Biology for Engineers, First Edition (Solutions, Instructor Solution Manual) [1 ed.] 9781439848661, 9781420077636, 1420077635

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SOLUTIONS MANUAL FOR

Biology for Engineers

by

Arthur T. Johnson

SOLUTIONS MANUAL FOR Biology for Engineers

by Arthur T. Johnson

Boca Raton London New

York

CRC Press is an imprint of the Taylor & Francis Group, an informa business

CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2011 by Taylor and Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed in the United States of America on acid-free paper 10 9 8 7 6 5 4 3 2 1 International Standard Book Number: 978-1-4398-4866-1 (Paperback) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts have been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com

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Biology for Engineers Solutions Manual Arthur T. Johnson Many of the problems in this book were intended to stimulate thought about biology and biological engineering. They are not very specific, and not difficult for the students to answer; only a little thought is required to answer them. Because of the nature of most of the problems, there are few right and wrong answers. What is more important than exact answers is the quality of student responses: did they give serious thought to the answers, and have they really given sufficient effort. Sometimes, students have shown amazing insight into a problem, and given unique and insightful or elegant answers. Expect these: these are the creative ones in your class, and they have great capability to go far. Solutions given to many of these problems are given in general terms, and student answers may not agree with the ones given here. That is to be expected. There are a few questions that have a particular twist deliberately incorporated in them. For those questions, the answers should match well with those given here. I have always formed groups in my classes, and assigned homeworks by groups. I usually give groups a choice of questions to be answered in each section. They can choose their own questions that they want to answer. For sections of the book that include Applications and Predictions, I ask that they answer the question from each section that asks students to add to the applications and predictions. Otherwise, they can answer one additional question of their choice from each section.

QUESTIONS Chapter 1 1.2.1. Give at least two biological examples of the stages of technology. Here, students may answer with many different examples. Make sure that each example that the students give have Random, Descriptive, Quantitative, and Control phases clearly labeled. 1.2.2. What do we mean by the “control phase” of technology? What does this phase mean for biological engineers? The control phase is the part of technology development that relates to the use or application of the phenomenon of interest. For biological engineers this means that they have enough knowledge of a biological system that an engineering design or

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application can be made either using that phenomenon or applied to some biological system. Students may give their own, valid explanations to answer this question. 1.2.3. Describe what you think engineering is. Students give their descriptions of engineering. The answer may contain the elements of scientific applications, creativity, professionalism, and service. Solving real-world problems requiring creativity and a strong math/science background may be part of the answer. 1.2.4. Are biologists who manipulate genes really “genetic engineers”? Students should give their opinions. In general, genetic manipulation is not genetic engineering unless the outcome of the manipulation can be anticipated. Most genetic manipulation is done to see what the outcome will be. On the other hand, if there is a purpose to the manipulation, and the exact gene is known that results in the desired outcome, then that may be called “genetic engineering”. Synthetic biology is headed in the direction of genetic engineering. 1.2.5. What are the differences between inductive and deductive fields of study? Induction involves extrapolation of data or results to new situations or to circumstances outside the range of the data. Extrapolation can thus be somewhat dangerous. Science is continually extrapolating in order to generalize specific results. Science involves a quest for new knowledge, and so extrapolation is a necessary tactic. Deduction involves working from the general to the specific. As long as the generalization is true, the deducted fact or figure must be true. Thus, deduction is generally safe. Engineering uses induction all the time. Deduction is a necessary method to create a new design or application for established knowledge. 1.2.6. How would you go about explaining an idea to a scientist? What if the listener were an engineer? Students may have a lot of different answers to the question. As long as the scientist specializes in the field of study that you both know, then there should be no trouble communicating between you two. However, scientists and engineers both have their particular jargon. It is often easier for an engineer to learn the catch words and phrases used by the scientist than for the scientist to learn how to think as an engineer, and thinking as an engineer is what is necessary for the scientist to communicate with the engineer on his or her own terms. The difference in the two sides thus comes down to the formation of concepts by engineers and the care and diligence exercised by scientists. Generalizations are dangerous, so these statements may not always hold true, but the burden is often on the engineer to speak with the scientist on the scientist’s terms.

