THE YEAR IN MICROBIOLOGY
I'm weight challenged because I have too many hunger receptorsThese stories illustrates the two unifying principles of biology upon which I anchor the biological phenomena covered in Micro 101/102.
Two men camping in the woods, climbed
out of their sleeping bags only to see an obviously angry Grizzly bear approaching. One of
the men grabs his running shoes and begins to put them on. |
A man goes into a clothing store and
tells the clerk that he wishes to purchase a suit. The clerk takes a suit off the rack and
invites the customer try it on. When the man comes out of the fitting room and examines
himself in the mirror he observes "This suit doesnt fit! It is too
big, one sleeve and one leg each are longer than the other, the jacket hangs lopsided and
the pants are baggy in the seat." The Clerk replies. "No
problem Sir, just twist your back this way, raise your hip up on one side, dip your
shoulder and hitch the pants up around your waist." The customer
complies and the clerk says "See Sir, it looks just fine.".
The customer agrees and proceeds to pay for the suit. As he limps out of the door, twisted
and hunched over, with his head bent to one side and his shoulder crooked, two men see him
and one says "Look at the terrible shape that poor cripple is in.".
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Many non-science majors protest that the remorseless quantity of unfamiliar and complex esoteric material they are exposed to in biology classes overwhelms and discourages them because it is difficult to understand and little of it seems to relate to their everyday life. Dumbing down the courses is not an answer as the goal in every GER biology course, is to produce graduates that learn and retain a basic understanding of modern biology so as to be able to participate in an ever increasingly complex technology-based world. How then can this desirable end be achieved?
| Jonathan Swift observed: "You cannot reason a
person out of a position he did not reason himself into in the first place."
So, if science is taught as just a collection of (assumed-to-be) facts, it is nothing but
dogma. Dogma stoutly resists subsequent displacement by reason. From this site. |
A common problem with biology instruction is the prevailing teaching style that presents topics in separate compartments (e.g. Chapters, or Sections). This invites the student to learn solely for the purpose of passing the next exam. Under such conditions students fail to merge recently acquired knowledge with previous information thus impeding subsequent learning, retention and knowledge integration. With no firm linkage to common themes, poorly understood and assimilated information is quickly forgotten or, worse, becomes confused with myth, superstition and pseudoscience; in which case students may be functionally more ignorant than they were before taking a biology course.
My goal in Micro 101/102 is to present the quantity of necessary information while preserving a coherence that promotes learning, understanding, retention and a continuing interest in biology. The approach I employ in Micro 101/102 is that of reductionism. Reductionism is the strategy scientists use to penetrate the awesome complexity of nature. Reductionism is the breaking up of nature into small, easily grasp concepts and information packets. Consider, for example, the human eye. To ever hope to understand the workings of the eye it is necessary to dissect it into its many component parts and then to study each. The ultimate goal being, that through an understanding of these basic elements, to reconstruct and understand the workings of the whole organ. In doing this science identifies the hidden designs and elemental principles of nature.
These "elemental principles" constitute the body of "natural laws" that apply everywhere throughout the universe (e.g. Laws of Gravity & Thermodynamics). Knowledge of these natural laws demystifies nature and coalesces it into something we can begin to grasp.
The approach used in this course emphasizes that life is based on two, easily grasped, elemental principles. I use this methodology to describe various biological and microbial phenomena at the reductionist level, but I then relate them to the two overarching principles describe next.| I. EVOLUTION |
| II. THE SPECIFICITY OF INTERACTIONS BETWEEN LIGANDS AND RECEPTORS (LOCK & KEY) |
These principles are at the core of every biological phenomena discussed in this course. They hold the key to understanding all biological phenomena; indeed it is reasonable to conclude that they hold the "key to understanding life". Without comprehending these principles it is impossible either to make sense of biology or to develop reasonable approaches for solving the remaining puzzles of biological life. Failure to define the whole of biological knowledge in terms of these principles dooms one to wander aimlessly through a wasteland of seemingly unrelated facts and observations whose complexity beggars understanding. These principles draw all the biological knowledge together in a form that is both awe inspiring and understandable. In their absence one is left with little more than a enormous collection of seemingly unrelated facts, boring terminology and seemingly random observations.
