Orientation Lab - Student Version

				Part 1 - Intro to collaborative learning - TAs need to take the time to tell students about the new expectations that come with a Collaborative Learning approach - students need to be aware that this approach requires that they do some of the learning on their own - point out that working in groups can give the student insight into how "real scientists" work, as much of science involves collaboration. This is helpful if they're planning on science as a career. Even if they aren't planning on science as a career, understanding how scientists work in order to better grasp the issues is an important part of being a global citizen.

Part 2 - What is biology

	BIOLOGY - WHAT'S THAT MEAN?
	It's typical for a book to lead off by setting up its basic definitions and terms, and this will be no exception. This is all about biology, the study of living things (which are also known as organisms, a nice catch-all term that includes anything considered alive). And generally, biology is thought of as more that just study, it's really the scientific study of living things. We'll get to what makes a study scientific before long; right now, let's deal with what makes a living thing alive.

	WHAT MAKES SOMETHING "ALIVE"?
	This is the first place that we get to deal with a recurring theme in this book: biology is a practice, a set of behaviors, done by human beings, which means that some of the "rules and regulations" can be partly understood from the standpoint of general human compulsions. First, humans like to name / label and categorize things, put them in neat little symbolic boxes, which helps us in our second endeavor: humans like (one could say that they need) to explain how things work. The science of biology provides one area of explanation, and what qualifies as a living thing falls into the area of labeling. It's important to remember that human explanations are always limited by our knowledge at any given time, and that labels and categories are limited by how well real objects squeeze into the constraints we put on them. Life goes on whether we understand it or not, and living things care not a whit whether they're in one or another of our little labeled boxes. And, in biology, labels and explanations must be somewhat loose. For example, a species description of dogs must be broad enough to include all dogs. You may need to lose a tendency that most students, being human (or so they claim), bring to a biology course - they think that Life works in the same patterns that you see in humans and other big fuzzy animals. The sooner you come to the realization that there are lots of other ways of doing things than how it works in people, cats, and horses, the better off you'll be. Although "life" may seem at first like "art" - "I know it when I see it" - it needs to be better defined for a science to be built around it. We're going to develop a list of features that can be applied to living things everywhere. Virtually every biology textbook in existence has a list like this, but if you were to check, you would find that the lists rarely match each other point-for-point; some things are separated into distinct features, while others may be lumped together. But if you look closely enough, the features found here themselves are all in those other lists somewhere.

	ORGANISMS ARE GENETIC SYSTEMS
	"Oh, genetics, I've heard of that!" Of course, that doesn't mean that the term means anything to you. What exactly is a genetic system? In this instance, it means that living things are able to reproduce in a way that passes features, or at least information about making features, along from a parent to its offspring. For living things on the planet Earth, this feature is usually based on information stored in Deoxyribonucleic Acid, or DNA. Genes are made of the material DNA, and this is the basis of the term "genetic." This molecule, about which much more is covered later on, holds the code by which proteins are made - and proteins are the workhorse molecules of earthly organisms, producing directly or indirectly the "traits" people commonly connect to "genes." But features can be passed along in non-DNA ways - some features found in your cells are there because they were in your mother's egg cell, and some of your traits and tendencies may be linked to the chemistry that surrounded you in the womb while you developed. Another type of example would be this book, and all of the sorts of information that can be passed on through learning. Inheritable traits that are not strictly in our DNA are called epigenetic - later, when things like evolution are discussed in terms of passing on traits, this is something to remember: all that we are, all that we pass on is not just in our genes. This also opens the door for many of what we might call machines to have this aspect of life - is transferable computer code sort of genetic? Embedded in this feature of Life is reproduction - it's hard to pass traits on to offspring without reproducing, although I suppose you could imagine a living thing that is immortal and never reproduces (no one has found such a thing, though). In our world, reproduction falls mostly into two camps: asexual reproduction, where offspring are genetic copies of the parent (they can be genetic copies yet not to be physical copies, because of how genes work), and sexual reproduction, where offspring are a mix of gene sets from two sources (and which may or may not involve two separate parents). You might not think so by looking at these definitions, but there is a gray area between these types as well, where copying happens but some mixing is allowed. As we'll see later, there are advantages to each and disadvantages to each (and, as a trend you'll eventually notice in these kinds of biology pairs, the advantage of one reflects upon the disadvantage of the other). A side effect of reproduction is growth and development: without growth, each generation would get progressively smaller beyond their ability to survive; without development, the next reproduction phase could not be timed properly. Growth is a fairly simple property, while development can be a simple switch in a cell that says, "Don't divide yet," or the many complicated stages that multicellular organisms go through between one zygote (the very first cell, usually created from the fusion of a sperm and an egg cell) and the next generation's zygote-generating adult. An old biology proverb states that, "An adult is just a zygote's way of making another zygote." You might have heard a variation: "A chicken is just an egg's way of making another egg."

