Consumer Reports: My Energy Comes from Plants?

A "Consumer" Report

Ladies and gentlemen, we are consumers. Newsflash! I know, I know... it's America. Capitalism, materialism... these are familiar concepts. But I'm a biologist. It's what I do (observe the world around me critically). And lately I've been thinking about consuming in a biological context. Surprise, surprise. Recall, I've been using this blog to refresh readers (and myself) about the basics of biological science (click here to see where this started). Consumer Reports is a popular magazine complex interested in reviewing and rating products in hopes of helping consumers make smart buying decisions in the American (and global) marketplace. Today, I'll be submitting my own Consumer Report. This report, however, focuses on the underlying biological mechanisms--those relating to photosynthesis--responsible for the energy in what we consume. As always, I will attempt to paint a picture of photosynthesis from an evolutionary perspective.

You and I consume other living things, from which we obtain energy in a variety of different forms, mostly as proteins, lipids, and long chains of sugars called carbohydrates. As I have just discussed (last couple of posts), our bodies are made of millions and millions of cells capable of using energy bound up in the foods we eat after converting it to energetic currency called ATP through the processes of glycolysis and cellular respiration (if oxygen is present in our cells). But we never serve as the origin of any energy we use.

While our bodies can transform basic chemical compounds into more complex and useful forms (e.g., 10 of the essential amino acids used to synthesize proteins), we are constantly converting energy from one form to another (remember that first law of thermodynamics?). The question eventually arises, where does all this energy come from in the first place? The short answer isn't found on mother earth. It's the sun. A more fruitful explanation lies in the study of plants and other organisms (cyanobacteria, green algae), which we call autotrophs or producers, which can convert solar energy into chemical energy.

Evolution and Photosynthesis

First, a little digression... Evolutionary biologists (like myself) are scientists interested in all aspects of the evolution of biological species. While most evolutionary biologists do not concern themselves with the origins of life, other scientists' work often focuses on evaluating and empirically testing the significance of other kinds of evidence (i.e., astronomy, geology, early earth biochemistry, et cetera) about the archaeology of early life and the ancient earth environment. Sometimes scientists intend to demonstrate the validity of different theories about these latter phenomena, while at other times scientists make discoveries with implications for how we think about the history of life, while this was not their original intent; this second class of discoverers simply realize the implications of their new knowledge after laying it bare. Because photosynthesis is thought to have played a pivotal role in the evolution of life on earth, I choose this perspective as my starting point.

Isotopic studies of meteorite tungsten demonstrate confirm the long-held and well-supported idea that the earth is very, very old--around 4.6 billion years, give or take 10 million, to be more precise (Jacobsen 2003). Evidence suggests simple prokaryotic cells evolved between 3 and 4 billion years ago (Line 2001). Later, the processes of life's evolution generated single celled eukaryotes just over 2 billion years ago, which were first very simple then engulfed proto-plastids and evolved into photosynthesizing eukaryotes (as described in an earlier post, which you can read here) (Margulis 1970; Campbell and Reece 2005). Because a by-product of photosynthesis is oxygen, these creatures, which increased exponentially in number, played a major role in setting the environment up for more complex lifeforms (i.e., animals and land-dwelling plants) by increasing the atmospheric and aquatic O2 concentrations of the early earth (Dismukes et al. 2001; Campbell and Reece 2005). Recently, molecular sequence data of cyanobacteria chloroplasts are consistent with these other findings in demonstrating an ancient origin of photosynthesizing cells (Xiong et al. 2000). Not surprisingly, photosynthesis is still generating crucial oxygen used by most species today. Now that you know a bit about the evolutionary significance of photosynthesizing organisms. Thus, we turn to the process of photosynthesis itself.

Photosynthesis

Everyone who knows anything about this important process knows photosynthesis occurs in plants. Those more erudite scholars among you might even know this happens, more specifically, in the chloroplasts evolved from early plastids I mentioned. Those with heads high in the heavens (even concocting a nosebleed) of scientific knowledge might even remember that plant chloroplasts are divided into different parts and that different sub-cellular pathways carry out what are call "light" and "dark" reactions, that there are different photosystems, and or that electrons are involved in chemiosmosis during the sequence of super duper photosynthetic events. Allow me to clarify for those of us who aren't as smart as the nosebleeders.

Chloroplast Ultrastructure

Chloroplasts, like mitochondria, have two outer layers--outer and inner membranes--and are filled with interconnected networks of membranous sacs known as thylakoids. Chlorophyll is a special pigment in thylakoid membranes that give plants their green color, as you shall see.

As I mentioned, photosynthesis involves two different phases. These are the light reactions and the Calvin cycle. These are crucial to your life and mine and to life's evolution.

Light Reactions use solar radiation to convert carbon dioxide and water into useable chemical forms

Generally, light reactions convert solar energy into chemical energy trapped in the form of ATP and an electron carrier, NADPH (similar to NADH and FADH, from discussion of cellular respiration). By solar energy, I mean light. Let me explain. Light is electromagnetic radiation or energy travelling in the form of waves with the properties of particle packages of energy, or photons. Different wavelengths of light are visible and invisible (see electromagnetic spectrum). Light with low wavelengths is intense (has more energy; e.g., violet light) while the converse is true of long wavelength light (e.g., red light). When light from the sun (which emits all wavelengths of light) hits objects on earth (mostly visible light reaches the surface), some visible light is reflected by those objects, which may absorb or transmit (allow to pass through them) other wavelengths. Chemicals called pigments absorb many frequencies of visible light and reflect a narrow range of wavelengths. So, we see that the chemical composition of matter is highly variable, thus objects take on different colors because their pigments or absorption characteristics (absorption spectra) allow only certain colors to be reflect and processed by visual sensory organs of living things, (e.g., our eyes). And that's a simple (albeit incomplete) explanation of why we perceive objects to be different, specific colors!! Isn't that cool? Nonetheless, there are deeper truths these facts hold in store for photosynthesis.