The first of these two principles, evolution, is the causality of life. Evolution, in turn, is driven by the engine of natural selection. I will discuss every aspect of microbiology presented in this course from an evolutionary/natural selection perspective. The first question that will be asked of every phenomena is "How did Natural Selection decide on a given characteristic?". My approach is illustrated in the opening stories:
The specificity of interactions between ligands and receptor molecules is the molecular mechanism whereby evolution operates the entirety of lifes processes. I will present all biological phenomena through the double lens of these two unifying themes; all explanations of biological systems will be initiated and terminated by reference to these two principles.
So it is with the ligand/receptor relationship. A LIGAND is a small molecule, or a small portion of a larger molecule, that binds to a RECEPTOR. A RECEPTOR is an arrangement of atoms in/on a molecule to which a specific ligand tightly and specifically binds. The rules of the ligand/receptor game are simple:
Traditional discussions of biological phenomena (e.g. #enzymes-substrate reactions, #antigen-antibody reactions, #virus maturation etc.) concentrate on the unique historical terminology used to describe them, which persuades students to focus solely on learning the "designated vocabulary". The almost inevitable result of this approach is that students, while memorizing these scraps of terminology (however important for communication), often overlook the common threads that connect of lifes processes together. I will attempt to correct this predicament using this unifying approach. I suggest that this approach will not only make it easier for the student to understand the common processes behind biological phenomena, but that the required vocabulary (which is always in flux) will be more easily remembered and understood when it is fitted rationally onto these two principles.
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The earth was formed ~4.0-4.5 billion years ago (give or take a few million years). Approximately 3.5 billion years ago something extraordinary happened on earth. This incredible event ultimately resulted in the production of a structure (the human brain) with the capacity (the mind) to contemplate its own emergence, its fate and its reason for being. That seemingly improbable event was the coalescence of nonliving material into the form of the first living cell, C-Prime. The outcome of this wondrous incident remains, if we are lucky and clever, to be written in the distant future. Of all the nervous systems evolved by living organisms in the intervening 3.5 billion years, only that of man has developed the capacity to understand the laws of the physical universe and to apply then to an understanding of the origin of life. The one question, "Where did I come from?", might even be considered to be the line that, once crossed, forever differentiated humans from all previous species that have inhabited the earth. For as far as we can tell, while some other animals think to the extent that they can solve problems, retain memory of past events and even use rudimentary tools, only man contemplates his origins, his reason for being and his ultimate fate. Further, man is the only animal to gather data and perform experiments on these esoteric questions. Barring the invention of a Time-Machine, it is unlikely that we will ever know the exact conditions that led to the formation of C-Prime. However, the scientific knowledge gained in the last 200 or so years does allow us to make some reasonable guesses as to what may have occurred.
As far as we can determine bacterial-like microbes were the earliest primitive #cells on this planet. One favorite theory suggests that as the hot, primitive earth cooled over millions of years a point was reached when it became possible for liquid water to exist on its surface. Gradually, over eons of time, as the skies poured rains upon the steaming rocks, water accumulated into lakes, rivers and oceans. For tens of millions of years these waters remained hot, only slowly cooling. The high temperatures extracted minerals from the rocks and accelerated chemical reactions. The minerals, along with the carbon dioxide, nitrogen, ammonia, sulfur, methane, carbon monoxide and other gases in the fiery primitive environment interacted chemically in a billion billion different ways to produce a cornucopia of chemicals that formed a chemical soup in the earth's oceans and ponds. The prebiotic earth can be viewed as a massive chemical beaker in which compounds were continuously forming, breaking down and reforming again in new and varied configurations. This chemical soup was also bombarded, throughout the ages, with powerful UV radiation and with lightning from massive storms that raked earth for millions of years. The energy from these sources induced additional bizarre chemical