	ORGANISMS ARE DYNAMIC UNITS
	Both parts of this term are important - dynamic refers to how living things are always changing as their internal chemistries use resources, convert energies, and produce wastes (this chemistry is known as metabolism); units refers to how living things exist as individuals, separate entities with particular needs. Internally, living things are a storm of interactive atoms and molecules, extremely tiny objects, not themselves considered alive, whose complex relationships, involving energy and particle transfers, make up the activity of life on its tiniest level. This is the most modern area of biology, and a good example of science as reductionism: the assurance that any large activity can be totally understood if you understand how all of the tiny pieces work. Again, being human makes us feel in our guts that all of the little labeled components must add up to the whole, even though biology commonly exhibits what are called emergent properties that appear when several complex systems produce effects that seem to not be a product of the pieces. Anyone familiar with computers has seen examples in those complex systems as well - behaviors that can't easily be explained by knowing how each piece of software works by itself. Of course, computer people and biologists are often sure that even emergent properties can be reduced to understandable components, and they may be right. Just as a warning, when activity on an atomic / molecular level is covered later, you may find it the most difficult section to grasp. It is essential to have a good understanding of molecular issues as a foundation for most biological fields, but the basic mindset of budding biologists does not tend to match that of chemists, so the material may not come as naturally as other concepts, and in fact may need to be learned by rote until later exposure brings it into better focus. The units of life begin on the small level (much bigger than molecules, though) with cells, contained bags of many floating chemicals sealed inside an oily membrane that allows a large degree of control over what enters and leaves. Organisms can be just one single cell (the vast majority of living individuals on Earth are unicellular, made up of only one cell), or they can be a collection of cells that divide up duties (multicellular organisms). In keeping with the odd reality of the world, there are also colonial organisms made up of individuals that are technically "independent" but virtually cannot exist without others in the colony - this applies to collections of unicellular organisms, ants, and possibly even people. Unicellular colonials are somewhat intermediate between unicellular and multicellular organisms.

	ORGANISMS INTERACT WITH THEIR ENVIRONMENT
	Living things, as stated before, are dynamic as their internal chemistries use resources, convert energies, and produce wastes. These changes cannot be sustained in a locked chamber with no connection to the world around them. Organisms must pick up materials, release materials, and try to avoid circumstances that would kill them, either from immediate threats (such as something trying to consume them, or a toxin, or potentially-harmful germ) or long-term needs (examples would be finding needed resources, or preventing its own wastes from poisoning it). These needs require the ability to pick up cues from the environment and respond to them, something that can be very simple, as some molecule-based "switches" are, or as complex as the information to absorb and process and the responses you produce every minute (Hello, you are responding, right...?). The level of interaction depends upon the "size" of the environment being discussed ("environment" is a very flexible word). Each cell exists in an immediate locale of atoms and molecules, usually in a water-based soup. Individuals exist in microenvironments that are just their immediate surroundings and fit into ecosystems that includes, in theory at least, all of the factors in the world that influence them and which they influence. Not surprisingly, any practical discussion requires limits be imposed when defining any particular ecosystem. Ecosystems have niches, kind of like functional "slots" into which types of organisms fit - most earthly ecosystems have a niche or niches for Top Predator(s), defined by factors including available prey but also territory and water availability. This is another area where biology is reductionist, assuming that the workings of any ecosystem can be understood and predicted by a knowledge of all the "pertinent" niches; this is also another area where emergent properties can be very inconvenient.

