an understanding of a system by describing its subsystems (components)

Powerful Approach: living systems are very complex, so describing the STRUCTURE can give insights into FUNCTION.


Gaining an understanding of a system by describing its subsystems (components)

But the functioning of a complex system is not entirely described by the ADDITIVE EFFECTS of their components… The system functions as a consequence of how these subsystems INTERACT… these aspects are called EMERGENT PROPERTIES


Medicine: Anatomy (reduction) and Physiology (systems approach)Natural History: Taxonomy (reduction) and Ecology (systems approach)Genetics: sequencing (reduction) and Functional Genomics (system approach)

-Methodological Approaches:1. REDUCTIONISM2. COMPARATIVE METHOD


The function of complex systems may be understood by comparing them with simpler systems (with fewer subsystems).


The function of complex systems may be understood by comparing them with simpler systems (with fewer subsystems).

How could a complex system like a camera eye, composed of mutually dependent parts, have evolved through a stepwise sequence?(This is Paley’s (1802) ‘argument of design’, currently repackaged with molecular and cellular examples by the ‘Intelligent Design’ movement.)

Half an eye (lens) can’t work…

2. COMPARATIVE METHODThe function of complex systems may be understood by comparing them with simpler systems (with fewer subsystems). Visual systems in molluscs:

2. COMPARATIVE METHODThe function of complex systems may be understood by comparing them with simpler systems (with fewer subsystems). Visual systems in molluscs: Half an eye

(retina) CAN work…

2. COMPARATIVE METHODWhy is this method so powerful in biology? Is there a REASON why different organisms might have similar structures and functions?

2. COMPARATIVE METHODWhy is this method so powerful in biology? Is there a REASON why different organisms might have similar structures and functions? Yes… common ancestry.

This is why the use of model organisms (E. coli, fruit fly, house mouse) illuminates the field of medicine

And the most dramatic examples of homology are in the hox genes, as well.


In fact, the homology is so good that lineages of eyeless flies lacking that hox gene can have the ability to grow eyes restored by adding the homologous gene from a mouse…and flies develop compound eyes with the mouse hox gene for eye development, even though mice have camera eyes…HOW COOL IS THAT!?


And, human diseases have been identified as hox mutants by identifying homology with fruit fly hox genes, and they have been found in the genome with ss-DNA (probe) from the fly homeobox region of that gene.


And, human diseases have been identified as hox mutants by identifying homology with fruit fly hox genes, and they have been found in the genome with ss-DNA (probe) from the fly homeobox region of that gene.And, because of

evolution and common ancestry, we can use model organisms like flies to learn about how heredity and development work in all animals … including humans.

-Methodological Approaches:1. REDUCTIONISM2. COMPARATIVE METHOD3. EXPERIMENTATION (EMPIRICISM)

-Methodological Approaches:1. REDUCTIONISM2. COMPARATIVE METHOD3. EXPERIMENTATION (EMPIRICISM)

Observe repeated, correlated physical phenomena/patterns

“On Caribbean Islands with lizards, there are no spiders”


“On Caribbean Islands with lizards, spiders are rare”GOAL: is this relationship causal?

GOAL: create a falsifiable (testable) causal hypothesis

Bring other observed facts to bear“They use similar habitats” (could live

together)“Lizards eat spiders”

“Lizards and spiders eat other insects”“They disperse differently” (so they may have

gotten to different islands by chance)“Hawks eat lizards but not spiders, so maybe it

just happens that hawks and spiders are together”

“Some warblers eat spiders and not lizards, and maybe it just happens that warblers and

lizards are together”“Lizards run around and may break spider webs

and starve them inadvertently”










lizards are together” “Lizards run around and may break spider webs



“On Caribbean Islands with lizards, spiders are rare”GOAL: create a falsifiable (testable) causal hypothesis







lizards are together”“Lizards run around and may break spider webs


You can envision many alternative causal hypotheses …and there are nearly a limitless supply…you can’t test them all (so scientific facts aren’t eternal truths or PROOFS)… test the simplest explanation first = “principle of parsimony” or “Occam’s razor”




Hypothesis: Lizard predation causes a reduction in spider abundance on Caribbean Islands

Other observations





Alternative Hypothesis: Lizard predation does not cause a reduction in spider abundance… (maybe competition does or maybe it is just a correlated effect of something else…)

Other observations





Alternative Hypothesis: Lizard predation does not cause a reduction in spider abundance… (maybe competition does or maybe it is just a correlated effect of something else…)

Other observations

Here is a another critical element of a scientific hypothesis – it must be falsifiable – you must be able to envision data collected from the physical universe that would prove

your hypothesis is wrong.