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1.2.7. Make a list of engineering contributions that have enabled scientific progress. There may be many items on this list. Many will involve the products or processes reduced to practice by the engineer. Different kinds of instruments will probably appear on the list. In a more general vein, engineering works related to housing structures, vehicles, ventilation and refrigeration systems, roads, sanitation systems, manufacturing processes, food production, and others can appear here. The student should give a lot of thought to this, and realize that engineering supports scientific progress in many different ways. Lastly, engineering can lead scientific progress by modeling a scientific problem and implying what next steps should be taken to produce meaningful scientific data. 1.2.8. Give an example where an understanding gap is likely to exist between a scientist working in that area and an engineer who also wishes to work in that same area. How could you, as a biological engineer, help each to understand the other? Students can give examples as they conjure them. Such an example might arise when an engineer sees only the engineering aspects of a problem and doesn’t communicate well with the scientist. An example could be similar to this: engineers are working on an algorithm to treat the electrocardiogram (ECG) to extract certain traits that they have been led to understand are important for the treatment of disease. They forge ahead without knowing much about the workings of the heart, how the ECG is produced, or how it can change in response to other physiological factors. They marvel at their accomplishments, but the physiologists or physicians cannot comprehend what they did or why it is good. The biological engineer, being able to understand both engineering and biology, can bridge the communications gap. Other examples might deal with certain requirements to measure correctly. The engineer might understand these things, but the scientist may not know why these limits are important or even what they are. The biological engineer should be able to explain limitations in terms that the scientist can readily understand. 1.3.1. Why is the scientific method so powerful? proceed without using the scientific method?

Can any kind of science

The scientific method is so powerful precisely because it is supposed to be impassionate and impartial. The hypothesis is supposed to be proposed ahead of the experiment, and the data analysis method decided beforehand. Thus, the conclusion from the experiment comes from the data rather than from a preconceived notion about how things should work. Science doesn’t always work this way, but this is how it should work. Science did progress before the scientific method was practiced. Ancient science proceeded either through experimentation that was largely random, but sometimes guided by experience, or through thought experiments. An example of the first kind is

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the chemical knowledge gained by alchemists; an example of the second kind was Aristotelian science based on perfect models (such as spheres). Thought experiments are still carried out in the present, as exemplified by relativity, astrophysics, and quantum physics. So, the scientific method is not a requirement of scientific progress; however, even acceptance of Einstein’s theories had to wait for experimental verification. 1.3.2 Why is Koch’s method of proving a connection between a microbe and a disease so powerful? Are there other possible causes of the disease if microbes identified by his procedure pass all tests? Koch’s method is particularly powerful because it is thorough. The steps involved in Koch’s method include having to have the target microbe present in all cases of the disease, be grown in isolation, and, when injected into an animal which then comes down with the disease, be identified in all cases of the disease and be positively identified as the identical microbe that was first found in all cases of the disease. Koch’s method not only tests the positive, but also the negative, and it is redundant. It is possible that there could be other causes of the disease if the microbes appear to be the cause. For instance, there could be several microbes working together, or a microbe and a prion, or a microbe and a particular environmental condition that cause the disease. Koch’s method is not infallible, but it does reduce the chance of wrong conclusions to a very small number. 1.3.3 Name some diseases whose cause would not be able to be identified through Koch’s method. Not all diseases are caused by microbes. Koch’s method would fail for Alzheimer’s Disease or Bovine Spongiform Encephalopathy (BSE) that seem to be related to prions (or misfolded proteins). Koch’s method may not even work for Acquired ImmunoDeficiency Syndrome (AIDS) that is caused by a retrovirus that cannot be cultured easily in the lab. There are some hormonal diseases, such as diabetes, and perhaps Parkinson’s Disease, that would not be able to be identified with Koch’s method. Also, genetically-caused diseases, such as Cystic Fibrosis would defy causal identification with this method. 1.3.4 If you are told that a certain drug is effective against a disease, what kind of evidence should you look for in order to be convinced? You should look for evidence that the drug is more effective than a control. The control should be conducted with as much methodological commonality with the treatment as possible. The only difference should be the administration of the drug in one case and a placebo in the other. Both groups of subjects should be equivalent in all respects. The sizes of the control and treatment groups should be large enough that any effects seen have meaning. Statistical tests can be conducted to add confidence in the results. A double-blind experiment carries more weight than a single blind or open

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test because the likelihood of the test personnel influencing test results is much reduced. 1.3.5 State a principle of science. through theory to its present form.