	ORGANISMS EVOLVE
	Evolution is a change in type over time. It connects back to that human compulsion to label and categorize things, combined with a knowledge of how the world of the past was different than today's world. All sorts of things can evolve, so this may be the feature of Life found most often in things that are not alive. The current best explanation for how evolution works is the Theory of Evolution by Natural Selection, developed and written down originally by Charles Darwin and Alfred Russel Wallace in 1858, with many slight adjustments and additions by many people since. Generally, "disagreement" in scientific circles with this theory involves a dispute about how much Natural Selection influences evolution compared to other factors, not whether the basic ideas are accurate. A comparable theory might be the Theory of Gravity - scientists might disagree on the details of how gravity works, but no one suggests that gravity doesn't exist. What is Evolution by Natural Selection? Sometimes nicknamed "Survival of the Fittest," it would be more appropriate to call it "Reproduction by the Fittest." Simply put, since more detail will appear later, in any given group of organisms, there will be some variety of features that directly affect how good a chance each individual has of living to reproductive age and then successfully reproducing - who manages to live long enough to make little ones? As a general trend, each generation of offspring will, more and more, reflect features that are advantageous to their environment, which helped their forebears survive. The important detail here is that environments change over time - what was a good feature in one environment may not be so good elsewhere - and these changes in environment (the "Nature" part of Natural Selection) influence (the "Selection" part) which individuals live long enough to reproduce and what features preferentially wind up in the offspring. Over time, depending on an organism's suitability to the new environment, new features and combinations of features (called adaptations, a confusing term that does not always mean the same thing even to biologists) may spread through the population as a whole until the basic "type," or species (there will be a more particular definition of this term later) has changed significantly enough from the "type" of its ancestors that it needs to be relabeled. Evolution is not an "ever upward movement toward perfection," although that is what it often is portrayed as; species don't get better at anything other than fitting the environment of the day, which could change at any time. There is no target, no progress, no ultimate peak at humans (our brand of intelligence may not be a great adaptation, since it comes with a long list of self-extinction threats from our own meddling, including but not limited to weapons of mass destruction), and not everything evolves at the same rate, partly because the rate at which environments change varies considerably from place to place (and even pieces within environments vary), partly because some forms are more flexible and require little change for a new environment (think of humans - when faced with a new environment, we largely change the environment to suit us, a good thing on a small scale but a possible problem at larger scales), and partly due to how long generations last. Organisms that reproduce quickly also can evolve quickly if need be.

	RELATED DISCUSSION -
	Viruses - are They Alive?
	After defining the traits of living things, it should be made clear that there are things in this world that act alive but maybe don't hit the entire checklist of necessary features. Modern computerized construction robots (especially ones used to build more robots) can present an interesting debate, but the question of viruses is an old one. Viruses are extremely tiny things, usually well above molecular size, although the smallest ones get close to molecule-tiny, and well below the size of even the smallest cells. The basic structure of viruses varies widely and often is not considered cellular - no membrane! They float around the world, ejected from the last host cell, like set mousetraps, primed to become active if they make contact with another potential host cell. That is one of the problems: free of a host, they seem completely inactive, with no metabolism of any kind. Inside a host, their metabolism is totally focused on turning the cell into a factory to make more viruses, which will eventually be released fully-formed and "set" to infect the next cell - there is no growth and development in a virus, only construction. Viral diseases are hard to cure with drugs because viruses lack vulnerability - no working chemistry to interfere with when free, and active on borrowed cell chemistry, where interference could kill regular uninfected cells. Only the fact that, in some viruses, some of the construction chemistry is unlike what a regular cell would do gives drug designers a possible target to poison. Put these features together - no metabolism in the free form, no growth, no development, often no cell - and it's not surprising that many biologists refuse to consider viruses as living things. Some do consider them alive - after all, they do reproduce and evolve, and they do interact with the environment inside a cell in some ways (that's a gray area that can support either side in the debate). It may be useful to remember one important fact - no virus in the world cares whether we put it on a "living" or "unliving" list.