reactions causing a mixture of chemicals to rain from the sky. As a result of these activities every chemical compound allowed by natural law formed, was destroyed and formed again, each time with a new mix of other chemicals. With time, as the earth continued to cool, more and more chemicals that were stable at the cooler temperatures accumulated giving the chemical soup a new character. As a particular mix of chemicals began to accumulate the energetics of concentration (mass action) drove the formation of additional, complex polymeric compounds from the concentrated precursors. Because of the concentration of carbon on earth and the special chemical nature of the carbon bond, organic compounds were common in what has become known as the "organic soup" that virtually covered the earth. Since many of these unstable complex compounds tended to be larger molecules (#polymers) there was a gradual amassing of larger, more complex molecules many of which stored energy in #weak bonds. As these macromolecules grew in variety and complexity those that gained additional stability by taking on #shapes that augmented their survival further accumulated in the primeval organic soup. In other words the normal course of events were driving the chemistry in the direction of increasing complexity and size. Many molecules took on configurations or shapes that caused them to bind with various degrees of affinity to other molecules, which led to additional stability and to new types of chemical interactions and still another level of complexity. The actual sequence of events that produced what we would recognize as a living organism seem, in their complexity, beyond comprehension. However, considering the time scale involved; i.e., even though 10,000 or more years might pass between each of the individual steps leading to life, that period is but a tiny fraction of the millions of years available for something to happen. Further, as there was no life to digest the complex organic molecules that formed, they could remain available for extended periods, during which they could interact with billions of other molecules until, quite by random chance, a successful combination was stumbled upon. Fueling chemical variations was the continuous influx of energy from the planetary fires and the warming sun. This supply of energy provided ample fuel for endless chemical processes to occur.
As the number and variety of complex, interacting molecules increased in the organic soup the rate of molecular interaction grew apace due to the multiple possibility of #interactions built into large molecules. A form of molecular evolution occurred. On a cooler earth millions of unique environments of temperature, light, mineral concentration and other variables developed, each condition imparting its affect on the activity and character of the abundant organic molecules. A crude form of natural selection occurred, selecting and reselecting which molecules would survive in each environment. Some of these complex molecules took on the characteristics of organic catalysts, what we call #enzymes, in that they catalyzed the breaking or forming of specific chemical bonds. Molecular evolution favored those molecules that performed reactions that eventually produced more of themselves (e.g. by raising the precursor's concentration). This organic sea would contain #hydrophobic lipid-like, molecules that spontaneously clustered together forming #lipid membranes which, when shaken vigorously as in the action of waves, formed tiny hollow balls, inside of which were trapped a mix of other molecules present in the water when the ball or vesicle was formed. #Hydrophilic molecules that couldnt penetrate the lipid barrier were entrapped and isolated from the chaotic external environment in these closed vesicles. In this milieu randomly isolated molecules were concentrated under conditions that would allow them to interact with each other without interference by other molecules. In short, such vesicles could be considered proto-cells. One characteristic of lipid vesicles is that they easily fuse, mixing the contents of each and then subsequently break apart by mechanical action forming the equivalent of daughter proto-cells. This situation offers the possibility of separate, but limited molecular interactions occurring in billions of lipid vesicles over millions of years that would repeatedly fuse and split apart. Molecular evolution would inevitably lead to the increased survival of vesicles that contained molecules that would interact with the lipid membrane in ways that would stabilize it. Over time the random fusion and separation would bring together numerous, but limited, molecular groups. Some of these would interact in unexpected ways, one of which would be to improve the stability of the vesicle. Thus a form of super vesicle would gradually develop as tiny, incremental random additions led to the accumulation of survival characteristics.
