the Scientific Method   and  the Scientist

      "Equipped with his five senses,
                  man explores the Universe around him
                            and calls the adventure Science."

                                   Edwin P. Hubble
astronomer - 1948  

      The Scientific Method is the orderly process of asking
      and answering questions about the Natural World
      through repeated and unbiased observations and
      experimental tests...

                            end of scientific method lecture outlinenext A
















Gk:   Bios = life     Logy = study of                                    
the term biology was coined by Gottfried R. Treviranus
in 1802.

                    Biology is one of the Natural Sciences which also include...
     Physics is the study of atomic particles of matter that interact 
                  by a set of rules (gravity, electromagnetism, strong & weak nuclear
                  forces) that may be distilled into predictive formulas,
                       Golden ages = 16th (Galileo), 17th (Newton), and 20th (Einstein) centuries.

    Chemistry is a more complicated application of physics & its rules
                  to a few molecules interacting in a test tube.
                        Golden ages = 18th (Priestley O2), 19th (Dalton), 20th (polymers) centuries.  

       Biology, then is an even more complicated application of chemistry rules,
                  in a special test tube (a cell), which may run via predictive formulas?
                  but, as we'll learn, Biology's rules are messy and they're infinite...
                  the multitude of molecular interactions are almost impossible to predict
             Golden genomic age - 20th (Watson & Crick) and 21st (Doudna & Charpentier) centuries.


the end of
                      scientific method lecture outline










Biology is an activity carried out by thousands of researchers all contributing to a general picture of Life and the Nature that evolved on our plant, Earth,
and is commonly described as the...
Study of Life and  the Living Condition

Biology recognizes the CELL as the basic unit of life and attempts to describe the properties of the cell as the living condition, including its origins, growth, reproduction, structure, heredity, and evolution.

Biology attempts to understand HOW INANIMATE MOLECULES built a highly ordered and complex interactive system that exhibits EMERGENT PROPERTIES, which we characterize as cells being ALIVE.

Biology has established that all life shares a CARBON BASED CHEMISTRY, depends upon WATER, and is capable of SELF-REPLICATION, which defines a rich set of characteristics we refer to as the LIVING CONDITION.
    Neils Bohr (NP in Physics for Atomic Theory 1922)
       "We may look at a living organism either as a living organism or as a jumble of molecules".

The aim of modern biology...
  is to interpret the properties of living within the structure of their molecules.






   Textbooks explore biology, with a little detail, by looking at the the rich storehouse of discoveries
   made by
all the [rockstars] biologists who have come before us, such as...

                          Do you recognize any of these "famous" biologists?

   To explain the Biology of Living Things is too difficult for one to do in one's own generation time.
   It's for one to do a small bit, with certainty, now, and leave the rest for those who come after us.
(paraphrased from Issac Newton - 1643-1727)

   The Scientific Method is not trusting blindly in our past knowledge (your textbook)... or not having
   absolute faith in the accumulated knowledge of our forefathers. Science is a Human endeavor
   beset by social and cultural influences, irrationality and even fraud, but in the end science
   establish, with clarity, who is right and who is wrong.

   In science "I made a mistake" is often the best strategy to the truth and how the world functions.
                                      (paraphrased from Carlo Rovelli - Reality is Not What it Seems. (2017)    

    For now, we will begin our small bit by reviewing how they used the SCIENTIFC METHOD.

   fiber helix














the Scientific Method...         a Video Descriptionview@home-10 min

    Scientific Theories often have only 2 components:
   1. one component describes  PATTERNs  OBSERVED in the natural world 

  2. other component identifies PROCESS or MECHANISM  responsible for the pattern


            To solve a scientific observation/problem a scientist must first
                               Recognize and State the problem?

             a graphic of the steps involved in the Scientific Method*

       fiber helix
Let's take a closer look at these steps of the Scientific method?












read this a PROCESS for investigating Nature

      it's the methodology by which scientists, collectively & over time, attempt to construct
      an accurate, reliable, consistent, & non-biased representation of observed natural world

   is a process for investigating the things (patterns) we observe around us...

is a means for describing...  the mechanisms (laws/rules) that govern our physical world...

is a careful observation & measurement of patterns of living things & their processes

                           it employs rigorous methodology and

                           it devises
experiments to validate a clearly stated hypothesis...

