Concepts of Biology (BIOL115) - Dr. S.G. Saupe (; Biology Department, College of St. Benedict/St. John's University, Collegeville, MN 56321

Nature of Science

I.  What is science?  
    Latin - scientia, meaning to know or have knowledge.  By this definition, everything is science!

A.  Comparison of disciplines

Which is best?  None...each has its particular purpose and should not be used for the others.

B.  Definitions of science.  Among the many possible definitions, Science�.  (don't memorize these)

         tells us how many and how big, but not how beautiful

         is the systematic gathering of information from observation or experiment

         is an exploratory activity for the purpose of understanding the natural world (P. Medawar)

         is organized skepticism (M. Curd)

         is a self-corrective discipline

         is scrupulously applied common sense (Huxley)

         is the search for understanding, which is achieved by statements of natural laws applicable to a wide variety of situations, and that are tested experimentally (Goldstein & Goldstein)

         seeks to organize knowledge in a systematic way, endeavorig to discover patterns of relationships among phenomena and processes

         strives to provide explanations for the occurrence of events

         proposes explanatory hypotheses that must be testable, that is, accessible to the possibility of rejection

         is an interconnected series of concepts and conceptual schemes arising from experiment and observation and yielding new observations and experiments (J. Conant)  

    One of my favorite definitions is that �...all science is partly biological (George Gaylord Simpson - This View of Life)."  I like this quote because it highlights the importance of the observer in the scientific process.

C.  What science isn�t.
    Science isn't involved in moral decisions, social attitudes, or beliefs.  But, clearly science and scientists are influenced by them.

II.  Goal of Science.
    The goal of science is to understand the natural world and uncover underlying truths (facts).  Question:  what is a fact?  A fact is what most everyone agrees to be true.  Fact are real events that are/were observable.  Compare this to an inference � a deduction or conclusion drawn from facts that tend to be predictive, and do not describe real events that occurred.  

A.  The "problem" with facts.
    Just because everyone agrees, does that make a fact necessarily true?  Nope, they are only our best guesses at the time.  Why?  Simple � a fact is a fact only because we believe it.  And, since facts are perceived with the instruments available to us, including our senses, who can say that our senses aren�t being fooled (i.e., optical illusions)?

    We know that there is both a physiological and psychological component to vision/seeing.  For example, individuals blind since birth and then able to see as the result of, say a cataract operation, have to be �taught� how to see.  Thus, seeing is in part a �learned experience.� 

B.  Paradigms
Facts are theory laden, encumbered by the prevailing ideas, or paradigms, of the day.   A paradigm is a way of looking at the world.  A paradigm is essentially your perspective or outlook on a situation.   It is difficult to escape and see past the current paradigms. Here's a simple example � not too long ago my wife and I attended the wedding of one of my former students, Tim. While sitting in church we saw some friends, Dennis and Betty, that we hadn't seen in quite awhile.  During the ceremony I wondered how they knew Tim since I didn't think they were associated with CSB/SJU.  After the ceremony we got chatting and it turns out that they were there for the bride, Kelly.  Duh!  Why hadn't I thought of that? I was blinded by my paradigm, "I was invited by Tim, so they must too".  The evidence was clear � Dennis and Betty were even sitting on the other side of the aisle in church �  but I just couldn't see past my preconceived paradigm.

    There are plenty of scientific examples of paradigms throughout the history of biology.  Two important ones include the explanation for the cause of disease and the origin and evolution of life.  The table below summarizes these paradigms.

Table 1.  Paradigms Old and New


Old/Original Paradigm

New Paradigm

Cause of disease

diseases are caused by spirits (i.e., miasma theory -  diseases were caused/ transmitted by bad air, called a miasma. 

diseases are caused by germs (i.e., Pasteur & Germ Theory)

Origin and evolution of life

Creationism (God created life in the form we now find)


Existing paradigms are always being challenged, tested.  Those that don't fit with the evidence are discarded as new ones are adopted.  Paradigms change over time and when they do it tends to be some of the most intellectually-stimulating times.  Two medically-related paradigms that have changed recently are: (a) the switch from a focus on disease to wellness; and (b) recognition of some types of alternative medical therapies (i.e., herbal remedies)

III.  Philosophy of science.

A few years ago, a supermarket tabloid reported that the actor/singer Tom Jones reportedly almost drown in a rip tide, but a large wave threw him back on shore.  What explanation can we suggest for his miraculous rescue?  Well, perhaps God grabbed him by his shorts and tossed him back onto the beach.  Alternately, a large wave just happened to roll in and catch him.  The first explanation is vitalistic - based on the notion that the universe is controlled by supernatural processes whereas the latter, is mechanistic.  This idea originated with the Greeks and essentially assumes that the universe is orderly and rational and is governed by predictable laws.  It should be no surprise that religions are vitalistic while science is mechanistic.   Thus, a scientist wanting to explain the Tom Jones �miracle� would look at it from a mechanistic perspective.  This allows the scientist to develop a hypothesis to explain the event and to collect evidence that would support or disprove this hypothesis.  For example, one hypothesis is that Tom was swept up in a beachward current.  However, there is no way a scientist could determine whether God actually helped.