Thylakoid membranes are peppered with chemical complexes called photosystems. In broad terms, photosystems consist of chemical complexes (groups of large molecules) containing photosynthetically important plant pigments (which I expand on later) surrounding a central region where special pigment molecules are housed. The light reactions of photosynthesis depend upon the excitation of electrons in photosystems and the transport of these electrons down protein chains to generate energy bound in ATP and NADPH.

To elaborate, there are two photosystems at work in plant cells, photosystem I and photosystem II. Here's how they do the work of the light reactions. Pigments in photosystem II abosorb light from the sun at wavelengths of 410-510 nm and 610-700 nm (both are approximations). This light is in the form of an individual photon which energetically must exactly match the difference between excited electron states and the ground state of the pigment molecule (most commonly discussed are chlorophyll a, chlorophyll b, and carotenoids). The photon's energy is transferred directly between pigment molecules in photosystem I's outer complex until it reaches the base of the inner region, where two special chlorophyll molecules are located. These molecules, because they absorb light best at 680 nm, are termed P680's. Absorption of the photon powers a single electron from one of the P680's to a higher energy state, a higher orbital (if you know chemistry). The excited electron reduces a molecule called the primary electron acceptor. Nearby, an enzyme quickly breaks a proximate water molecule into its constituent parts: oxygen, two protons (H+), and two electrons. The electrons drop back to each fill the void left in each P680 molecule at the base of the inner photosystem region from giving electrons to the primary electron acceptor. (hang with me here!) Next, the primary acceptor drops its newly gained electron in one of two places, electron transport chains (ETC; we'll call them electron transport chains one and two, ETC1 and ETC2!). For now, we consider what happens down each individual ETC.

ETC1 is similar to the ETC found in mitochondria, which functions in cellular respiration. As with mitochondrial ETCs, ETC1 breaks the explosive change in energetic state of the electrons from photosystem I into a small series of steps, each yielding ATP. Eventually (quickly), our little electron is passed to photosystem I. That's right! Electrons go from photosystem II to photosystem I. Kind of weird, huh? The explanation for this apparent misnomer is that the photosystems were named in order of discovery, with scientists later determining the order of electron passage contradicted the nomenclature.

The last compound in ETC1 drops our electron directly onto the special pigment molecules called P700's, chlorophylls that absorb light best at 700 nm (go figure), which are at the base of the central region of photosystem I. Again, this transfer of energy blasts electrons from P700's to an excited state, which reduces photosystem I's primary electron acceptor. This acceptor, in turn, drops the electron down the other ETC (i.e., ETC2), where, upon reaching the bottom of the chain, it is passed on to an enzyme called NADP+ reductase. This enzyme requires two electrons from the light reactions (photosystem I) to reduce NADP+ to NADPH, an electron carrier molecule. And that's it for the light reaction phase!

ATP generation

I told you that electrons dropping down ETC1 make ATP and those funneled down ETC2 cause NADP+ to be reduced to NADPH. What I said was true. However, I was holding something back; namely, the mechanism responsible for these changes. It is a familiar mechanism, chemiosmosis (if you don't know what this means, read this)! This is the same mechanism driving the generation of the majority of ATP in aerobically respiring living cells, oxidative phosphorylation, a process of cellular respiration.

As I have stressed in talking about cellular respiration, ATP is generated by an enzyme, ATP synthase, as a result of a H+ gradient in mitochondria. The same is true of photosynthesis. In mitochondria, ATP is made as H+ are pumped down their concentration gradient from the mitochondrial intermembrane space into the inner space of the organelle (mitochondrial matrix), where ADP is phosphorylated into ATP. In plants, things are not much different. Obviously, the electron transport chains are different. Less obviously, however, is the fact that another similarity exists. In mitochondria AND thylakoids, the ETC's and ATP synthases are embedded in the same membrane (the inner membrane of mitochondria, the only membrane in thylakoids) and ETCs supply force to pump H+ into a different space (against their passive transport directionality, therefore requiring active transport) which accumulate and run easily through ATP synthase literally turning the machinery to generate energy for ATP production. Whew! Clear as mud right? But where does that ATP go next? How is it actually used in cells of plants? What kind of work do these cells accomplish and why is it important to you and me as consumers? Simple (ha ha).

The Calvin Cycle

In brief, the Calvin cycle uses ATP and NADPH to turn carbon dioxide into polysaccharides that benefit consumers like us! In a sense, this process is partially analogous to a reversal of the citric acid cycle (CAC). On the one hand, the CAC uses oxidized sugars to generate chemicals storing energy. On the other hand, the Calvin cycle expends energy to make sugars, which are stored in plant tissues and consumed by animals as food. The Calvin cycle is comprised of three phases, (1) carbon fixation, (2) reduction, and (3) regeneration of the starting materials (carbon dioxide). While some think of the Calvin cycle as generating sugars directly, this is not the case. Instead, it yields three carbon sugars which are also intermediates in CAC's, glyceraldehyde-3-phosphate, or G3P. Enzymes separate from the Calvin cycle use G3P as a starting material for glucose genesis, which only involves a few steps.

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Dismukes, et al. 2001. The origin of atmospheric oxygen on earth: the innovation of oxygenic photosynthesis. PNAS 98(5):2170-2175.

Jacobsen, S.B. 2003. How Old Is Planet Earth? Science (Washington). 300(5625):1513-1514..

Line, M.A. 2001. The enigma of the origin of life and its timing. Microbiology 148:21-27.

Margulis, L. 1970. Origin of eukaryotic cells. New Haven, Yale University Press.

Xiong, et al. 2000. Molecular evidence for the early evolution of photosynthesis. Science 289(5485):1724 - 1730.

For info on other citations, see References post.

References

This post will be an on-going list of some sources I reference frequently or which are integral to a lot of stuff I review here about basic biology. Those include:

Campbell, N. A., and J. B. Reece. 2005. Biology. 7th Edition. Benjamin Cummings: Boston, MA.

Wilson, E. O. 2006. The creation: an appeal to save life on earth. W. W. Norton & Company: New York, NY.