           "Science is what scientists do, and there are as many scientific methods as there
are individual scientists
. The scientific method is what working scientists do."
     Cartoon                                   Quote by... Percy Bridgman, "On scientific method," in Reflections of a Physicist,
                                                                                       New York: Philosophical Library, 1955

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SCIENTIFIC METHOD... often involves a number of COMMON PRACTICES:

 1. Observations...  an accurate description of a phenomenon or group of phenomena.
             i.e., a gathering of the data...  either directly  or  from previous studies...
       an observation: 
Bil 150 students sitting in the top of a lecture hall, often fall asleep?

Begin to ask Questions: about how's & why's (mechanism) of things you observed.
                      What is the process or mechanism responsible for them falling asleep?
In the scientific method  questions must be framed in measurable terms.

Begin to look for ways to Ask a Testable Question:
others may have asked & even answered the same type of question...
literature searches:   textbooks,  journal & internet articles...
                          reading other people's findings may lead to more interesting questions,
                          and help define  or  modify your testable question better. 




                      It is known that warm air rises so, pose a testable question...

            "Does sitting in warmer air at top of lecture hall promote student sleep"?
















2.  Postulating the Question... 
i.e., Formulating an explanation (testable hypothesis) of the
        observations &
the posing of a critical and experimentally testable question is hard - 
        If students fall asleep in class... 
Does warm air at top of auditorium promote sleep?
     Develop possible explanations:        
         Formulating a Hypothesis*... an explanation, based upon observations and,
assumptions, that leads to a formal testable prediction
         is a proposed explanation for our observation, which is experimentally testable...
         our observation:  compare numbers asleep vs. awake in hot & cold temperatures...
fiddle with the air conditioning &/or thermostat in the room...
                                          hot..., hot...cold etc....
         One must state the testable hypothesis as precisely as possible and must list
         list the expected predictions that the hypothesis might make

                 "warmer air at top of lecture hall promotes sleep"

often involves critical analysis  &  critical thinking
                        and there may also be alternative hypotheses  -
                            ... sitting in the top or back of the classroom keeps a student
                            ... out of reach of instructor  &   its quiet & cozy...
... or maybe "it's a boring lecture that promotes sleep". 








3. Experimental Testing and Predictions...

             a hypothesis is making a prediction
to be experimentally tested. 
    "Lowering the temperature at the top of the auditorium can prevent their sleeping"

            Designing an experiment to test a Hypothesis is a big part of Scientific Method:  
                  Experiments requires experiencecreativity and sense of what is  practical.
                       √    read methods published by others - modify them to your purpose,
                       √    brainstorm with others - different perspectives are helpful,
                       √    you may be limited by equipment availability, costs, and time.

             Let's look at a BUSINESS ANALOGY that is similar to hypothesis testing?
      Experiments are best designed to FALSIFY, not to prove a hypothesis.
When an experiment works, it does NOT prove the hypothesis,   
more likely it just does not falsify the hypothesis being tested.      

          There is often no proof in science, only 'disproof' :
                   the scientific method is all about disproving what was once believed
                   to be truth & reality,
but evidence may be collected in support of a hypothesis.   
           When scientists publish their data, they never say "results prove..."
but rather "results suggest..."    or    "results provide support for..."










DESIGNING the Experiment    is a hallmark of the scientific method..
the design of an experiment should be to...  FALSIFY the HYPOTHESIS  
          and experimental methods need to meet certain CRITERIA including:  
          - being unbiased...
          - defining the variables... factors that are liable to vary or change during experimentation:

Example Experiment
            plant hormone
* (used in the stem elongation experiment below)...
  dependent variables:
the variable being modified by treatment
                      such as - cell, stem or root length in mm, etc.., number of parts, etc...,
                      must be measurable & observable units;

independent variable: only one variable being manipulated, which may change...
                      height, weight, age, sex, amount of hormone, etc..., often it is time.
controlled variables:  all other factors kept constant and not allowed to change,
                   all experiments must have a control...  standard for comparison (a challenge)

            Variables plant growth hormone auxin in the plant stem growth experiment:
                               dependent variable:      cell, stem, or root length (growth).
       independent variable:   growth over time at one auxin concentration

 next           and controlled variables:      temp, humidity, day length, amount of fertilizer.