ALTERNATIVE PROPOSALS II. Comets, meteorites and space dust have been found to be rife with organic molecules like those found in living organisms. The bombardment of earth during its early post-formative years with space debris containing a wealth of organic, and other, molecules has been suggested as explaining how it accumulated much of the raw materials of life. Even today space dust adds about 30 tons of organic material to earth every day. Such space debris may have seeded the planet with enough organic materials to explain why life seems to have appeared within 100 to 500 million years after the earth became habitable. |
Further speculation as to the order of the events that ultimately led to the first living cell is not profitable here. However, it is reasonable to assume that the first cell was probably woefully inefficient (by today's measurements) at everything it did. That is, compared with the lean, mean, competitive cellular machines of today, C-prime wouldn't last 10 seconds; it would be as a lamb among famished tigers. But no matter, as C-prime's advantage over chaos was monumental and might be likened to that of a sighted person in a land where everyone else is blind. Consider that C-prime found itself in a rich medium, a virtual world-wide cornucopia of organic wealth, that it had only to float through while plucking the occasional molecule it required. This Eden-like existence could not last, as physical demands would require that some form of reproduction occur, if for no other reason than to limit the size of the growing C-prime, gorging itself at the worldly table of goodies. The resulting daughter cells that broke off would, in turn (as children are prone to do), demand their share of the organic Eden. Random mutations would inevitably lead to mutant cells that regulated their reproduction and other biochemical activities so as make them MORE EFFICIENT. These mutants would be at a competitive advantage in that odd small (or large) puddle with its limited supply of organic goodies. Once this path was taken it was impossible to stop as mindless competition for increasingly limited resources invariably leads to the brutal application of the "survival-of-the-fittest" natural law (natural selection). Thus as the daughters of C-prime spread across earth into billions of different environments countless contests for survival occurred as each cell sought, through the blind chance of random mutations, to gain an advantage in the ceaseless struggle for life. Once taken there was no way to leave this path and live; the rule was: COMPETE SUCCESSFULLY OR DIE.
FAQ: "If the formation of life on earth was inevitable, given the unique environmental conditions and the long time available, did it happen more than once?".
ANSWER: While that possibility can not be precluded, life probably didn't arise more than once. However, proto-life may have arisen frequently, only to be snuffed out by random events (e.g. meteors). Even the most ardent evolutionist would admit that while the formation of life might be inevitable, given the time frame, the randomness of the events leading to life would make it highly unlikely that two such independent events would occur close together (e.g. within a million years of each other). It is also assumed that C-prime would hold such an advantage over any following living cell (C-late-comer) that its ascendancy would doom any subsequent, less robust, life form to an early extinction. However, some have proposed that life developed numerous times during the earth's existence, but that it was destroyed by various cataclysmic events, only to pop up again. What appears abundantly clear from the life that currently dominates the planet is that it (including MANKIND) arose from one common ancestor which subsequently evolved into the multitude of life-forms we see around us today. So even if life did develop more than once during the history of our planet, one form won the evolutionary jackpot (i.e., it ATE its competitors).
FAQ: "Can we create life in the lab?".
ANSWER: Starting with a flask containing the components of the primitive earth (the contents of which we don't know for certain), probably not, unless we plan to follow it for several million years or so. Even then we could never repeat the exact environmental conditions that were crucial to the formation of life. But what would happen if we fudged a bit and started out with a mixture of the known organic makings of life; like say grinding up a rat or two, removing all forms of life (don't forget the inevitable viruses) and putting this mixture in a sealed flask and stirring for a while? Frankly, I don't have a clue, but I do suspect that it would be difficult to get money for such a project.
FAQ: "How do you know that GOD didn't create life if you can't recreate it in the lab?"
ANSWER: Obviously, science can't prove that GOD did or didn't create life, making this a circular argument. All the reproducible data we have supports the contention that the universe operates on unbreakable laws. Everything we have learned about life indicates that it works within the framework of these natural laws; i.e., it is not "miraculous". Science does not deal with the origin of the natural laws, but only with identifying what the Natural Laws are (in this universe) and understanding how nature works within their confines. If people wish to believe that GOD wrote these natural laws, so be it. There is no credible SCIENTIFIC data to indicate that GOD has broken any since they were first "written". In this case GOD might be viewed as a coach who wrote the rules to the game but who now sits in the stands as a spectator.
The emphasis in this course is on bacteria, which seems appropriate since they are the life form that has been around the longest. In this sense it seems only fitting that they should receive the lion's share of our attention. After all, being the first they are our ancestors in every sense. All subsequent forms of life can correctly be viewed as variations and/or modifications of the bacterial theme. Viewed this way, the study of bacteria is a study of ourselves, for whatever abilities we have, including our ability to think and reason, arose in a primitive form first in the bacteria and has only been modified and augmented over time to meet the changing needs of evolutionary adaptation. For example, many bacteria sense specific wavelengths of light ; i.e., they see colors. Our eyes are simply an expansion (albeit a significant one) of that ability.
For another perspective visit this site.
EXTRA CREDIT COMMENTARY:
PROLOGUE A |
Copyright © Dr. R. E. Hurlbert, 1999.
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