Trace its evolution from isolated facts

Students usually do not answer this question, but, if they did, they could mention general principles related to such things as cause and effect, believing observational data over speculation, and the reproducibility of data. More specific principles might be, for example, principles of physics or chemistry. Newton’s Laws of motion could be given, or his theory of gravitational attraction. Students would most likely have to look up the history of the development of these principles. 1.3.6 Ohms law (I = E/R) was originally published with an additive constant term (I = E/R + C). Ohm spent the rest of his life trying to amend his original mistake. If you were George Simon Ohm, how would you go about doing this? It is very difficult to retract something you have written once it is published and disseminated. One way to do this is to write a retraction letter to the journal in which the original article was published. This is embarrassing to you, the journal, and the reviewers of the paper. However, it must be done. In Ohm’s day the publishing process was different. Authors often self-published papers they wrote, and read them in front of learned societies. Copies were distributed among scientists (philosophers) in civilized societies. In this case, a retraction letter to the publishing journal was not possible. One could read such a letter in front of the society that heard the original paper, but there was no guarantee that those to whom the paper was distributed would know about the retraction. However, because of the embarrassing nature of the retraction, Ohm would probably not want to take his actions past the step of reading a retraction. 1.3.7 Give an example where some physical or biological phenomenon is explained with a human motivation. How could you go about proving or disproving the explanation of the event? Human motivation is projected all the time on our pets, for instance. We often say that our dogs and cats do or don’t want to do something because they are thinking about others’ reactions or because they want to share, or something else. Some of us talk to our cars, especially when they get stuck, don’t work, or are in danger of doing either. “If you will only get me home, Betsy, then I’ll take care of you tomorrow”. We talk to our computers all the time, and our plants, our tools, and even our food, projecting onto them some presumption of human understanding. We could very well set up an experiment to test whether the object of our attention has the motivation we attribute to it. For instance, we could determine if our plant grows well because it likes us by projecting hate on plant and treating it exactly the same as before. This could be difficult to do unless we set up a double-blind test.

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The trouble is that we really wouldn’t like to set up such a test because we really know how the results would turn out. 1.4.1. Give an example of a model that includes both theoretical and empirical elements. How can one be distinguished from the other? When is it necessary to use empirical models? When is it desirable to base models on theory? Many engineering models include both theoretical and empirical elements. Even if a mathematical model starts out as a theoretical model, the calibration and validation steps incorporate empirical information to evaluate parameter numerical values. Students may have come across some model that they are familiar with to illustrate the answer to this question. There are books dedicated to presenting models of biological or physiological nature, and some of these that I have found useful are: Davidovits, P.. 1975, Physics in Biology and Medicine, Prentice-Hall, Englewood Cliffs, NJ, ISBN 0-13-672352-7. Edelstein-Keshet, L., 2005, Mathematical Models in Biology. The Society for Industrial and Applied Mathematics (SIAM), Philadelphia, PA. ISBN 0-89871-554-7. Haefner, J.W., 1996, Modeling Biological Systems. Principles and Applications, Chapman and Hall, New York, ISBN 0-412-04201-0. Johnson, A.T., 2007, Biomechanics and Exercise Physiology. Quantitative Modeling, Taylor and Francis, Boca Raton, FL, ISBN 1-57444-906-0. Keener, J., and J. Sneyd, 1998, Mathematical Physiology, Springer-Verlag, New York, ISBN 0-387-98381-3. Murray, J.D., 2002, Mathematical Biology I. An Introduction. Third edition. Springer, New York. ISBN 0-387-95223-3. Murray, J.D., 2003, Mathematical Biology II. Spatial Models and Biomedical Applications. Third edition, Springer, New York. ISBN 0-387-95228-4. Distinguishing empirical model elements from theoretical elements can be done with two judgment criteria: 1) are the elements based on generally-accepted first principles taught in basic math or science classes? and 2) numerical values are normally obtained empirically, at least for engineering models. It is necessary to use empirical models when theory has reached the limit of its applicability. Theory applies only to ideal situations; empiricism is based on real life. Theory can be used to frame an original model, but empirical (experiential) results are used to extend the model to describe actual phenomena.