          a big part of experimental design is
materials & methods (the procedures used)
          based on previous published works, colleagial suggestions, intuition, etc...


          our auxin hypothesis... 
              if auxin
is added to DWARF PLANTS, we predict stem lengths will increase


          our experimental design will analyze effect of auxin on dwarf plants:

              1. auxin controls  negative control:   dwarf plants NOT given auxin
                                            positive control:    normal plants NOT given auxin 

               2. determining the proper auxin concentration levels:
                                 should not be too low (no effect detected) nor too high (toxic);
                                 should be within physiological range [10-6 to 10-10M] of cells


must be recordable quantitatively measureable, such as stem length (mm)

4.  must be replicable...  redone several times, to be statistically valid
experiments ought to show consistent results
                                  again and again, from test to test















  to help make predictions about an outcome, experiments
may involve making a MODEL...
       a picture is worth a 1,000 words... a drawing can be a model of how a structure might work.
purpose of a Model (a kind of analogy or mental image) is to give one a conceptual
            likeness of how something functions...
  water waves is a model image to emulate light waves.
waves                      light waves       

Protocols to help model a hypothesis:         

      Hypothetico-Deductive Model...  which involves the formulation of the hypothesis,
         conceivably falsifiable by a test of observable data, and from experiments one
         may deduce a general answer to the hypothesis...   .
       often involves...     

  Deductive Reasoning...    (from general case to the specific)
IF...THEN deductive logic
                            IF all birds have feathered wings,
and a robin is a bird,
THEN robins have feathered wings.     
 - in daily life*

              Inductive Reasoning...    (from a specific case to a general principle)
         it is the ability to deduce intuitive/creative principles...
             objects fall to ground when dropped...
                thus, a force
  [gravity]  must act on the object...   
                  "sparrows are birds... birds have wings... thus birds can fly" 














   Additional aspects of the Scientific Method include... 
Scientific Method is cumulative...
            - no endeavor of humankind rivals Science in its incremental processes
                               toward a more complete understanding of the observable world.
               "The beauty of science is that all important discoveries are made
                 by building on the discoveries of others
     JC Venter...A Life Decoded, 2007

        Scientific Method must repeatable...
            - everything that science "knows"  - even long established theories -
                               are subject to reexamination as new information is collected.
                            "all scientific knowledge is tentative, and open to challenge"


        Scientic Method shows
not all experiments are clear cut, scientific results must fit into known facts.
            - something is purposefully changed by the researcher in the environment
            - random assignment of multiple study groups is often employed.

     Now let's recall our auxin experiment hypothesis and its predictions:
               negative control:    dwarf plants treated with water   =   remain short (dwarf)
               positive control:     normal plants treated with water =   remain normal height
               test treatment:       dwarf plants treated with auxin   =   grow taller (normal)

                              so let's do the experiment  and  collect some data...












  The Collection & Interpretation of Experimental Data...
   Data collection often draws upon previously known knowledge...
     and scientists fit the new knowledge into framework of what they already know...


   Observations and Measurements must always use the same criteria (Standardization)...
in our Auxin experiments: plant height always measured from pot rim to shoot tip

          Variability in data from experiment to experiment must be estimated via ...
statistical analyses:
    some common statistical methodologies include ...

                      t-test         - compares the means of two groups

                      ANOVA     - compares means of three (3) or more groups

                      chi square - compares how closely the observed or measured data
                                                  is to the expected results
  (ex: genetic crosses)

                       linear regression - a single independent variable (time) is used to
                                                 predict a value of a dependent variable (mm)

            What are some of the ways that biologists present their collected data?*   


















     Organizing Data...   raw data is often expressed in tables and figures. 

         tables:  often used to emphasize numbers themselves, rather than a trend

         figures:  graphs show trends;   pictures,  photos,  diagrams are

                         line graphs - show effect of independent variable on  X-axis - (time)
                                              the dependent (measured) variable on  Y-axis - (length)

                         bar graphs - compare sets of data that may be discontinuous
                                                  i.e., maybe different groups

         the best way to display your data often depends on what you want to show

aim is to show when maximum growth rate is reached after several weeks

         sometimes data may be misleading:   Will chocolate lead to a Nobel Prize*?
urban legend:   younger scientist make the great discoveries

                                                                            Homework Assignment
















It's may seem easy in the Hypotheical-Deductive model to make an initial hypothesis...

         but it's hard to make an effective CORRELATION between CAUSE and EFFECT.