Cellular Respiration: Brief Look at the Citric Acid and Oxidative Phosphorylation

Just recently, I blabbed about cells and cellular respiration. Then toward the end of my last post I got really excited about cellular respiration as fundamental to all living creatures, including you and me. But all I had really talked about was the fundamental units of biological organization, the smallest living things, thermodynamics and biological chemistry, and how we get a little ATP and a bunch of energy stored as pyruvate from each glucose molecule that gets broken by glycolysis. Nothing very important, really...

Perhaps you remembered vaguely when you first learned this material. Perhaps you wondered why anyone would care. Perhaps you were amazed to be reminded of the chemical basis of all life on earth, the far-reaching implications of the chemistry which forms the foundation of biological science. If you're in the latter group, right on! And read on! Because glycolysis is only one process linked to cellular respiration. It is not considered a part of real respiration because oxygen is not involved. And it yields a relatively small amount of ATP dividends per unit starting molecule and per unit effort (10 steps, two molecules of ATP burnt off). What really gets my engine burning, and hopefully yours too, are the citric acid cycle (CAC) and oxidative phosphorylation (OP).

Before I talk about these, allow me to just say that these aren't just singular discoveries written down in books so that students get a view of the big picture from their biology education--at least, that's not all these are. Instead, the CAC and OP pathways represent active areas of scientific research. Recent studies illustrate this point: a group of scientists from Germany and other places have been looking into fluorescent imaging of CAC intermediates (here), while American scientists have examined the origin and self-organization of biochemical cycles, not to mention the evolution of the enzymes involved.

So, on to CAC and OP and what these should mean to you and me.

The CAC (Fig. 1 below) is an eight-step biochemical pathway turning pre-packaged Acetyl-CoA (a modified form of pyruvate from glycolysis; two per glucose molecule, just like pyruvate) into two molecules of CO2, three NADH, one ATP, and one FADH2 (an electron carrier similar to NADH). On the other hand, OP takes electrons from NADH and FADH2 made available from glycolysis and the citric acid cycle and uses these to generate up to 32 or 34 molecules of ATP per starting molecule of glucose!!! As an aside for now, Acetyl-CoA used in the CAC may also come from proteins and lipids--not just glucose--but this is beyond the scope of our discussion. All in all, factoring in CAC and OP in view of the classical glucose metabolism perspective, each molecule of glucose broken down in your cells has the potential to generate up to 36 or 38 molecules of ATP!!!


Figure 1. The citric acid cycle (Orgel 2000, see link at end of text).



So, we see from this overview how oxidative phosphorylation and chemiosmosis (linked processes) are together responsible for the majority of ATP produced by the respiration of our cells (eventually linked to the respiration we do with our circulatory system and respiratory systems, or blood and lungs). These ATP generated by OP and chemiosmosis are largely the result of what is known as the electron transport chain (ETC), making this one of the most important sub-cellular structures in living things.

The ETC is a collection of multiprotein complexes found all over the inner membrane of our mitochondria. NADH and FADH2 deliver electrons to specific pieces of this chain. In turn, these electrons move down the chain using well-known avenues. At the end of this chain, the last protein in the ETC sequence (these proteins are mostly particular kinds, called cytochromes. My DNA Barcoding work studies cytochrome oxidase 1 to explore nearshore fishes of the Carribbean/Western Central Atlantic for cryptic speciation events), "Cyt a3," transfers its electrons to oxygen (O2), which grabs two hydrogens to become water (H2O). Because electrons from FADH enter the ETC at a different protein complex than those donated by NADH, they provide less energy for ATP synthesis than those from NADH.

So, electrons release energy as they fall down the ETC. "But how is this energy harnessed to make ATP?" you might ask. Simple. Coupling electron transport to ATP synthesis (exergonic reactions coupled to endergonic ones, as mentioned elsewhere). This is accomplished by the process of chemiosmosis.

Chemiosmosis is the phenomenon whereby motion of an ion across its gradient through a membrane releases energy which is used to do cellular work. ATP synthase, also found in the inner wall of the mitochondrion, is the enzyme responsible for ATP formation from ADP (the "used up" form of ATP in our cells) and inorganic phosphate (P-). In the case of ATP synthase, the ion used to generate the energy of ATP regeneration is hydrogen, which accumulates in the mitochondrial intermembrane space as a result of the action of the ETC. This combined action of the ETC and chemiosmosis make up what we know as oxidative phosphorylation, what I have called OP. One key difference between this process and the ATP-yielding pathways we've discussed, glycolysis and the citric acid cycle, is that OP generates ATP from phosphorylation using these two processes instead of substrate-level phosphorylation, the method of glycolysis and CAC. Are you with me??

Hope so.


There you have it... in a nutshell, the difference between glycolysis and cellular respiration, the difference between glycolysis/CAC and oxidative phosphorylation (ETC + chemiosmosis/ATP synthesis), and all fit into an overview of how we get chemical energy from our food. Holla!

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See Campbell and Reece (2007) for more information, or try a search of Google Scholar to learn more about cellular respiration, glycolysis, the CAC or OP. Or, read this Orgel (2000) paper. Peace out ~ JB

Cellular Respiration: Cells, Energy and Glycolysis

Living cells perform work. Essentially, work is the amount of energy transferred by force, thus energy is required for work to take place. My fingers are performing work by pressing down on and transferring their kinetic energy to the keys on this keypad. This is a coordinated effort of nervous impulses in my brain receiving and dictating signals to and from the muscles and other tissues of my eyes, hands, and fingers. An input of energy is required for each type of tissue involved to accomplish the task of each keystroke. My brain cells are not performing the same type of mechanical work as my hands and fingers; however, they are costing my body an enormous amount of energy through maintenance and metabolic costs from not only my mental activity, but also the basic needs of my neural cells. Recall how two major themes of biological science are (a) that energy flows through ecosystems from the sun to producers to consumers and (b) that living things place energetic demands on their environments in order to do the work characteristic of life. At this point, we will delve into these in greater detail, all from the standpoint of cellular respiration.