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It is desirable to base a new model as much on theory as possible because the model has a firm basis, and would be found to be generally acceptable by others in the field or in the company. Theory is used as the first step to design a completely new product, whether the product be a physical widget or a mathematical model. 1.4.2. Someone tells you that they have an equation that nearly perfectly fits the data, and so that equation is the best description of the phenomenon. You inquire, and find out that parameter values for the equation were obtained from the data set for which the fit is nearly perfect. Why should you be suspicious about the value of the equation? What could you do to determine how good the equation is? An empirical equation based on one set of data fits that data as well or better than any other equation of the same type. However, robustness has not been proven. The equation has not been validated. Another set of data, especially obtained independently, is not as likely to contain the same biases as the first set, and may give entirely different parameter values. To check the equation, see how it fits other data sets. There are times when it is either impossible or impractical to obtain a completely different data set. The next best thing is to split the original data set in half, maintaining the same data range as the combined data set. Calibrate the equation with one half of the data, and validate it with the second half. 1.4.3. How can a mathematical model help an experimentalist? experimental facts be used to guide model development?

How can

A mathematical model can help guide the experimentalist in determining what parameters need to be tested, and the range of treatment (independent variable) values to use. Hence, a mathematical model formulated ahead of the experiment can help to design the experiment. I have seen at least one instance where a grad student spent years trying to show something experimentally that a later mathematical model showed was impossible. In this case, the mathematical model would have led the student to change his project before he wasted all that time. Experimental information is necessary before a mathematical model can be formulated seriously. First of all, experiments identify phenomena needing further attention (the quantitative stage of technology development). Second, experiments shed light on the way phenomena are related. Third, experiments are necessary in order to calibrate and validate the mathematical models. 1.5.1

Give your own additional descriptions for biological engineering.

Here, students can give their own impressions of biological engineering.

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1.5.2

What part of engineering is science and what part is art?

Engineering designs are based on scientific knowledge in order to predict behavior of new designs. The art comes in creating the design in the first place, putting together concepts in an original manner. 1.5.3 What is meant by a “specialist in technical diversity”? “specialist”?

Why a

A specialist in technical diversity is an expert who can look at the broad picture with a perspective that few others have. While other experts may study details of a fairly narrow technical specialty, the specialist in technical diversity studies how things go together to form a whole system. The specialist neither knows as much about a specific topic as the expert in that topic nor is capable of applying the depth of detail that a more specialized expert can. However, developing the ability to appreciate the whole system, and to know when to call on other experts, takes just as much study. That’s why it is a specialist in technical diversity. 1.6.1 Give an example where unintended consequences resulted from some attempt to fix a problem. There are many possible answers to this question, especially because the example doesn’t have to involve biology. There are many societal examples, including tax breaks intended to foster some societal goal leading to conflict with another goal. The Federal government’s policy to work toward energy independence by subsidizing ethanol production from corn has led to higher corn prices and higher production costs for meat and eggs. One student suggested that a good example is the equipping of the Taliban to fight the Russians in Afghanistan. We gave them American weapons that they used against us when we went into the country in 2001. A biological example might be the war against microbes that cause disease. We cleaned up our homes, our bodies, and our children. Then we used prophylactic antibiotics directly against the microbes, even if they hadn’t caused disease. We routinely put antibiotics in animal feeds to make them grow faster. What we ended up with are stronger microbes and weaker immune systems. 1.6.2 Should there be other expectations of biological engineers? If so, what and why? Students can give their opinions on this. Some will have well thought-out answers. 1.6.3 If the gene controlling the protein to draw oxygen from the mother’s blood were able to be turned on to cure sickle cell anemia, what unintended consequences would you suspect would happen? One part of a biological process is usually not isolated enough that it doesn’t affect other parts, so it is likely that changing the protein will have other consequences,