Online Introduction to Biology (Advanced)
Copyright 2003 - 2006, Michael McDarby.
Reproduction and/or dissemination without permission is prohibited.

Biology: The Science of Our Lives | Back to Top
Biology literally means "the study of life". Biology is such a broad field, covering the minute workings of chemical machines inside our cells, to broad scale concepts of ecosystems and global climate change. Biologists study intimate details of the human brain, the composition of our genes, and even the functioning of our reproductive system. Biologists recently all but completed the deciphering of the human genome, the sequence of deoxyribonucleic acid (DNA) bases that may determine much of our innate capabilities and predispositions to certain forms of behavior and illnesses. DNA sequences have played major roles in criminal cases (O.J. Simpson, as well as the reversal of death penalties for many wrongfully convicted individuals), as well as the impeachment of President Clinton (the stain at least did not lie). We are bombarded with headlines about possible health risks from favorite foods (Chinese, Mexican, hamburgers, etc.) as well as the potential benefits of eating other foods such as cooked tomatoes. Informercials tout the benefits of metabolism-adjusting drugs for weight loss. Many Americans are turning to herbal remedies to ease arthritis pain, improve memory, as well as improve our moods.
Can a biology book give you the answers to these questions? No, but it will enable you learn how to sift through the biases of investigators, the press, and others in a quest to critically evaluate the question. To be honest, five years after you are through with this class it is doubtful you would remember all the details of meatbolism. However, you will know where to look and maybe a little about the process of science that will allow you to make an informed decision. Will you be a scientist? Yes, in a way. You may not be formally trained as a science major, but you can think critically, solve problems, and have some idea about what science can and cannoit do. I hope you will be able to tell the shoe from the shinola.
Science and the Scientific Method | Back to Top
Science is an objective, logical, and repeatable attempt to understand the principles and forces operating in the natural universe. Science is from the Latin word, scientia, to know. Good science is not dogmatic, but should be viewed as an ongoing process of testing and evaluation. One of the hoped-for benefits of students taking a biology course is that they will become more familiar with the process of science.
Humans seem innately interested in the world we live in. Young children drive their parents batty with constant "why" questions. Science is a means to get some of those whys answered. When we shop for groceries, we are conducting a kind of scientific experiment. If you like Brand X of soup, and Brand Y is on sale, perhaps you try Brand Y. If you like it you may buy it again, even when it is not on sale. If you did not like Brand Y, then no sale will get you to try it again.
In order to conduct science, one must know the rules of the game (imagine playing Monopoly and having to discover the rules as you play! Which is precisely what one does with some computer or videogames (before buying the cheatbook). The scientific method is to be used as a guide that can be modified. In some sciences, such as taxonomy and certain types of geology, laboratory experiments are not necessarily performed. Instead, after formulating a hypothesis, additional observations and/or collections are made from different localities.
Steps in the scientific method commonly include:
    1.    Observation: defining the problem you wish to explain.
    2.    Hypothesis: one or more falsifiable explanations for the observation.
    3.    Experimentation: Controlled attempts to test one or more hypotheses.
    4.    Conclusion: was the hypothesis supported or not? After this step the hypothesis is either modified or rejected, which causes a repeat of the steps above.
After a hypothesis has been repeatedly tested, a hierarchy of scientific thought develops. Hypothesis is the most common, with the lowest level of certainty. A theory is a hypothesis that has been repeatedly tested with little modification, e.g. The Theory of Evolution. A Law is one of the fundamental underlying principles of how the Universe is organized, e.g. The Laws of Thermodynamics, Newton's Law of Gravity. Science uses the word theory differently than it is used in the general population. Theory to most people, in general nonscientific use, is an untested idea. Scientists call this a hypothesis.
Scientific experiments are also concerned with isolating the variables. A good science experiment does not simultaneously test several variables, but rather a single variable that can be measured against a control. Scientific controlled experiments are situations where all factors are the same between two test subjects, except for the single experimental variable.
Consider a commonly conducted science fair experiment. Sandy wants to test the effect of gangsta rap music on pea plant growth. She plays loud rap music 24 hours a day to a series of pea plants grown under light, and watered every day. At the end of her experiment she concludes gangsta rap is conducive to plant growth. Her teacher grades her project very low, citing the lack of a control group for the experiment. Sandy returns to her experiment, but this time she has a separate group of plants under the same conditions as the rapping plants, but with soothing Led Zeppelin songs playing. She comes to the same conclusion as before, but now has a basis for comparison. Her teacher gives her project a better grade.
Theories Contributing to Modern Biology | Back to Top
Modern biology is based on several great ideas, or theories:
    1.    The Cell Theory
    2.    The Theory of Evolution by Natural Selection
    3.    Gene Theory
    4.    Homeostasis