Related ideas are causalism and teleology.  According to teleology, events in nature occur according to a predetermined plan, in other words, everything has a time and purpose.  In contrast, causalists deny predetermination, but rather, suggest that events occur in a stepwise fashion, each event setting the stage for the next.  A good example would be in the novel Bridge Over San Luis Rey.  The author (Thornton Wilder) wrote from a teleological perspective following the lives of the individuals who died, suggesting that they were destined (�it was their destiny� - Darth Vader) to die on the bridge.  In contrast, a caualist would argue that it was simply chance that those five individuals happened to be on the bridge.  Perhaps their combined weight was sufficient to break the bridge after years of weathering.

click here for more details

IV.  Types of Science.

  1. Observational or descriptive - accurately describe nature (i.e., anatomy, astronomy)

  2. Systematic or taxonomic - naming and classifying organisms

  3. Hypothetico-deductive or "Experimental" Approach - this includes the typical �scientific method� which usually includes a comparison of two groups (experimental vs. control) that differ by a single factor (variable).   The usual steps of the scientific method are:  (1) make observations/gather information; (2) develop a hypothesis; the hytpothesis is generated by deductie logic - formulated as If...then...statements;  (3) design an experiment to test the hypothesis; (4) collect data (results); (5) make conclusions; (6) report results; (7) repeat ad infinitum modifying hypotheses as necessary and/or generating new ones.  This is the type of science we will do during our first lab.

  4. Model Building - a variation of experimental science in which models are constructed and then tested to see if they fit the data. 

V.  Hypotheses.
A hypothesis is a tentative explanation for an observation.  It is your best guess.  For example, what if I think that Tom Jones was �saved� by a chance encounter with a large wave that pushed him into a beachward current.  If this is a good hypothesis must be:  

  1. testable - able to design an experiment or make an observation to determine its validity (I could test my hypothesis by studying currents in the area, the frequency and size of waves, whether it was high or low tide, etc.);

  2. falsifiable - the possibility exists that it could be false.  My hypothesis is falsifiable because it certainly could be potentially false.  For example, we could find after study that there are no beachward currents in the area.  Thus, we have shown it to be false, and must consider an alternative hypothesis; and 

  3. simpler than competing hypotheses (called Occam�s Razor).  As an example, I could propose that a dolphin happened to swim by, see Tom in trouble, swim underneath him then flick his tail and cast him up on shore - certainly less likely than our wave hypothesis. 

VI.  Nature of proof.

Technically, you can never �prove� anything in science.  The possibility always exists that another hypothesis is true � especially since it is impossible to test a hypothesis under all possible conditions and circumstances.  We can collect enough support that it will seem like solid �proof�, but we still haven�t absolutely proven it.  Conversely , we CAN prove an idea to be wrong since it only takes one case to show that a hypothesis is not true.   To take advantage of the ability to disprove hypotheses, we often state them as a null hypothesis - that is, we state that there is no difference between what we expected and what we found.  And, if we prove this to be false, then that means there must (�proved�) be a difference between the two.  This is a commonly used technique by �statisticians".  The take-home-lesson from this is that we can support an hypothesis, but we can't prove it. Don't say that you�ve �proved� your hypothesis �  instead, say that you've �supported� it.

VII.  Biology has few laws.
    The more data that support a hypothesis, the more strength that it has, and we presume the greater "truth".  The general scheme of increasing strength of support for an idea is:
hypothesis theory  law.  In practice, there is no clear distinction between law, theory and hypothesis.  For example, even though you hear of the �theory� of evolution, it doesn�t mean that biologists consider it is any less a fact that say, the �law� of gravity.

    Thus, biology is a statistical science.  Generalizations in biology are probabilistic - because there are often exceptions.  Why?  because living organisms are so diverse and exhibit exceptional variety.             

VIII.  A Case Study:  Ignaz Phillip Semmelweis and Childbed Fever (for more information see the article by Brown and Williams, 1990)  

  1. Background & Problem: 
        Semmelweis (1818-1865) was a Hungarian physician; received a medical degree and midwifery from the University of Vienna (1844).  He worked at Vienna General Hospital Obstetrical Clinic.  He noticed that many women in the clinics died of childbed fever.  The cause was unknown but was "hypothesized" to be caused by miasma.  Because of the high risk of dying from this fever which was associated with hospitals, most women had births at home.  Clinics were just for poor, unwed mothers.  Childbed fever is now known to be caused by Streptococcus pyogenes (Staphylococcus) - like one that killed Jim Henson (Mr Muppet) and the face-eating bacteria.