Cellular respiration (CR) might be defined as the sum of all the processes involved in the catabolism (breakdown) of food molecules (protein, carbohydrates, and lipids) into carbon dioxide, water, and energy bound in the form of ATP and heat released from chemical reactions involved. This relationship between different chemical and physical variables of cellular respiration is similar to the oxidation reactions generating motion in heat combustion engines. A major goal of any education in cellular respiration should be founded upon an understanding of the way cells arrive at ATP and the way this molecule is utilized by cells to supply the energy necessary for life. Before this can be grasped, however, it is necessary we embellish more on the nature of energy and metabolism in natural systems.

The first law of thermodynamics: Energy is neither created nor destroyed, it may only be transformed or transferred from one form to another. Second law of thermodynamics: all energy transformations and transferences increase the overall entropy of the universe. Notice how this second law of thermodynamics need not apply to individual transactions between organisms and their environment, whether the events we consider are single physical interactions of adults or we are concerned with development or evolution of populations. What I mean by this is that, simply, we learn from studying nature how many ordered phenomena coexist with random, chaotic, or stochastic processes and events. The order we find in the universe, in the beauty and symmetry of life or its evolution for example, does not contradict the second law of thermodynamics because these are single occurrences while organisms and their populations increase the entropy of the universe in other ways, including heat loss. Thus, while individual structures or events may decrease the entropy of the universe (by introducing orderliness; e.g., cleaning your room), the universe is more than its individual systems (organisms, ecosystems, planets, etc.), extending to includes each system’s surroundings (e.g., where heat is lost), so entropy may drop locally but is always increasing in the universe as a whole.

The Gibbs free energy (ΔG) of a system describes the energy available for work in a system, such as a cell, when pressure and temperature are constant. This quantity is equivalent to the total energy in a biological system minus the entropy change over a given time period at a given temperature. Spontaneous processes use available energy and in doing so decrease the energy in a system, and therefore are represented by negative Gibbs free energy values; conversely, a positive value of ΔG suggests a process is not spontaneous. Systems in the biosphere often run down energy gradients towards energetically more stable states, the most stable of these being that of equilibrium, where free energy change is near zero or positive and more work cannot be accomplished. Our cells represent dynamic systems where many different types of chemical and mechanical forces are at work to maintain and alter living things. Here, in our cells, reactions where energy is lost (ΔG <> 0), or endergonic reactions, may occur, often in simul. Because of the many chemical processes carried out in our cells, our bodies never reach a state of energetic equilibrium; rather, materials constantly flow through our physiological systems.

Biologists generally recognize three kinds of work cells accomplish using the energy harvested from biochemical reactions making up cellular respiration (oxidizing food particles into useful energy), (1) mechanical work involving movement of various cellular structures, (2) transport work which pumps substances across membranes against concentration gradients, and (3) chemical work, which involves supplying energy from outside of chemical products to force processes to completion which are not naturally spontaneous. Much of this work is accomplished through energy coupling, or using exergonic processes to generate energy fueling endergonic processes. I have already commented on the role of mitochondria in ATP production, the ability of this molecule to trap energy, and subsequently have alluded to its importance in cellular respiration and metabolism. But what is the structure and importance of ATP really like? Why, more specifically, is its role in the reactions of cellular respiration important, and what are those reactions themselves like?

Each ATP (adenosine triphosphate) molecule is composed of a nitrogenous base, adenine, linked to a ribose (pentose, or five-carbon ring structured) sugar, which is in turn connected to three inorganic phosphate molecules. The region of ATP containing these inorganic phosphate molecules is negatively charged and unstable, making ATP an effective reducing agent (it oxidizes other molecules). When bonds between ATP phosphates are broken by hydrolysis in our cells by enzymes, a P group is transferred to other molecules, which are then said to have been “phosphorylated” by ATP, which is oxidized to ADP, adenosine diphosphate. This process of phosphorylation represents a coupling of exergonic (ATP hydrolysis) and endergonic processes used by the cell to accomplish different tasks, i.e., cellular work—either involved in mechanical motion, transport, or chemical changes. ATP phosphorylation is a ubiquitous solution to problems involved in cellular work, which is taking place in our cells constantly and generates a high demand for ATP in our cells. Luckily, our bodies are equipped with mechanisms for quickly and efficiently regenerating hydrolyzed ATP from by-products of catabolic processes (more on this later).

Metabolic (energetic) and catabolic (break down) pathways of cellular respiration, as a whole, represent a complex and tangled web of biochemical interactions. Given this complexity, biologists have seen fit to break this complexity into two basic processes comprising cellular respiration: (1) the citric acid cycle (a.k.a., the Krebs cycle) and (2) oxidative phosphorylation. Broadly speaking, this order represents a potentially but not necessarily in-line time series of events classically taught from the perspective of breaking down glucose molecules into energy in the form of ATP. Now, we take a closer look at each of these steps in cellular respiration.

Glycolysis, considered by many the first stage of cellular respiration although making this designation is committing a semantic error (cellular respiration only means processes using oxygen in CR), refers to biochemical processing our cells carry out in the cytosol, or liquid matrix comprising the extra-organellar (NS) space within cells, which serves the purpose of breaking individual glucose molecules (6-carbon ringed polysaccharide monomers) into two pyruvate molecules (3-carbon chemical compound). This evolves a small amount of ATP. Glycolysis is comprised of a ten-step process. In the early stages, the energy investment phase, cells burn two molecules of ATP; in the latter half of the whole series of reactions, two molecules of pyruvate (3-carbon molecule formed from breaking the 6-carbon glucose ring in two using Aldolase), four ATP molecules (net of two per glucose molecule) and two molecules of NADH are generated per starting glucose monomer. Pyruvate, after being shuttled into the mitochondrion, may be further oxidized through the citric acid cycle (CAC) and or by oxidative phosphorylation (OP) machinery, but this only can happen if oxygen is present in the cell. Alternatively, NADH, the reduced form of NAD+, holds electrons which can be used by CAC and OP processes to yield waaaayyy more energy than glycolysis per unit glucose starting material (as you'll see next post).

What I really want to harp on here is that this stuff is important! Really, really, really important, actually. Everyone should be interested in learning about this because biology is everyone's problem by virtue of our biological nature. Learning about biology is learning about your history, your form, your function, your relatives, your disease, your world. No biological entities could move or do any work without a means of converting energy in food to useable form in our cells, which are uniquely equipped with machinery to carry out highly specialized functions maintaining life as we know it. Next, I'll review another troubling set of ideas forming the remainder of cellular respiration: the citric acid cycle and oxidative phosphorylation.

