B. Limitations:

1. What is studied:
Science is limited to studying the physical universe; it is unable to address questions of morality, or those dependent on the assumed existence of supernatural agents. However, facts drawn from science and from nature may have implications in these areas. The physical universe is a pretty big and complex place; how can we even begin to try and understand this seemingly limitless complexity? Where do we begin and how do we proceed?

2. Philosophical/Methodological Approach:
Science is an empirical philosophical approach, meaning that a scientific argument or "truth claim" requires physical evidence that can be experienced "by the senses". But science is much more than "common sense" - in fact, it is almost the exact opposite. "Common sense" is a conclusion or "truth claim" that is accepted based on personal observation or opinion, alone--without thoughtful reflection or consideration of other alternatives. So, "common sense" would tell us that the Earth is flat, the sun orbits the Earth, solids are mostly matter (not space, as they are), and species are unrelated. By it's very nature, science does the opposite; it necessarily creates testable hypotheses that addresses at least one more important alternative--your idea might be wrong. Science tries hard to exclude personal opinion or bias in reaching a conclusion. That is why science is so quantitative and mathematical; numbers are impersonal and are less subject to opinion. So, the goal of science is to explain observations by testing falsifiable hypotheses of causality. "Testing" means gathering new physical evidence that bears on this question. Over time, scientists have found that FOUR major philosophical approaches have been very useful in describing the universe. None are unique to scientific study, but together they make a very powerful tool for understanding the physical universe.

        a. REDUCTIONISM:
        If you have a complex system (and all living systems are very complex), and you want to figure out how it works, try to 'break it down' into smaller, less complex subsystems. If you can figure out how the subsystems work, maybe you can then appreciate how the subsystems relate together to function as the cohesive whole. Consider a cell; it takes in material, break that stuff down and harvests the energy released by this breakdown, then uses that energy to maintain its own integrity (replacing broken stuff), and build new stuff (grow and reproduce). It is all incredibly complex, but maybe we can get a handle on how it all happens by looking at one step at a time.... even by looking at the structure and characteristics of what cells are made of - that's what we'll do in the first part of the course. However, it is important to appreciate that parts interact in a system; so knowing everything about the parts may not give you a complete understanding of the how the whole system behaves. In medicine, anatomy is important - but it does not explain all of physiology. In natural history, taxonomy is important - but it doesn't explain how the species interact. In genetics, we have sequenced the whole genome, and may eventually identify all of the genes in humans...but this will not allow us to completely describe how the genes all interact to form a functional genome. Properties that arise at each level of organization that cannot be explained by the action of subsystems are called 'emergent properties'.

        Another example is the "camera eye".  It is an extraordinary organ.  How does it work?  Well, break it down.  There is a retina that responds to visible light by sending neural impulses to the brain.  There is a lens that focuses light on the retina.  There is an iris that regulates the amount of light entering the eye.  There is a cornea that bends the light initially, and there are two gelatinous "humors" that give the eye shape.  WOW!  It is a complex system, but by breaking it down into its component subsystems and learning what they do, we describe--in part--how an eye works.
 

        b. THE COMPARATIVE METHOD:

            When any complex system is considered in isolation, the observer is impressed with its complexity, integration of function, and internal causalities, and the very complexity of it seems to make figuring out it's origin nearly impossible. When we ask "why an eye?" or even the more mundane question of "How an eye?", there seems to be no place to start.

            Here's where the comparative methods finally comes into play, particularly within biology and the context provided by evolution. If we hypothesize that eyes evolved from simpler structures, maybe we can COMPARE the camera eye to the visual structures used by simpler, more primitive groups. We know they function, so by definition, these primitive systems are internally plausible and evidentiarily true - they exist, they aren't hypothetical constructs. So,let's compare the'eyes' in molluscs.... from limpets to snails to nautiloids to squid.

             Hmmm.... retina first, lens second, humours third, cornea and muscles last. Functionally efficient at each step, satisfying the limitations of a functional non-random sequential process. Good answer to an initally apparently intractible, unanswerable question using reductionism and the comparative method in an evolutionary context. We'll see this argument play out again tomorrow.

The comparative method is a very powerful tool in biology, because there is a REASON that organisms might be similar in structure or function. That reason is common ancestry - all species share a common ancestor with one another. The more recent that ancestor is, the more genes the species share and the more similar we might expect them to be. Even organisms that are very different - like flies and humans - can trace their separate lineages back to a common ancestor - probably a very primitive bilaterally symmetrical animal of the pre-cambrian, 600 million years ago. Although flies and humans are very different, they share the same basic stages of animal development from a zygote through to the establishment of a bilateral embryo. And indeed, they share the genes that co-ordinate this early development, the establishment of a head and tail end, and cues to specify how intervening body regions will develop. This common ancestry, and this similarity in structure and function, is the basis for our ability to use other species as models for humans - we learn about human genetics by studying flies, and we learn about human disease by studying mice.

        c. EXPERIMENTATION: 
                    Finally, the most direct way to tease apart causality from a nearly infinite set of coincident events is experimentation. For instance, if you want to know how eyes develop, well, there are an infinite set of events occuring whe an eye is developing, including genetic events and environmental events.