            Drawing  a conclusion...     if experimental outcomes match your predictions,
                                                       then your hypothesis is not falsified, but is supported,
                                                       if not, then your hypothesis is negated.
Do your results agree with findings of others?
if not, do you know why not ???   
                          a different species or strain of organism, different model of instrumentation,
                          different methods, seasonal variation in reagents, etc???


Experimental Results are a TOOL
                 Scientists usually assume that no theory is 100% correct.
                     so  experiments provide a sense of direction for doing more experiments.
                                do NOT let predictions affect your objectivity.
                                do NOT make results fit your predictions (
personal bias).                     
                     you may modify your hypothesis to better fit the observed results...
                                    modifications of a hypothesis help scientists gain assurance
                                    that their explanations may eventually be valid.
Negative results are often more important than positive ones.






Affirmed data may let one formulate or substantiate a THEORY...
                                           ... a set of rules & mechanisms governing what was observed.
a THEORY is... a hypothesis that has stood the experimental test of time.

Theory of GRAVITY is always subject to testing & refutation as new ideas emerge;
       If experiments always support a hypothesis, it is regarded as a THEORY or LAW
           of nature, but if it doesn't we must scrap that theory...

Scientists are constantly double-checking their own ideas and, even if they don't, other
   scientists will do so. The goal is to get at the truth. Indeed, a good scientist should
   never hold firmly to their ideas and should be open to changing their viewpoint as more
   data comes in. Slowly. but surely, scientific ideas are refined by this process, getting
   closer and closer to the TRUTH

In scientific disciplines, the words "hypothesis",  "theory", & "law" may have different
       connotations in relation to acceptance or knowledge about a group of phenomena. 

A scientific theory or law represents a hypothesis, or a group of related hypotheses,
       which have been confirmed through repeated experimental tests over a long period of
       time and the results are considered to have general significance.

              "Nothing in Science reaches the level of Theory without a vast pool of facts
                    and tested hypotheses behind it
james rollins 'Black Order' (2006)

                    The great Theories of Biology may be compared, as creative
                           achievements, with the great works of art or literature. 

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  the Scientific Method has limitations...
     the scientific method can not deal with hypotheses
                               that are NOT EXPERIMENTALLY TESTABLE...  



  How  many  of  you  believe  there  is  life  elsewhere  in  the  Universe?*
                       A show of hands, please!


















fiber helix.gif (5957

"IRONIC SCIENCE"... (non-testable hypotheses, that appear scientifically based)

   previous example:  Is there life elsewhere in the Universe?  
         Human do not have the technology to answer that question yet.
             The vast size of the observable universe (93 billion LY in diameter) with up to
             2 trillion galaxies (many larger than the Milky Way) precludes human observation.  

   Some other examples of Ironic Science:             
        Nuclear winter
* or  a meteor* that causes dinosaurs mass extinctions?  ice ages?, etc.
            Can scientists do any experimentation to test these hypotheses???
            Mount St. Helens  image & impact*  +  MODIS Earth-on-fire*
                       Amazonian deforestation,    are they part of Global Climate Change ? ...


These are systems that involve great Complexity and make it difficult to predict exactly
   what is going to happen at any given time, in the present or the future.

                  Chaos theory deals with the behavior of nonlinear dynamical systems that are characterized
                  by sensitivity to initial conditions. Examples include the atmosphere, the solar system,
                  plate tectonics, turbulent fluids, economies, and many biological systems, as
population growth.


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Technology & Advances in Instrumentation...
plays a role as important as any hypothesis or concept.
       Scientific instruments extend our senses for observation of the natural world.

       Developments in instrumentation have greatly advanced cellular biology analyses... 
             examples:   1)  microscopy from mm to nm
(light to electron microscopy),
                                2)  rapid through-put DNA sequencing machines,
                                3)  tagging of molecules within cells stains vs. fluorescent markers.