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perhaps related to retarded maturation of the person, or perhaps related to oxygen supply to the tissues. One possible effect would be that oxygen from the lungs would be bound too tightly to the fetal hemoglobin to successfully supply oxygen to the tissues during stress. Thus, the person might not be able to perform sports, work, or perhaps even normal resting activities adequately. 1.7.1 What number am I thinking of? If the number is somewhere between 1 and 10, what is the number? If the number is odd, and between 1 and 10, what is the number? If the number is evenly divisible by the integers 3 and 9, is odd, and is between 1 and 10, what is the number? What does this game have to do with engineering predictions? The answer to the first question is any possible number. The second question narrows the choices down a bit to a number from 2 to 9. The third question removes 2,4,6, and 8 from the list of possibilities. The fourth question requires the answer to be 9. The more information that is known, the better the prediction can be. 1.7.2 Why can it be said that an engineer must be able to predict the future? How does prediction relate to design? Above all, an engineer’s designs must perform their required functions. The engineer must know ahead of the final design that, with a great deal of certainty, his design will be successful. This is prediction in the best possible sense. Contrarily, if the design is likely to fail, the engineer must know that too, so that failure can be avoided. 1.7.3 List five biological attributes that can be predicted and five that cannot. Justify each. There are some biological attributes that can be predicted reasonably well based on familial relationships. These might include general height, weight, facial appearance, and intelligence of individuals. A dog’s breed can be anticipated based on its parentage. The appearance of a flower or the taste of a vegetable depends on its genes. Environments affect eventual outcomes, however, so exact attributes cannot be predicted. 1.7.4 Give an example of an inductive argument and an example of a deductive argument. One student answer that was given for an inductive argument is the conclusion that a trial antibiotic kills bacteria, based upon data collected in a laboratory experiment. If the antibiotic kills bacteria plated on agar, then it should work for other purposes. The same example can be used for a deductive argument when applying the same antibiotic to a specific microbe in a specific instance. If it works for all other cases, then it must work for this particular instance.

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These aren’t exactly what one might call arguments, but the general idea of induction and deduction are important. 1.8.1 Give an example of a product of engineering design and the original concept that led to the final product. Many different examples could be used. Perhaps one that is familiar is an incandescent light bulb. The original concept was for a glowing hot object to give off light. Many trials were required to determine empirically what material that object had to be made from to give off enough light without being consumed in the process. Carbon filaments were used for a while before the switch was made to tungsten. The fluorescent light bulb used an entirely different principle, and now light-emitting diodes produce light in a different manner. Biologically speaking, the glow from certain insects involving lucerferin take this step further. This reaction doesn’t generate noticeable heat. 1.8.2 What expectations do you have for this book? What do you hope to learn? Students will give their expectations. It is important for the students to engage their curiosity and interest at the beginning of the course. That way they will be more receptive to learning new material. This question and the next are intended to have the students actively participate positively in the learning process. 1.8.3 Look through the Table of Contents. Are there topics that particularly interest you? Students like this question, and most choose this question to answer. I like their answers, too, because then I know two things: 1) what they are interested in, so that I may treat these topics with a little more information, and 2) that they have interests coinciding with the material in this book. That way, they will be more fun to teach. 1.8.4. Contrast the knowledge that you already possess about biology with the contents of this book. Does this look to you like a biology book? Most of our bioengineering students have taken other introductory biology courses before they enrolled in college. When they look at the material to be covered in this course, they remark about how different this course is from the others they have taken. Yet, this is still introductory material, an inch deep and a yard wide. Despite their previous course, we don’t allow them to bypass this course, because it prepares them for biological engineering careers, not biology careers.

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QUESTIONS Chapter 2 2.0.1. Explain in your own words how knowledge of physics aids understanding of biological systems. Physics is the basis for almost all of engineering. Physical laws also apply to biological systems just as they do to inanimate objects. Understanding how biological units cope with physical limitations and use physical laws to their own advantage can be very enlightening with respect to the wisdom of biology. 2.0.2.

How is biological engineering design related to the study of physics?