  2. Observations:
        There were two clinics at the hospital � one with medical students and physicians and the other with midwives.  The mortality rate was high in the First clinic that was tended by physicians and students.  The mortality was low in the Second clinic staffed by midwives.  Semmelweis observed that in the first clinic the physicians and students would perform autopsies, exams, and examine sick patients.  The midwifes cared for patients but performed no autopsies.  The mortality in the First clinic was high (about 10%) but low in the Second (about 2%).  The First clinic admitted patients on Saturday, Sunday, Tuesday and Thursday, while the midwife (Second) clinic admitted patients on Monday, Wednesday and Friday.  The delivery practices in the two clinics were the same and the deaths occurred in patients admitted on Saturday, Sunday, Tuesday and Thursday.  One of Semmelweis teachers died from infection received during autopsy; symptoms similar to childbed fever.

  3. Hypothesis:  
    The medical students and teachers are passing the disease from patient to patient

  4. Alternate hypotheses:  
    The patients sick before arrival.
        Miasma caused disease.   

  5. Predictions:  
    IF the medical students and teachers are passing the disease from patient to patient THEN, washing hands should prevent disease

  6. Experiment: 
        Semmelweis ordered everyone to wash hands with chloride of lime

  7. Result:  
        Death rate dropped.  

  8. Conclusion/Evaluation:  
    Semmelweis - Problem solved
    Others - Coincidence (especially because they stopped washing hands and death rate rose again.  End result:  Semmelweis' work NOT accepted especially because he didn't publish his work.  He spoke in 1850 at Med. Society of Vienna and physicians were on the verge of acceptance, but adidn't because he hadn't published (at least until much later in a rambling incoherent way).  He eventually died in an insane asylum at 47.  

         For a dialog about Semmelweis, click here


  1. Societal acceptance of/impact on science

  2. Development of hypothesis; tested by gathering evidence

  3. Control vs. experimental groups - indirectly

  4. Importance of publication

  5. Standard scientific method not always - usually have an opinion about what the endproduct of experiment experiment to support/prove yourself wrong.

  6. The time was not ripe for understanding of his discoveries

IX.  Case Study - Frog and Toad in the Garden. (not covered in class but fair game for exam)
This wonderful children's story by Arnold Lobel provides a look at experimental design and inappropriate conclusions (non-causal correlations) based upon a poorly designed (no control group) experiment.

 click here for details

X.  Case Study � Card Playing   (not covered in class, not on exam)
We will see if you can determine the pattern that I arrange in a deck of playing cards.  This exercise should focus on concepts of falsifiability, certainty, proof, alternate hypotheses, laws and biology.              

XI.  Case Study - Dodos and Trees (not covered in class, not on exam)
This story is included because it demonstrates nicely how scientists can study past events.  

A.  Observations.
    On the island of Mauritius, the native home of the now extinct dodo, Calvaria trees have not germinated naturally for 300 years (the age of the youngest tree), which is about the same time as the dodo went extinct.

B.  Question.
    Was the extinction of the dodo responsible for the failure of the Calvaria tree seeds to germinate?

C.  Hypothesis.
    Germination of the seeds of the Calvaria tree only occurred naturally after they passed through the gut of a dodo.

D.  Collect evidence/experiments.
We haven�t mentioned it yet, but technically what scientists do to support or disprove a hypothesis is to determine if predictions that arise from their hypothesis are true.  Let�s list some predictions from the hypothesis.  IF the dodo is responsible for the failure of the Calvaria seeds to germinate, THEN......

  1. there should be no trees younger than 300 years when the dodo went extinct.  (This is true)

  2. the dodo should have been big enough to eat the seeds (True)

  3. the dodo was small enough to prevent completely crushing the seeds (True, demonstrated by inference to other bird studies);

  4. dodos would eat seeds (True - seeds found in fossils)

  5. passage through a dodo gut should cause the seeds to germinate (True - from studies force-feeding turkeys).

E.  Conclusion.
The extinction of the dodo has lead to the near extinction of Calvaria trees because the seeds have a very hard pit that can not be broken down.  The evidence seems to be very strong in support of the hypothesis.  But, does this prove our hypothesis?  No - remember we can never �PROVE� our hypothesis - it�s always with the realm of possibility that an alternative is true - for example, perhaps the seeds aren't germinating because of a climate change, or a new disease, or pollution in the water, etc.  In fact, this article was published in one of the premier journals of America science.  It stimulated a flurry of research and thinking and now has been discredited.  

XII.  Case Study - van Helmont and his willow(not covered in class, not on exam)
We will analyze this classic experiment that was very important in the history of plant physiology.  Interestingly, it had some �flaws�. 

Click here for details.

XIII.  Case Study - Willow Cuttings 
(not covered in class but fair game for exam)
             Click here for details.


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