Transformers

Went and saw Transformers with family and friends last week. My take: blown away. I am still just pumped by the overrunning excitement of that experience (late show: 9:30 – 12:00 midnight). Not only was it a real stepping stone to take some time and connect with my family through an entertainment experience like that (because it’s something we haven’t done together in a long time), but also there’s something in being able to watch dreams of your childhood come to life on the big screen, with a bunch of cinema magic in the mix. An added feature of seeing transformers was that I noticed in myself more maturity in my analysis of the world around me; in other words, it was fun to think about what I had just seen critically and to personalize the analysis by looking inward at what the experience meant to me. It was really great to see that my intellectual development is something that has branched out to other areas of life. So, what a deal!

Transformers was a great movie, not just a great movie-going experience. So, it would be fruitful to think about why this was the case. What made this movie so good? The science fiction aspect certainly has its benefits. Also, one cannot leave the Transformers experience and, after thoughtful analysis, conclude that this was a simple set of interactions going on, that it was the perfect film; rather, the movie proved more complex and multi-faceted with its own problems. I will consider both of these perspectives, the pros and cons, in more detail.

Again, in the best light, Transformers was really great. I think this has its foundations in an interesting story relating concepts involved in my imagination and play as a child, the action (graphics and sound) were incredible, the cars and techie stuff were cool and relevant to the times (new versions of fighter planes and beefy automobiles), comic relief was well-placed, and the movie’s underlying themes were provocative yet open to interpretation (thinking parents would get more out of this movie than good ole’ fashion good guys vs. bad guys, shoot-em-up, save the world stuff).

On the other hand, the film was not without its faults. After taking a reality check on the drive home from the theater, I realized this film had many difficulties. I will provide a few examples. First thing, the boy-girl story was unrealistic.

Megan Fox and Shai LaBoeuf (sp?) in Transformers.

Also, the alien robots (transformers and the other bots) took on distinctly human-influenced physical and emotional forms so as to be palatable to the human audience, which seems weird given this may be viewed as taking away from the “alien” nature of the story line. Another problem was that the audience was left without closure in some spaces; for example, some parts of the plot, which wove through several group’s stories (e.g., the computer hacker people and secretary of state), were dropped, never to be fully resolved in time and space on the screen (at one point in the movie, they just never show these characters again). In a skeptical context, certain claims in the story were never substantiated (e.g., the sector seven commando played by the guy from the Adam Sandler films used an unknown technology to knock out a small robot created from the black guy’s cell phone using power from “the cube,” but this was never explored or explained further by virtue of the timing of the Megatron invigoration). Furthermore, the whole autobot back story may be viewed as too short and or too shallow for the tastes of some moviegoers altogether. In other words, showing more of the whole cube’s story might have been fruitful. Also, what did it do in pre-war autobot society, why did it survive the transformer planet’s destruction, what was its power used for, etc.? Last but not least—and I could go on—the parent scenes and hottie girl’s “juvie record,” as in police record, stories could easily have been left out. Given these substantial lists of problems, one would be tempted to think the movie sank; however, the experience of the moviegoer, if like my own and potentially even acknowledging plainly each of these faults, tells a different story, a story of success, a story of entertainment and enjoyment. So, even though the problems could have fatally injured other films, for some reason this wasn’t the case with Transformers.

I conclude with reflection on the major themes of the movie. One cannot help but leave the cozy chairs, popcorn, and soda cups, not to mention THX surround system, of AMC theaters without having come away with two, maybe three essential themes of the film. I give several possibilities: (1) the failure of “I-know-more-than-you-do” and “rules-and-bureaucracy” leadership (i.e., big US government and national security, typical parenting issues) (2) the idea that the greatest achievement, the greatest good and virtue is sacrificing for a good cause—others, something bigger than yourself (e.g., the fate of the planet or the fate of the good guys, the autobots in this case), and (3) the idea that there is more to life than what you think, "more than meets the eye." I also thought it was cool how the autobots considered themselves living creatures, with humans representing more primitive species (don't get it, but interesting nonetheless).

Maybe, you'll hear more about this later...

The Cell

It would be difficult to imagine life on earth without cells. In fact, it is not very easy to explain whether or not life would be possible without cells. The cell is to the organism what the nephron is to the kidney or the atom is to a chemical molecule or the individual employee is to a thriving coroporation, it is the smallest unit of the whole—in this case, the smallest unit of life. As we have already learned, below the cellular level, the parts of biological systems are usually thought of as non-living. Thus, it is the cell which has the capacity to be the smallest living thing. I have described how life forms, including our human bodies, are made up of millions of different cells comprising different levels of our form (tissues, organs, etc.). Now, we turn our attention to where we think cells came from, what cells are, what kinds of cells make up living things, what structures differentiate different cells, how these structural variations correlate with functional plasticity of cells, and how biologists study cells.




Figure 2. Generallized prokaryotic (left) and eukaryotic cells (right). (coming soon)

Today, cells are broadly classified into two different groups, (1) eukaryotic cells and (2) prokaryotic cells (Fig. 2). Further, eukaryotic cells may be subdivided into plant cells and animal cells based on different characteristics. Eukaryotic cells and prokaryotic cells—all cells in all living things—share several features, including DNA, cytoplasm, ribosomes, and a cell wall. Eukaryotic cells, thus eukaryotes (organisms comprised of eukaryotic cells), are differentiated from prokaryotes by possessing membrane-bound organelles, including a membrane bound nucleus, a kind of command center for the cell where the hereditary information is stored, and mitochondria, the “powerhouse of the cell.” Also, prokaryotes are single-celled organisms lacking distinct nuclei.