Basic physical laws and equations are used to calculate forces, stresses, heat flow, mass transfer, and fluid flow. All of these and more come from the study of physics. Understanding physics aids understanding of biology and helps to calculate aspects of engineering designs by biological engineers. 2.0.3. Physical, chemical, and biological components of the environment interact with loving things. Give examples of the physical environment of organisms. The physical environment includes temperature, humidity, pressure, stresses, energy sources, gases present, abundance of water and nutrients, and many other environmental factors. Animals, plants, and microbes must adapt to the presence or absence of these physical factors. 2.0.4. Can you think of additional physical principles that relate to biology? If so, list them. Let’s see if they come up with anything good. 2.1.1. Describe the behavior of a biological organism. In this description identify the effort and flow variables. Remember that effort variables don’t describe things that move; that is what flow variables do. An organism eats food. It does so by applying a force to a piece of food and putting it in its mouth (or other ingestion orifice). There are several effort variables here: hunger is one, and it results in food ingestion (the flow variable). Force required to move the food is effort, and the velocity is the flow variable. The organism moves around in the same way (force=effort and velocity=flow). The muscles work by depolarization (flow) accompanied by a voltage (effort). These movements generate heat (flow) that can lead to a higher temperature (effort). Nutrients in the food are distributed through the body by a circulatory system with fluid movement (flow) propelled by a pressure source (effort). From the circulatory fluid to the cells,

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nutrients move (flow) by diffusion caused by a concentration difference (effort). The organism searches for a mate (flow) because of a desire to reproduce (effort). 2.1.2. Describe the effects of resistance. If resistance did not exist in a plant or an animal, what would be different? Resistance limits flow for any given effort. Many basic variables are effort variables. If there were no resistances, there would be no limit to the amounts of resulting flows for even minute effort differences. For instance, swimming in the ocean would completely dry an animal if there were no resistance to water flow from the skin due to the difference of salt concentration between the body and ocean water. 2.1.3. Give examples of ways living things have to overcome resistance in some of their functions. Here, many answers are possible. Terrestrial animals overcome resistance of terrain and air in order to move around. Aquatic animals, including microbes, overcome water resistance to move in the aquatic environment. Chewing animals overcome mechanical resistance of food when they chew the food into small pieces before swallowing. Overheated plants and animals overcome thermal resistances when they cool. Plants must overcome resistance of the soil for their roots to grow, and they must overcome chemical resistances to absorb water and nutrients from the surrounding soil. Microbes must overcome resistances imposed by the immune systems of their victims in order to infect their hosts. Friction resistance in the joints must be minimized and overcome in order to move the limbs. Electrical resistances of the heart, muscles, and nerves must be overcome for proper operations Courtship requires a certain resistance to be overcome before mating can be consummated. Even learning has a certain amount of resistance to overcome before it happens. Any of these and more can be named by the students. 2.1.4. Give examples of ways living things have to reduce resistance in some of their functions. Resistance to heat transfer can be reduced by increased convection. Resistance to flow, or movement through a fluid medium can be reduced by aerodynamic shaping. Resistance to chemical reactions can be reduced with enzymes. Resistance to electrical current flow can be reduced by making current paths shorter and conduits larger in diameter. Resistance to learning can be reduced by providing a proper learning environment. There are many examples of these and others in nature that can be used as answers to this question. 2.1.5. Give specific examples of the appearance of resistance in an ecological community.

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There may not be many students who will voluntarily answer this question, because it may require a different interest than most who take this course. However, ecological communities can be at many different scales, so a great many answers are possible. Resistance is defined as the ratio of effort variable to flow variable. Any specific variables are allowable as long as they are consistent and conform to the geral definitions of effort and flow variables. In an ecological community of any scale, the implication is that the resistance involves something passing among different entities. Ecological communities of microbes might involve the passage of different biochemicals from one microbe to another. These may be used to signal the need for certain responses, such as in group signaling. Resistance to such a flow would be found in the intermicrobial fluid and the cellular membrane. This would require a certain concentration difference before significant amounts of biochemical messengers reached their targets. It can be said that the organs in a body are an ecological community. Hormones pass from one organ to another, just as the chemical messengers pass between microbes. Again, there is resistance to this chemical flow. There is also heat transfer from hotter to cooler organs. There is resistance involved here as well. In a macroecological community there are many types of resistances. Dense growth of plants resists fast movement of animals; Plant canopies present resistance to the passage of light to undergrowth; there is intergenerational resistance to learning of necessary cultural knowledge; feeding of one species of another involves resistance as well if the prey resists predation. There are many examples that can be cited. 2.1.6. Describe the meaning of capacity. Give examples of the appearances of capacity in living things. Capacity is the ability to store flow variable, whatever it may be. Capacity allows excess flow to be stored for later use during a deficit. Capacity in living things is given, for example, as the storage of glucose, creatine phosphate, or ATP in living cells, water in specialized storage structures of desert plants and animals, excess numbers of offspring in a population, sperm in males, or heat in the oceans (OK, so the ocean isn’t exactly a living thing), and many others. Students can use their imaginations to come up with good answers to this question. 2.1.7. Give examples where capacities in biological systems should be minimized. Give examples where it should be maximized. Because capacity involves storage, minimum or maximum capacity depends on the survival advantage conferred by such storage. Capacity usually cannot be avoided as long as there is flow variable. Thus, it is present at some level almost everywhere. Minimum capacity would be found where significant flow variable storage would be detrimental, as in the storage of fat-soluble vitamins, or retention of excess fluids in