       "Although concepts and ideas occupy a central place in the grand sweep of our under standing
         of the nature of the world around us, it is a mistake to imagine that they play a greater role than
tools and techniques in achieving scientific progress". 
Few scientific revolutions are concept driven
                           Human Genome Project, J.M. Thomas,1994 

        "Progress in science often depends upon  new techniques, new discoveries, and new ideas,
               probably in that order
                                                                  Shimomura, Chalfie, Tsien win 2008 Nobel Prize for GFP

        "Advances in Science are enabled by technology advances that allows us to see what we have
                not been able to see before
."                  Lloyd Watts, Computational Intelligence: The Experts Speak.  IEEE Press, 2003.







    What about
ERROR in scientific experiments happens... it may have have several sources...

    1.  No instrument measurements are absolutely precise.
Accuracy is limited by the smallest division an instrument can measure.
               There's also intrinsic error in
instruments  -->   RANDOM ERROR... or
unpredictable variations in measurement
* signals (background noise). The precision
               of a measuring instrument and accuracy may be improved by making multiple
               measurements of the same thing with the same instrument an expressing the variation.
               Knowing the
Limits of Resolution of an instrument is critical to accuracy.
2.  There is NON-RANDOM or systemic error, due to factors which may bias the results.
               No experiment, can be perfectly precise..
          A.  Human error:
failure to follow procedures, failure to use the equipment properly,
               failure to prepare solution correctly, measurements made by 2 researchers,
               simple arithmetic errors, etc... 

  Fudging data:
               Another common mistake is to rule out or
ignore data which do not support
               the hypothesis...  Humans have psychological tendency to find "
something wrong",
               with data, which does not support
their hypotheses.
   see: Bungles, Lies, & Fraud












 ERROR cont.

      C. a scientist's personal BIAS can effect the outcome of an experiment...
           most fundamental error is
to mistake the hypothesis for an explanation of a
, without performing experimental tests. Sometimes "common sense"
           and "
logic" can tempt us into believing that no test is needed.
...teacher can intimidate student in front to keep awake    Bias is Unavoidable*read@home 
                  ....humans have implicit biases, yet we often ignore them.


           Bias may be overcome... via open communication among members of the scientific
           community because experimental tests are repeated by different scientists...
           using different types of experimental setups... again and again.

           Sharing your results...    the  "PUBLISH or PERISH" Rule
1.  in a paper in a referred (peer-reviewed) journal publication +
Open Access
 2.  at a poster session at a scientific meeting
3.  via seminars at scientific meetings or symposiums














             Over a period spanning a variety of experimental tests (usually many years),
consensus develops in scientific community, as to which experimental results
             have stood the
test of time and become     ---->     THEORY.
     the word   THEORY... 
         to scientist the word THEORY means ESTABLISHED FACT or TRUTH,
            but, to lay person (nonprofessional) the word THEORY may mean...
a speculation, a guess, an unknown,
or a lack of knowledge.
the end of scientific
                        method lecture outline
                             Scientific Insanity:       doing the same experiment over & over,
                                                             but expecting a different result each time     

              If Science is what scientists do, then  What Makes a good Scientist?   

paradigm - an
                            archetypal model   <--Paradigm             back to Bb    Scientific Societies*                           
  copyright c2023,   Charles Mallery, Department of Biology, U. of Miami.         










         previous material no longer relevant

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            on what the Scientific Method is...    &     who is a

  The scientific method was initiated by the Greek philosophers [2600 years ago].  
(590 bc) is considered the founder of the scientific method...
   The prime question asked was..
"what differentiates living from non-living".





  "Science is what scientists do, and there are as many scientific methods as there
are individual scientists
. The scientific method is what working scientists do."
     Cartoon                      Quote by... Percy Bridgman, "On scientific method," in Reflections of a Physicist,
                                                   New York: Philosophical Library, 1955  


   What experimental results from hypothesis testing tell us...

            a Hypothesis is always open to further testing (i.e., not proven correct)...
                           but, a
Hypothesis can be falsified
(proven wrong) or refuted

            Experimental testing can support the hypothesis as a likely explanation,
            not by proving it is correct, but rather by finding that it is NOT FALSE.

There is often no proof in science, only 'disproof':
but evidence may be collected in support of a hypothesis...

             When scientists publish their data, they never say "results prove..."
but rather "results suggest..."    or    "results provide support for..."