Alternative Hypothesis: Lizard predation does not cause a reduction in spider abundance… (maybe competition does or maybe it is just a correlated effect of something else…)Here is a another critical element of a scientific hypothesis – it

must be falsifiable – you must be able to envision data collected from the physical universe that would prove

your hypothesis is wrong.

Conduct an experiment in which data supporting either hypothesis is equally possible. This is a specific case derived from a general hypothesis … deductive logic.

Conduct an experiment in which data supporting either hypothesis is equally possible. This is a specific case derived from a general hypothesis … deductive logic.

IF: - lizard predation is responsible for low spider abundance

AndIF: - I add lizards to specific islands and remove lizards from others, with appropriate controls for the manipulations,

THEN: - Spider abundance should decline where I add lizards and increase where I remove lizards, and spiders should be a major component of lizard diets (gut content analysis).

IF: - lizard predation is responsible for low spider abundance

AndIF: - I add lizards to specific islands and remove lizards from others, with appropriate controls for the manipulations,

THEN: - Spider abundance should decline where I add lizards and increase where I remove lizards, and spiders should be a major component of lizard diets (gut content analysis).Then you do it and see!!! And you generalize from your specific experiment to nature (inductive logic). You use logic and evidence from the physical world to reach a conclusion about how nature is and how it works.(Usually by statistical inference…which we will demonstrate in lab…)

Then you do it and see!!! And you generalize from your specific experiment to nature (inductive logic). You use logic and evidence from the physical world to reach a conclusion about how nature is and how it works.

Many lines of independent evidence…



can support a single general explanation



can support a single general explanation…

These Explanations are THEORIES. They are supported by experimental results and they can be tested by subsequent experiments

-Methodological Approaches:1. REDUCTIONISM2. COMPARATIVE METHOD3. EXPERIMENTATION (EMPIRICISM)4. METHODOLOGICAL MATERIALISM

-Methodological Approaches:1. REDUCTIONISM2. COMPARATIVE METHOD3. EXPERIMENTATION (EMPIRICISM)4. METHODOLOGICAL MATERIALISM

Philosophical materialism – the material is all there is.Methodological materialism – the material is all we can test.

III. Context: Ways of KnowingA. Why You Know - Searching for Truth1. Faith: Webster’s – “unquestioning belief not requiring proof or evidence”

III. Context: Ways of KnowingA. Why You Know - Searching for Truth1. Faith: Webster’s – “unquestioning belief

not requiring proof or evidence”2. Logic: “the science of correct reasoning;

science which describes relationships among propositions in terms of implication, contradiction, contrariety, conversion, etc.”



science which describes relationships among propositions in terms of implication, contradiction, contrariety, conversion, etc.” Evidence is a "clean argument“, but it does not have to describe a physical reality.



science which describes relationships among propositions in terms of implication, contradiction, contrariety, conversion, etc.” Evidence is a "clean argument“

3. Science: Logical argument and physical evidence.

III. Context: Ways of KnowingA. Why You Know - Searching for TruthB. Different Problems, Different Tools“If the only tool you have is a hammer, you tend to see

every problem as a nail.” – Abraham Maslow, American Psychologist

III. Context: Ways of KnowingA. Why You Know - Searching for TruthB. Different Problems, Different Tools“If the only tool you have is a hammer, you tend to see

every problem as a nail.” – Abraham Maslow, American Psychologist

Science can’t answer questions about supernatural things (“God exists”) or morality (“Abortion is right”) – it is a bad tool for those questions.

But for questions about the physical universe, science has demonstrated that it is the best tool. And all technological applications support that claim.

I. What is Biology?Begs two questions – “what is science?” and “What distinguishes living systems?”II. What is Science?III. Ways of KnowingIV. What Distinguishes Living Systems?

IV. What Distinguishes Living Systems?A.Characteristics

1. O__2. R__3. R__4. G__5. E__6. E__


1. Order – highly complex and non-random systems requiring energy input for their maintenance. They are open systems that can achieve greater order by an input of more energy or greater efficiency.


1. Order2. Reproduction:

asexual/clonal/fragmentation

sexual: production of new genome

Inexact reproduction (through mutation and sex) creates hierarchical patterns of relatedness among organisms over time:

genealogies and phylogenies

Me brother 1st cousin you!

Genealogy of Human Populations

Genealogy of Primates


1. Order2. Reproduction3. Response to the Environment (internal

and external): - physiologically (cells/tissues) - behaviorally (organisms) - genetically (populations

adapt/evolve)


1. Order2. Reproduction3. Response to the Environment4. Growth:

- single cells get larger (but less efficient)

- increase size by increasing cell number


1. Order2. Reproduction3. Response to the Environment4. Growth5. Energy Transformations –

Metabolism: - take in energy (radiant and/or

chemical) - use some, waste some (can’t

violate second law) to link atoms together into biomolecules.