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congestive heart failure. More often, however, storage capacity helps to overcome fluctuations in the availability of necessary factors in the environment. Internal storage of water in desert plants and animals helps to overcome uncertain availability of water in the environment. Similarly heat capacity helps arctic and desert animals overcome environmental temperature fluctuations. Storage of food energy as fat is used to overcome uneven presentation of food. Ocean storage of heat helps to maintain a temperate environment on Earth conducive to life. 2.1.8. Describe the effects of inertia on living things. Give examples of inertia. The presence of inertia means that movement of the flow variable doesn’t start quickly and without a little extra effort. Likewise, stopping the flow variable takes effort as well. Inertia is most readily seen in physical movements, such as in walking and running, moving the arms, or in contraction of the heart. Many other examples can be given. 2.1.9. Why is inertia important in biological systems? What effect does inertia have on the amount of energy needed by a biological system? Inertia is important because it slows the ability to make rapid changes. Predators are often physically larger than their prey. Thus, they have greater amounts of inertia. Prey can sometimes outmaneuver their predators because they can change directions faster. Inertia also causes overshooting of an action or reaction, and can sometimes lead to instability because of this. The presence of inertia requires higher energy expenditures than if there were no inertia. One consequence of this is that the predator may decide not to pursue a certain prey animal because the energy cost might exceed the energy available. 2.1.10. Why are absolute values of physical quantities nearly (if not absolutely) impossible to make? Nearly all of the physical measurements made depend on the senses. If we can’t sense the presence of something then it doesn’t exist for us. The reason that we can sense electrical and magnetic fields is that we transform them into things we can sense, like the visible movement of a needle on a dial or the lighting of a light-emitting diode. As long as these measurements depend on human senses, they are fundamentally relative. 2.1.11. Add to the list of Applications and Predictions. The answer to this question will be highly individual. Be sure that the answers make sense and that they don’t duplicate applications and predictions already in the text. If done correctly, this question can spur students to consider the implications of what they have read.

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2.2.1. Describe the number of cells in the human body in terms of a balance. The number of cells in the body is the number of cells stored. Thus the balance becomes: Number of cells gained from the environment – Number of cells lost from the body + the Number of cells generated = Number of cells in the body The absolute form for the balance is appropriate here because we are interested in totals, not just changes. The balance must either start at the first embryonic cell and accumulate cells from that point on, or start at some known number of cells and accumulate from there. The first term in the balance, (Number of cells gained from the environment), would normally be zero except for situations like organ transplants or blood transfusions. The second term, (Number of cells lost from the body), is normally not zero, because cells are continually being sloughed off the skin or intestinal lining. The third term, (Number of cells generated), can include the birth of new cells and the death of old cells, and so may be either positive or negative. 2.2.2. If the concentration of cells in a bioreactor is increased, how would this affect an oxygen balance written for the bioreactor? How would it affect a heat balance? Cells in a bioreactor use oxygen (assuming they are aerobic cells) and produce heat. If the concentration of cells increases, the rate of oxygen used term (as a negative rate of oxygen generated term) in an oxygen balance increases. In order to keep the cells functioning correctly aerobically, the rate of oxygen in term must also increase (strictly speaking, it’s the difference between rate of oxygen in and rate of oxygen out that must increase). Likewise, the rate of heat generated term would also increase. If there were no change in bioreactor temperature, then the rate of heat loss term would also have to increase. 2.2.3. If resistance, capacity, and inertia of the circulatory system are known, what additional information must be obtained in order to determine blood pressure? Blood pressure is determined from resistance times flow rate, volume divided by capacity, and rate of change of flow rate times inertia. What is missing, then, is blood volume, flow rate, and acceleration. 2.2.4. Describe an experiment to measure the rate of a chemical into a cell, given that the rate cannot be measured directly. What assumptions must be made?