Cellular Evolution, Form and Function

Most biologists agree the evidence suggests eukaryotic cells originated through a series of events described by what is known as the serial endosymbiosis theory (SET), which explains the organellar (sp?) differences in prokaryotic and eukaryotic cells, hence the origin of eukaryotic cells. Serial endosymbiosis theory is founded upon the established idea that prokaryotic cells arose first in the evolution of life, then exploited and changed the early earth environment. A symbiosis is a cohabitation of living things, one joined to the other physically, as in the case of rumen bacteria-cow and gut living protist-termite relationships, or ecologically, in which both organisms benefit. SET suggests ancestral prokaryotes formed a symbiotic relationship with aerobic heterotrophic prokarytes after engulfment as undigestable food or infiltration of the original prokaryote by the second through parasitic means. It is also believed that photosynthetic proto-plastids, the ancestors of today’s chloroplasts, were also prokaryotes similarly engulfed by ancestral prokaryotes which had developed membrane-bound nuclei, forming photosynthetic eukaryotes. Since all eukaryotes possess mitochondria but many eukaryotes do not possess plastids, we infer that mitochondria preceded plastids in eukaryote evolution. Recent DNA sequence data support the earlier versions of SET by illustrating a monophyletic origin of mitochondria and plastids (Gray 1993, more later). So, this provides a background for understanding the origin of cells, but what is a cell anyway?

Cells were discovered in the 17th Century A.D. Specifically, this feat is attributed to the English scientist Robert Hooke, who used rudimentary light microscopy to view and describe the cellular components of cork (the first major discovery of cells, 1665) and other living tissues, plants and animals (NS). Most prokaryotic cells fall within a statistical range of 1-10 micrometers (μm), while most plant and animal cells are 10 μm to 100 μm in size. These cells are usually too small to be viewed with the naked human eye. Therefore, modern biology has developed a variety of microscope applications for looking at cellular and sub-cellular structures. These include light and electron microscopes.




Prokaryotic cells are interesting and the subject of study in numerous medical and evolutionary studies in modern biology. However, the bulk of our discussion will focus heretofore upon animal and plant cells, their form, function, and evolution.




Animal cells differ from plant cells by several features. First, virtually all animal cells contain lysosomes, centrioles, and flagella, while plant cells lack these. Alternatively, plant cells possess chloroplasts, central vacuoles, tonoplasts, rigid cell walls, and plasmodesmata which animal cells do not.




It is one thing to know the difference in animal and plant cells based on their distribution of organelles; however, it is another thing altogether to understand the interaction of these cellular components and to be able to say something about their different functions within plants and animals, especially their importance in reproduction and survival, thus evolution of populations. Thus, what follows is a list of the different plant and animal organelles and their different functions (Fig. 3).


Figure 3. Animal and plant cell organelles and their functions.

Together, the nuclear envelope, rough and smooth endoplasmic reticulum, golgi apparatus, lysosomes and, in plants, central vacuoles, comprise what is known as the endomembrane system. This system regulates the flow of membrane lipids and proteins through the cell and performs metabolic functions. All organelles in this system have membranes. Subsequently, all membranes in the endomembrane system are linked through direct or indirect transfer of membranes and sacs, such as small vesicles, which are tiny spheres of membranes that move through the cell for different purposes. It will be helpful to look at each piece of this system in more detail.



The endoplasmic reticulum exists in two forms, smooth and rough, segregated by the absence or presence of ribosomes on the surface of the membrane, respectively. These two kinds of ER may also be thought of differently in terms of function. For example, the smooth ER is heavily involved in lipid synthesis, carbohydrate metabolism, calcium storage, and detoxification processes. As a result, tissues functioning in detoxification, such as liver tissues, often display a higher density of smooth ER than tissues which carry out detoxification processes to lesser degrees. An important point about smooth ER function is that we be clear about the distinction between different kinds of lipids—steroids and other hormones are kinds of lipids, as are oils and the phosphate-containing lipids making up the bulk of cellular plasma membranes. Because smooth ER is active in the synthesis of hormones, cells of tissues that specialize in hormone synthesis, such as human gonads and adrenal glands, are rich in smooth ER. On the other hand, rough ER has its own set of form with different functions. Many cellular and super-cellular processes rely upon proteins produced by rough ER ribosomes, including insulin, which is a secretory protein. Rough ER is also responsible for membrane production.



Golgi apparatus can be thought of as the manufacturing and shipping center of the cell. Golgi has no special meaning, other than being the name of this structure’s discoverer (NS). But golgi apparatus has a central function integral to cell function: the golgi provide a crucial link between structures in the endomembrane system by modifying carbohydrates, manufacturing macromolecules, and shipping different cellular products by budding vesicles from its surface and sending them out into the cytoplasm to be directed toward different locations.

Lysosomes, peroxisomes, and vacuoles are some of the simplest compartments in the endomembrane system. These are basically bags containing hydrolytic enzymes, hydrogen peroxide, and cellular wastes and water, respectively. Lysosomes digest engulfed food particles and degraded organic material beaten by cellular wear and tear. This latter function is called autophagy.
Campbell and Reece summarize well, “The cytoskeleton is a network of fibers that organizes structures and activities in the cell.” The cytoplasm actively provides structural support to cells. Also, it plays a role in cellular locomotion, as in pseudopodia formation and movement in amoebas, and cell motility, which may not mean whole-cell movement, but rather indicates movement of cellular parts. There are three main structural elements in cytoplasm: microtubules, microfilaments, and intermediate filaments. Microtubules are formed by coiled strands of tubulin dimers, polymers formed by alpha and beta tubulin subunits, which are hollow in the center. Microtubules are the only cytoskeletal elements considered to be organized and originate from the centrosome (pair of centrioles). Microtubules function in cell motility as parts of cilia and flagella and facilitate chromosome and organelle movement by providing substrates for motor proteins to move along. Microfilaments are composed of two strands of actin subunits wrapped around one another. Microfilaments are smaller in size than microtubules and help cells, tissues, and organisms by facilitating shape change, providing a substrate for cytoplasmic streaming, aiding in cell motility (pseudopodia) and cell division (cleavage formation), and providing a substrate for myosin ratcheting during muscle contraction. Intermediate filaments receive their name because they exist in diameters which are smaller than microtubules but larger than microfilaments. These structures are composed of proteins in the keratin family and vary from cell type to cell type; however, they maintain certain cell functions wherever they are found, including structural support, nucleus anchorage, and formation of the nuclear lamina, a netlike mixture of proteins which maintains the shape of the nucleus. For all of these reasons, tubulin, actin, and keratin represent some of the most important cellular proteins know to cell biologists.