Part 3 - Careers in Biology

	BIOLOGY CAREERS - POPULAR SUBFIELDS
	Students don't really go on to become "biologists" today - eventually, they will settle into one of the vast number of subfields within biology. Students in a Introductory Biology course have a wide variety of motivations for being there. Some have the course as a requirement for their non-biology major, some have a clear idea of what they want to do eventually, and some have only the most vague concept and may not even be sure that taking such a starting course is a good idea. If you feel strongly that your future career will involve science, you may want to read this reference about the educational choices you will need to make along the way. It is a very general primer that applies to many scientific disciplines, not just biology. In biological disciplines, many first-year students are intending to go into medicine. Be warned! Getting into medical school, or veterinary school, is extremely difficult and comparable to getting into the best universities as an undergraduate: not only will you need close-to-flawless grades, but the deciding factors may be extracurricular, everything from ethnic background and hometown to what sorts of extraordinary accomplishments or training you may have. It is an unfortunate fact of life that the vast majority of freshman who see themselves as "pre-med" or "pre-vet" will not even finish their undergraduate education still in the sciences; the fraction of these freshman who go on to medical careers is probably less than the fraction of college athletes who become professional ones (that, barring gathering of statistics, is a hypothesis). There is, however, a lot of medical research going on that is not done by doctors, so not making the grades for medical school will not necessarily keep you from a career in medicine. In fact, most biologists doing research are most likely in a field at least related to human health - it's where the money is. Some other biology subfields are popular but offer small hope of a successful career - there just aren't that many jobs available. These would include marine biology, wildlife biology, and paleontology. Careers in marine and wildlife biology may lead to the handful of marine research labs, but both will probably only lead to jobs as college professors at research universities.  CURRENT POPULAR SUBFIELDS:  The next book section deals with biology of the molecular level, which is the level at which most of modern research is aimed. Molecular biology, genetics, neuroscience, immunology, embryology and development, and other similar fields left the "see it with the naked eye" region long ago and are investigated in terms of what the molecules are doing. Ecology is less molecular-based, but is primarily a statistics-driven field. Statistics figure prominently in several other areas as well. Genetic engineering may become during your lifetime what computers became during your parents', as applications beyond medicine may play out their wide-ranging potential. Bioinformatics represent the intersection of sophisticated computer systems and biology, mostly molecular biology. The type of analysis, data collection, and database establishment that can be done with computers has led to this specialty of biotechnology.