                    1) The first element is REPLICATED OBSERVATION - you have to observe something alot of times to get a feel for which events happen concurrently and might be putative causal agents. For instance, you might be watching the development of a fruit fly and you might notice that the eye begins development on a rainy day. Well, did rain cause eye development? NO WAY TO TELL. But, if you observe eye development in 100 flies over a period of time, you will probably notice that eye development occurs on rainy AND sunny days, so neither rain nor sun correlates with eye development and thus are probably not causal agents. Through careful observation and some knowledge of the system, a subset of factors possibly responsible can be determined. So, observation does not invovle looking at ONE thing - it involves looking at MANY THINGS and observing patterns of correlation among these things. Where to from here?

                    2) The second step is to construct a HYPOTHESIS; a statement of causal relationship.  What is actually causing the phenomenon that you observed?  For a hypothesis to be scientific, it must be falsifiable with evidence from the physical world.  You see, science is NOT the process of dreaming up ideas and then only seeking data that confirms this idea.  The fundamental process of science is testing falsifiable hypotheses.  What does this mean?  Well, a falsifiable hypothesis is one that could be proven false—it is a statement for which you can envision contradictory evidence.  For example, the statement that “humans evolved from other primates” is a falsifable statement.  We can envision collecting data that would disprove it.  If, for example, we found human fossils DEEPER in sedimentary deposits than any other primates, then this would suggest that humans lived before all other primates and thus could NOT be descended from other primates.  We TEST hypotheses by looking for BOTH contradictory and supporting evidence in an unbiased way.  So, we dig deeper into sedimentary strata in places we haven’t dug yet.  We don’t know what is there, so it is an unbiased search.  We could find human fossils (which would disprove the hypothesis), or we could find only other primates (which would support our hypothesis).  The KEY is that, in an experiment, both falsification and support is possible. In this way, questions about the past are testable, too; not just things that are happening today.

                    3) The third step is DESIGNING an EXPERIMENT to test the falsifiable hypothesis:

                          Let’s put this all together to see the process in action:

                            a. observation of nature - recognition of a patterns in nature that can be observed by others
                                    a. In the caribbean, when lizards are rare, spiders are abundant
                                    b. Lizards eat spiders

                            b. FROM THESE SPECIFIC OBSERVATIONS, AN INDUCTIVE HYPOTHESIS IS MADE: -
                                    Lizard abundance affects spider abundance in the Caribbean

                            c. Design an Experiment to Test the Hypothesis:
                                    - create a controlled situation in which the hypothesis could be supported OR proven false. This is critical to science; the hypothesis must be falsifiable; the experimenter must be able to envision data that would DISPROVE the hypothesis. - Move lizards to an island that had low lizard abundance, and observe if there is a decrease in spider abundance. - Remove lizards from an island and see if there is an increase in spider abundance. - Through this process, you are using deductive logic. IF the hypotheis is true (a general claim), and IF I add lizards to islands, THEN, in this specific case, I should see spider abundance decline. I have reached a prediction by deductive logic.

                            d.      - CONTROLS: groups that are treated in the same way, but without the change in the critical variable. Walk around on islands and catch lizards, but release them on the same island (Controls for trampling effects by humans, and disturbance of lizard populations.)

                             e.     - Possible Results:
                                        Adding lizards causes spiders to decline (relative to controls) SUPPORTS HYPOTHESIS
                                        Adding lizards has no effect on spider abundance FALSIFIES HYPOTHESIS

                       4) Results - Analyze the results - involves determining the statistical probability that the pattern could have occurred by chance. If this probability is small, then chance probably is not responsibile for the pattern.  In this case, your manipulated variable is probably responsible for the pattern - you have proven causality to a statistically significant degree.  that is often "truth" in science  - probababilistic significance.  We will emphasize this in labs.

                       5) Conclusion - Hypothesis is supported or rejected, or modified. Maybe, while you are doing the experiment, you notice that lizards mostly eat insects, and only occassionally eat spiders. You also see that spiders eat insects. Maybe the inverse relationship in abundance is due to COMPETITION FOR THE SAME FOOD RESOURCE and not direct predation. This is a confounding hypothesis - a decline in spiders when lizards are added would support this hypothesis, too. So, you need to do another experiment to distinguish between these two alternatives. But you now know that lizard abundance has an effect on spider abundance. The next experiment will figure out what the mechanism of that effect is.

