Revision Portal> 2012 First Semester Revision

Class content > Introduction to the class

Two hundred years ago, biology was mostly about figuring out what kind of living organisms there were and how to describe and classify them.  (cf. Linnaeus)  But by 100 years ago, scientists like Darwin, Mendel, deVries, Fischer and others began to develop an understanding of how living beings worked and how they fit with their environments and with other organisms.

Today, and very likely for the next few decades, the most exciting developments are in the areas of figuring out how biological organisms work -- how they function in detail, through an understanding of their structure down to the biochemistry and the atomic and molecular level, and how they interact -- how populations and communities of organisms behave, through an understanding of ecology and evolution.  

Biology remains highly complicated, and there are large sets of terms to learn.  But the trends in modern biology means that a biologist or health-care professional who wants to keep up with developments needs to understand the difference between two kinds of scientific thinking:

• Phenomenology
• Mechanism

(Of course this is a bit of an artificial distinction. One is very rarely doing only one or the other in any discipline. That is just not how human cognition works. We see something happen, we try to describe it, but we are often simultaneously attending to causality. And in attending to causality means choosing aspects of the phenomenon to focus on. I don't think a clear distinction between these two modes of thinking really exists. More importantly, I don't see it is useful to draw students attention to this.)

Phenomenology

The term phenomenology basically means the study of phenomenon -- what there is and what happens.  It's largely descriptive. (Back to the section on disiplines, this speaks to the idea  that biology courses are NOT organized in terms of phenomena. Yes, 100 or so years ago.  Not today.  Bio courses are organized by principles and processes.)

Mechanism (I think your sense of mechanism is what in some cases we would call a process. a process is a sequence of mechanisms or steps that underlie or explain a phenomena. I think there may be a distinction between mechanism and process, but that may be too picky. )

The term mechanism means considering a phenomenon at a finer-grained level (finer-grained than what? this is an arbitrary distinction. mechanistic explanations can be made at various levels of abstraction depending on what you are trying to explain (I see that you do get to this below). again, this hierarchy makes the distinction between phenomenology and mechanism a bit to blurry to be of use).  What parts does it have?  What are the relations of the parts to each other?  What is are the chain of events that lead to a transformation taking place. Mechanistic thinking is analytic -- it breaks things down. Mechanistic thinking is valuable not just in science. It helps you understand whether your plan to organize a party for your friends will work and whether a politicians plan for the country makes sense.

Any science involves both phenomenology and looking for mechanism -- description and analysis.  (THE SIMPLIFICATIONS IN THIS SHORT SUMMARY OF PHOTOSYNTHESIS DO A GREAT DISSERVICE.  YOU DONT WANT TO INTRODUCE GROSS MISCONCEPTIONS IN YOUR SUMMARY OF THE PHENOMENOLOGY.)

•  In biology, the phenomenology of photosynthesis (GRAMMAR-- THE PHENOMENOLOGY DOES NOT SAY ANYTHING.)  might say is that plants convert use sunlight to make into sugars and starches that can serve as food for the plant and for organisms that feed on the plant, such as fungi and animals.  Biologists provide an understanding of this phenomenology  by studying and articulating  Understanding the mechanisms of photosynthesis.  fFor example what wavelengths of  light from the sun are effective (only certain very specific colors of light can be used to produce sugars work), what chemicals in the environment are converted to sugars, what chemicals exist in the plant carry out that results in this transformation, and what is the pathway sequence of chemical transformations that take place? 
• In physics, we can observe that when we hook a battery up to two identical bulbs connected in a row, the bulbs are dimmer than when we only hook up a single bulb.  That's phenomenology.  If we analyze the circuit by identifying the relevant properties of the battery, bulbs, and wire (voltage, resistance, and current) and figure out the relationships between them, we are exploring mechanism.  

Note that analyzing mechanism can occur at many levels.  With our batteries and bulbs, understanding currents, voltage, and resistance is a macroscopic  mechanism.  If we learn more and understand that currents in a battery and bulb circuits are electrons that are separated from their atoms and moving through the wires, we can explore a microscopic mechanism.  In biology we can go up or down in scale.  The mechanism of photosynthesis described above -- in terms of chemistry -- is a microscopic mechanism.  But we might also consider how photosynthesis evolved in terms of the interaction of different organisms and in an ecological context -- a mechanism at a level above the functioning of a single organism. 

Since physics "sets the rules", constraining how things can behave, physics is particularly important when trying to understand biological mechanisms.

Joe Redish 7/10/11