Cilia and flagella, as I mentioned, are locomotory organelles of cells extending beyond the main plasma membrane. These exist in different sizes, are found in different types of cells, and exhibit different types of stroke patterns; however, the fine structure or ultrastructure of these organs are homologous. Each is formed by microtubules connected by an orderly arrangement of proteins, all bound by a plasma membrane continuous with that of the remainder of the cell. Through the main body of cilia and flagella, microtubule sets are arranged in a “9 + 2” configuration of doublets; however, microtubule triplets form the anchoring region of cilia and flagella, known as the basal body, and are analogous in form to the centrioles. The motion of cilia and flagella cannot be explained by these microtubule-based structures joined by structural proteins alone. Instead, a large protein complex known as dynein is responsible for the bending and stroking motions of cilia and flagella. When fueled with adenosine triphosphate (ATP), dynein molecules can perform work in the form of a “walking” motion, a complex series of steps resulting in their movement along a microtubule doublet and subsequent movement of anything the polypeptides are bound to, such as another microtubule. In the absence of constraining forces, this motion would move microtubule doublets found in the main bodies of cilia and flagella in a parallel fashion. However, because microtubules of these structures are bound by cross-linking proteins, they are cut off from their potential range of parallel motion in such a way that causes cilia and flagella to bend. It is believed that synchronized dynein movements are responsible for orderly bending and stroking of cilia and flagella, although this is not very clearly understood.

THE IMPORTANCE OF CELL WALLS, EXTRACELLULAR MATRIX, AND INTERCELLULAR JUNCTIONS ARE NOT DOWNPLAYED, BUT SKIPPED.

What is Biology?

Philosophy of science is a vibrant area of philosophical discourse, which attempts to reason about the way we can come to know more about the universe through science and its methods. Philosophy of biology works to test biological practices and concepts for logical soundness, both as a kind of system of checks and balances and a method of perpetuating new ways of thinking about what biology is and what it ought to be like. Because it is so foundational, philosophy should spill out of any good description of what biology is and of what science is. One reason for this is students must fully grasp what science is before they understand what biology is, so it is only natural to begin our discussion of what biology is, what its theories are like, and what biologists do with a focus on philosophy of science and biology. However, it is important to realize that philosophy of biology is distinct from biology itself.


First, and foremost, biology is a science. Science is simply any study of how the world works reasoned out using naturalistic explanations. The highest goal of science is knowledge, so science can be thought of as the quest for knowledge, which may also be viewed as an innate part of the human experience. Often, our concept of science is synonymous with our understanding of scientific methods. And in the real world, the concepts lay people have about biology are based upon the relationship between what they know about biologists and their work.


If science is a way of seeking out answers to our questions about ourselves and the world around us, then how is this accomplished by biologists? Biology, like other sciences, is based on the idea of inquiry. Campbell and Reece (2007) define this as “the heart of science… a search for information and explanation, often focusing on specific questions.” If science is inquiry and inquiry is the quest for knowledge about the world and explanations of this knowledge, then it follows that the work of biologists must be centered upon observation and explanation; indeed, this is the case.

Observations are made by using our human senses to record qualitative (non-numerical) and quantitative (numerical) information about the world around us. We call this information, which are in essence facts about how the world is, data, which scientists use to make explanations about the natural world. Biologists make diverse observations from the color of fish fins to the size of neurons. Conclusions based on observations are drawn by a type of logic known as inductive reasoning, which is used to make generalizations from scientific data we gather. Explanations of generalizations based on facts represent the next logical step in scientific inquiry. After gathering facts and making generalizations, biologists and other scientists often develop hypotheses, which are educated guesses about specific questions making predictions that can be tested using another important scientific method, the experiment. Hypothesis-based science makes the jump from generalizations to understanding specific interactions, forces, structures, and so on, responsible for biological phenomena by using deductive reasoning (deduction), which creates a logical flow oppositely oriented with respect to inductive reasoning discussed above. In other words, deduction is the process by which we make the transfer from generalizations to specific results. This process allows scientists to draw the testable predictions integral to hypothesis-based science.


Here, it is important to emphasize that the straightforward scientific method of primary education (observation, hypothesis, prediction, test, etc.) in science represents only one description of the order of scientific methods. Many times in their career—even during one experiment or project (set of experiments)—biologists may use different methods or different ordering of research priorities to answer biological questions. In fact, some biologists never even conduct experiments, because in many cases they would be biologically harmful and or morally unacceptable!Another way to begin thinking about biology as a science might be to ask, what real world forces or tools are responsible for the advancement of science, of biology? An important point might be how the breadth of biological inquiry, not unlike other fields of science, has always been intimately linked with technological and theoretical advances. Many of these have been perpetuated by workers in the field of biology, however many important innovations in biology owe themselves to advances in other fields of science. Technological and theoretical advances are important because they detail the options available to biologists in terms of method and concepts upon which their inquiry is based. Thus, technology and theoretical improvement lead to better solutions of biological problems, including more rigorous tests of better equipped hypotheses. So, we see that it would be unrealistic to view biological science and other disciplines of scientific study as mutually exclusive entities. In his book, The Creation, E. O. Wilson (2006) notes,

“The ongoing explosive growth of knowledge, especially in thesciences, has resulted in a convergence of disciplines and created the reality,not just the rhetoric, of inter-disciplinary studies. Biology, for example, istoday a swiftly evolving kaleidoscope of hybrid subdisciplines… As aconsequence, what was once perceived as an epistemo-logical divide between thegreat branches of learning is now emerging from the academic fog as somethingfar different and much more interesting: a wide middle domain of mostlyunexplored phenomena open to a cooperative approach from both sides of theformer divide.”