 C. Theories

                        - Scientific theories are explanatory models of how the physical universe works.
                         - they are predictive
                         - they have been tested and validated by experiment.

                         - UNTESTED ideas are called hypotheses..... comprehensive, tested models of how the universe works are theories:

              Physics: Atomic Theory  (no one has seen an atom, but this theory explains how matter behaves)
              Astronomy: Heliocentric Theory (no one has stood outside the solar system, but this model predicts where the planets will be in relation to each other and the sun.)
              Chemistry: Bond Theory  (no one has seen atoms share electrons, but this theory predicts which the binding properties of chemicals)
              Biology: Evolutionary Theory (no one has seen a living dinosaur, but morphological, paleontological, geological points to a relationship with birds, and this predicts where subsequent fossils are found).

III. Ways of Knowing

A. Why You Know - Searching for Truth

1. Faith: Webster’s - unquestioning belief not require proof or evidence
2. Logic: the science of correct reasoning; 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.

B. Tools and Questions

1. Each way of knowing has its strengths and weaknesses, and is best applied to some questions and not others.
2. "Should abortion be illegal?" Science - can’t answer it. Use logic and ethics, often based on faith.
3. "How old is the earth?" Physical evidence is available - let’s date the oldest rocks.... 3.8 Science is the best method, because the question concerns the physical world.
4. Creationism: is not science because it assumes the existence of supernatural agents and mechanisms that, by definition, are beyond nature and can not be tested by science.

IV. What Distinguishes Living Systems?

A. Characteristics

Living systems are not distinguished from non-living systems by one single characteristic. Chemical reactions are not unique to living systems; reproduction is not unique to living systems; even evolution is not unique to living systems - computer programmers have created algorithms that introduce variation into replicated algorithms and select from this pool based upon some production/efficiency criterion. But, life IS distinguished by expressing a suite of characteristics together. And, since life is such a rollicking good time, you might remember these characteristics by remembering that "life is an O-R-R-G-E-E".

1. Ordered Organization – All living systems, from a cell to the biosphere, are highly complex, non-random systems. How is this order created and maintained? I'm sure you are familiar with the dictum that "entropy increases". In short, this means that, in a closed system that is not exchanging energy or matter with other systems, energy that can be used for work will decrease over time and any 'orderliness' in the system will decay. The key here is that living systems are NOT closed systems. They are open systems that can achieve greater order through harvesting more energy or using energy inputs with greater efficiency. This does not violate the second law of thermodynamics... (uh, it can't, cuz that's a LAW). The second law stipulates that no energy transformation is 100% efficient - so, when a transformation occurs, some energy is 'lost' ... usually as heat. So, as transformations proceed, the tendancy will be for useful energy to decline in the system, as it is transformed with less than 100% efficiency. So, how can living systems maintain their complexity in the face of this tendancy for energy to erode? They simply take in more than they are losing to entropy. You radiate huge amounts of heat energy from your body, representing energy lost through the inefficient metabolism of food and the inefficient conversion of chemical energy (food) to mechanical energy (movement). You are an entropy MACHINE, rapidly converting lots of high energy stuff into heat! How can this continue? Well, stop eating, drinking, and breathing and it won't. Although energy is pouring out of you, you can actually increase your energy content and complexity (creating more cells) by taking IN more energy than you are losing entropically.

Order and organization occur at many different heirarchical scales of biological and material organization. The reductionistic approach has allowed us to describe the structure at these different levels; at each level, new energent properties are expressed as a consequence of interactions between components. It is striking how wide range of spatial and temporal scales across which living systems react. You are not responsible for memorizing the measurements, but you should remmeber the order of these scales (such that molecules are smnaller than organelles, that are smaller than cells, etc.).

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 m
• Largest Organism: Fungus covering 37 acres (7 x 10² m)

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

Atoms are mostly space… matter is 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).

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 years
5. Oldest Vertebrates: 5.0 x 10⁸ (500 million)
6. Oldest Land Vertebrates: 3.6 x 10⁸
7. Age of Dinosaurs - Mesozoic: 240-65 million
8. 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

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. The history of the human species, spanning 200,000 years, is linked together by the continuous reproduction of individuals that lived - on average over the course of that span - about 20-40 years. It may seem like a trivial observation, but you are only here because each and every direct ancestor of yours - over the last 200,000 years - had a child that survived to reproduce.