5. Energy Transformations - Metabolism

First Law: Energy is neither created nor destroyed, but can be transformed

Second Law: No energy transformation is 100% efficient; some is lost as ‘entropy’ (often heat).

Metabolic process are usually coupled reactions, pairing a constructive (anabolic) reaction that builds molecules with destructive (catabolic) reactions that provide the building blocks and energy.


1. Order2. Reproduction3. Response to the Environment4. Growth5. Energy Transformations –

Metabolism6. Evolve:

Populations change over time. One way they change is to adapt to their environment. Organisms with useful traits reproduce more successfully than others (Natural Selection); the frequency of these traits change over time and populations diverge.

IV. What Distinguishes Living Systems?A.CharacteristicsB. Patterns of Organization

1. Spatial Scales:1. Biosphere: Earth is ~4 x 107 m in circumference 2. Ecosystem: drop of pondwater (1 x 10-3 m) to Amazon Rain Forest (5 x 106 m).3. Community: equally variable 4. Population: equally variable 5. Individual: Smallest Mammal - Pygmy Shrew: 2 inches (5 x 10-2 m)

Largest Animal Ever - Blue Whale: 100 feet (3 x 101 m) Human - 6 ft... 2 x 100 mLargest Organism: Fungus covering 37 acres (7 x 102 m)

6. Organs: variable 7. Cells: Liver Cell: 2 x 10-5 m (2/100ths of a mm)

E. coli Bacterium: 2 x 10-6 (1/10th of a liver cell) Virus: 2.5 x 10-8 (1/100th of a bacterium)

8. Organelles: Ribosome: 1.8 x 10-8 m Mitochondrion: 2.5 x 10-6 m (about bacteria sized)

9. Molecules: Hemoglobin (average protein): 6.8 x 10-9 m (1/1000th of a bact.) Phospholipid: 3.5 x 10-9 m

Amino Acid: 5.0 x 10-10 m 10. Atoms: Carbon: 1 x 10-10 m (1/10,000,000,000 m - a ten billionth of a meter)

(a ten millionth of a millimeter) (a ten thousandth the length of a liver cell)

11. Nucleus: 2 x 10-15 m.

So, the nucleus is only 1/50,000th the width of the atom.

Atoms are mostly space.

In fact, a cubic centimeter of nuclear matter (no space) would weigh 230 million tons (Physics by J. Orear, 1979)

Analogy: If a basketball 1 ft. in diameter represents the nucleus of an atom, the edge of the electron cloud would be about 5 miles away in either direction; the atom would be 10 miles wide (~ 50,000 ft.)… that’s a lot of empty space.

Analogy: You and the Earth are separated by 7 orders of linear magnitude. A millimeter (about the size of a bold-faced period) and a carbon atom are separated by 7 orders of linear magnitude. So, to a carbon atom, the period is it's Earth.... mind blowing... Cells make up living systems that can be 12 orders of magnitude larger (cell to biosphere).

B. Temporal Scales:1. Age of Earth: 4.5 x 109 yrs (4.5 billion)2. History of Life on Earth: 3.5 x 109 years 3. Oldest Eukaryotic Cells: 1.8 x 109 years 4. Oldest Multicellular Animals: 6.1 x 108 years5. Oldest Vertebrates: 5.0 x 108 (500 million)6. Oldest Land Vertebrates: 3.6 x 108 7. Age of Dinosaurs - Mesozoic: 240-65 million8. Oldest Primates: 2.5 x 107 (25 million)9. Oldest Hominids: 4.0 x 106 (4 million – 1/1000th of earth history)10. Oldest Homo sapiens: 2.0 x 105 (200,000)11. Oldest Art: 3.0 x 104 (30,000; 1/100,000th of Life's History)12. Oldest Agriculture: 1.0 x 104 (10,000)13. Oldest Organism: Bristlecone pines: 5 x 103

14. Human cell: brain/muscle 70 yrs Red Blood Cell - weeks Skin cell - days

B. Temporal Scales:

15. Supply of ATP in cell - 2 seconds

16. Rates of chemical reactions - milliseconds (3.1 x 10-10 milliseconds/year).

The history of life, spanning billions of years, is dependent on reactions that occur at a temporal scale separated by 19 orders of temporal magnitude.

Just a diagram to put things on a scale we are more familiar with… you are not responsible for the actual physical scales (in meters or seconds) of these phenomena… just their order for now…

i. what is biology?. a. definition: webster’s new world dictionary: "the science that deals...

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