Biology is continually advancing in new directions fueled by technology and theory, but a proportion of biological advances must always be attributed to the momentum generated by this middle domain and by the academy as a whole, resulting from the more generally intertwined nature of fields of science. For example, and a specific one at that, as chemical experiments reveal more about pieces of biological phenomena, biologists are better informed about their studies and therefore their work is accelerated.But if academia, if all of science is intertwined in this way, what features of biology distinguish it from other realms of science? Is there a point where the other sciences end and biology begins? There are minimally two approaches to solving this problem for the novice, explaining what makes biology similar to other fields of science then venturing on to its uniqueness, or explaining away what biology is not and should not be. Alternatively, one might go directly into the big picture of what biology really is beyond formal distinctions about science and its philosophy, then focus in on its more specific attributes. Now that we have discussed what science is and how biologists conduct scientific investigations, I will take the first step toward accomplishing the end of this alternative goal.


In simplest terms, biology is the study of life. More precisely, modern biological science represents a multi-faceted discipline exploring the complexity of living things, their history, their interactions with each other and their environments across fine (microscopic) and broad spatial (global) and temporal (historical) scales. Biology is divided into many specialty areas of research, which include, but are not limited to, cell biology, genetics, anatomy and physiology, ecology, systematics, and evolutionary biology. An educated view of what biology is best approached by a top-down approach. So, before we go any further, we should begin with the big picture.The earth is our home, our place in the universe, the only life-bearing planet of its kind known to humanity. Much of the earth’s mass is composed of rocky and molten geophysical components, yet a thin film of life surrounds the globe at its surface. The biosphere is the name given to all the places on earth sustaining living things. Notice this concept does not include the whole planet necessarily, but we do know that most of the earth’s surface is habitable. The biosphere, in turn may be subdivided into ecosystems composed of communities, which are groups of populations. Populations are a little tricky to define, but the traditional definition is that of all the individuals of a particular species in one place at one time. Populations are subdivided into individual creatures which are all engaged in a fight to survive and reproduce in an often changing environment.

Figure 1. Hierarchical organization of biological systems from molecules to the biosphere (http://www.mie.utoronto.ca/labs/lcdlab/biopic/fig/1.9.jpg).


But biological organization goes further still. Based on years of study, we know that individuals are composed of organ systems or tissue layers that are in reality groups of specialized cells, fundamental units of biological structure and function. Some organisms are actually single cells, while others are multicellular. At the level of the cell, a whole new universe of biological interactions open up. Using different imaging techniques, including microscopy and histological sectioning, we observe that cells are composed of many different cellular features, many of them specific to the type of cell in question. So, we see that organic, biological nature can be studied by the biologist at a number of different levels of naturally occurring hierarchical organization (Fig. 1). Differences in levels of organization chosen for study by biologists are responsible for the subdivisions of biological science mentioned above. From this short discussion, we see that biology covers an enormous range of living phenomena and that biologists have an immense amount of living material available to work with.


There is a level of biological organization that I have failed to mention. I will address this level after briefly digressing to discuss a familiar phrase that you might hear in an introductory biology class. One way of viewing the relationship between biology and the other sciences is captured in the familiar axiom, “All biology is chemistry, all chemistry is physics, and all physics is mathematics.” This phrase may be interpreted in a variety of contexts. Many, including myself, consider it a gross and sometimes unhelpful oversimplification. It does, however, have a few interesting things to say about biology and science which cannot be doubted. First, it brings an important biological paradox to light, namely that at smaller scales all biological entities are composed of non-living chemical substances. It is very important that the student recognizes the biotic (living) and abiotic (non-living) levels of biological organization: below the cellular and organelle levels, life breaks down into chemical constituents, which can be further subdivided on the basis of their structure and function as they relate to one another and the rest of the biosphere (more later). Second, it highlights the important link between natural and physical sciences. Third, it notes the connection of all sciences with what some (mostly physical scientists, statisticians, and mathematicians!) consider the most basic and inescapable truth of the universe, mathematics. Ultimately, standing alone, this phrase fails in helping us understand what biology really is, but it does offer a great road map for rounding out our knowledge of hierarchical biological organization as I have shown—by including biochemical substances.


Campbell and Reece (2007) list eleven themes that unify biology (p.27), including (1) the cell as the basic unit of structure and function; (2) the idea that the continuity of life depends on the inheritance of hereditary information encoded in the form of specific nucleotide sequences of deoxyribonucleic acid (DNA) molecules; (3) the interconnected facts (a) that biological systems are more than the sum of their parts, (b) that the biosphere shows a hierarchical kind of organization, and (c) new properties emerge as we travel up the hierarchical structure of living things which were not apparent at lower levels; (4) the ubiquity of regulation in biological systems, where we find that feedback mechanisms and other forms of regulation attempt to maintain stable physiological or chemical states; (5) the idea that living things are important parts of their environment, interact with it, exchange energy with it, and thus change their environments; (6) two related ideas that (a) living things place energetic demands on their environments as a function of the caloric costs of their metabolism involved in the work organisms carry out from sub-cellular to organismal levels and that similarly (b) energy flows through the biosphere from the sun to producers and on to consumers, and this energy leaves ecosystems and organisms in the form of heat energy; (7) while a great phenotypic diversity is seen in the biosphere, (a) the great variety of biological forms and their interactions arise from a much less diverse (similar) pool of genes and (b) all living things arose from a single common ancestor some billions of years ago; (8) evolution is the unifying fact of all biology which explains the unity and diversity we observe in the living world; (9) structure and function are intimately linked throughout the hierarchical organization of biological systems; (10) as I have focused upon thus far, biology is inherently scientific, thus based on inquiry and subject to the methods and philosophy of science; and, finally, (11) biology is not disconnected from other fields of inquiry, but has important applications and implications for individuals, society, other sciences, technological innovation, human societies, and the planet at large.


HERE: I'M SKIPPING BASIC CHEMISTRY, BIOCHEMISTRY, AND RELATIONSHIPS BETWEEN THESE VARIABLES AND THE FITNESS OF THE NATURAL ENVIRONMENTS OF THE EARTH FOR SUSTAINING LIFE. NOTE: The cell, genetics, and mechanisms of organic evolution will comprise the focus of the following discussion.See "References" Link for more information about sources and extra reading materials (If not on sidebar, it's coming).