2. Reproduction - Living systems reproduce - making copies of themselves. However, other non-living things reproduce, also, in a manner of speaking. A rock that is split is now two rocks, for instance. Some organisms reproduce in much the same way - simply by splitting or fragmenting. This type of reproduction does not create a new set of genes, however; it simply copies and perpetuates the same existing set. This is called 'asexual' reproduction. In sexual reproduction, new combinations of genes are created. As a consequence of the inexact/incomplete transfer of genes through time from one generation to the next, heirarchical patterns of genetic relatedness are created within families (genealogy) and among species (phylogeny) over time.

Family Genealogy	Ancestry of Human Populations	Phylogeny of Primates

3. Response to the Environment (internal and external) - Living systems all respond to the environment in some way. The nature of the response often depends upon the scale of organization. For example, tissue like blood vessels in your skin respond to hormones and temperature and dilate when you are hot - increasing blood flow through surface capillaries to dissipate metabolic heat (entropy!) to the environment. This is a physiological response. Organisms can also respond behaviorally - if you are hot, you might get out of the sun and find some shafde or air conditioning! Populations may respond to the environment, too; a population might shrink in size during drought/heat stress as mortality rates increase. Because heat-sensitive indiciduals in the population would be more likely to die than heat resistant individuals during this drought, the genetic structure of the population (in this case in terms of the relative number of genes for heat sensitivity and heat tolerance) of the population would change, too. this would be a genetic response - or evolution.

4. Growth - As a consequence of taking in more energy and matter than they expel during a particular amount of time, living systems like cells, organisms, and forests can grow. since all living systems are composed of cells (really another characteristic), growth can occur by increasing cell size, or by increasing cell number, or both. For reasons we will discuss later, most cells are small. So, to increase dramatically in size, most living systems increase the number of cells they have (by cell reprouction).

5. Energy Transformations – As described above, living systems absorb and transform energy to grow and to maitain and increase in complexity. These energy transformations are collectively referred to as "metabolism". As mentioned above, these transformations are governed by the laws of thermodynamics. The First Law of Thermodynamics states that "energy is neither created nor destroyed, but can be transformed". This means that you (as a living system bound by the first law) can't make new material - like a muscle protein - from NOTHING. You have to get the carbon, nitrogen, oxygen, and hydrogen atoms from somewhere. It also means that you can't magically "poof" them together into a protein. Linking atoms together takes an input of energy, and you have to get that energy from somewhere, too (cuz it can't be 'created').

So, living systems acquire energy and matter from their environment, and they simply transform this matter into new shapes and atomic configurations. These transformations, however, are not 100% efficient - that's the second law described above. So, you can't eat 10 grams of cow muscle protein (meat) and transform that into 10 grams of your own muscle protein. Although it is pretty similar, the cow muscle proteins must be broken down into amino acids that are reassembled into a new order to create your muscle protein. So, although these reactions are performed, they are not produced with 100% efficiency. In fact, mammals are only about 10% efficient metabolically... so you would be lucky to make 1 gram of muscle from the 10 grams you consumed.

Energy transformations often involve breaking material down and then building something new from the parts. 'Catabolic' reactions break large molecules into their components; 'anabolic' reactions link small molecules together into larger products. Often, 'catabolic' and 'anabolic' reactions are linked - so that the energy released by catabolic reactions can be used to 'drive' the anabolic reactions that are making something.

So, these are the characteristics that all living systems express - either as an emergent property of the populations to which they belong, or as a reductionistic process of the organisms and cells and molecules of which they are composed. Biology, then, is the scientific study of these systems. Phew! That was one long-winded explanation of biology!

Study Questions:

1.  Place these entities in their correct order, from small to large: molecule, atom, cell, organelle, organ, organism

2. What two types of reproduction do many living systems perform?

3. Why are living systems dependent on energy transformations? Explain in the context of the two laws of thermodynamics.

Study Questions:
1) Define biology and science.
2) How do correlation and causality differ? Relate this to the difference between observations and good experiments (and the use of controls).
3) Why must hypotheses be falsifiable to be scientific?
4) If statistics determine the probability that chance caused a pattern, how are they used in science to determine whether that pattern was caused by the independent variable? (from lab).
5) How is the term 'theory' use in science? How is it misused by the public?
6) Describe why scientific creationism and "intelligent design" are not scientific ideas.
7) Describe the two limitations of science.
8) Explain reductionism.
9) Why is the comparative method so useful in biology? Why should we expect things to be similar?
10)Place these entities in their correct order, from small to large: molecule, atom, cell, organelle, organ, organism
11) What two types of reproduction do many living systems perform?
12) Why are living systems dependent on energy transformations? Explain in the context of the two laws of thermodynamics.
13) Distinguish between three types of response, making sure to describe the biological scale at which these responses occur.