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The simplest of these is to monitor concentration of the chemical in the surrounding medium. Knowing the volume of the medium then gives the mass (or volume) of the chemical. In the medium is a known number of cells (obtained by counting cells in a sample of the mixture). As the concentration of chemical declines, the mass must have moved into the cells (or degraded chemically in solution). In this way, a mass balance can be used to infer rate of mass into the cells from the decline in mass storage. Assumptions made are that there is only one fate of the chemical being monitored (it goes into the cell), and that all cells take up the chemical at the same rate. Other experiments may be described. They can be checked for logic and practicality. 2.2.5. Under what conditions can the rate of energy storage in a microbe be zero if the organism is incapable of generating its own energy? If rate of energy into the microbe exactly equals rate of energy out, and rate of energy generation is zero, then the rate of energy storage must be zero. This could be a homeostatic condition. In the case where the microbe is incapable of energy generation, the microbe is likely dead. 2.2.6. Explain how the rate of oxygen perfusing a tissue is related to a balance on the capillaries. The source for oxygen into the tissues is the blood, and, specifically, capillary blood. Hence, rate of oxygen out of the capillaries equals rate of oxygen into the tissues. 2.2.7. Add to the list of Applications and Predictions. Let’s see what the students come up with. 2.3.1. What is the concentration of oxygen in air? How does concentration relate to density? The concentration of oxygen in the air depends on absolute temperature, pressure, and volume, as given by the ideal gas law. At standard temperature (0˚C) and pressure (1 atm), 1 mol of oxygen, with a mass of 32 g, occupies a space of 22.414 L. Thus, its density is 32g/22.414 L = 1.428 g/L . Concentration is equivalent to density, which also has units of g/L . 2.3.2. What is the vapor pressure of boiling alcohol? The vapor pressure of any boiling liquid is 1 atmosphere, 101 kN/m2. 2.3.3. Look up atmospheric pressure variation with altitude. At what height would human blood boil?

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The answer to this problem, at least for a first approximation, is found at the altitude that air pressure is equal to the vapor pressure of water at body temperature of 37˚C. From page 636, Johnson, A.T., 1999, Biological Process Engineering, John Wiley and Sons, New York, the saturated vapor pressure of water at 37˚C is 6266 N/m 2. From Wikipedia, a formula for atmospheric pressure with altitude is: P = Pb·exp﴾-g0 · M · (h-hb)/ R·Tb﴿ where Pb = 22632 N/m2 g0 = 9.80665 m/s2 M = 28.9644 g/mol h = altitude where blood boils, m hb = 11000 m R = 8314.32 Nm/mol K Tb = 216.65 K Solving for h gives an altitude of 19,144 m. This is almost twice as high as Mt. Everest. The actual value of the altitude at which blood boils will be higher than this for several reasons. First, blood is not pure water. There are solutes in solution and particles in suspension. The solutes, especially, reduce the vapor pressure of water in the blood. Reduced vapor pressure would correspond to higher altitude. Second, tissues surrounding the blood vessels exert a pressure on the vessels similar in effect to an elastic bandage. The difference between blood pressure and atmospheric pressure would be ameliorated somewhat by tissue elasticity. Third is the complication due to blood pressure. Blood pressure may tend to burst through the surrounding tissue and expose escaping blood to reduced atmospheric pressure. However, the 19000+ m altitude is a first approximation. 2.3.4. Classify the type of solid represented by: cell membrane bone tendon muscle skin The cell membrane is both distensible and composed of two double layers of lipids and proteins. It acts as if it were a composite polymer. Bone is crystalline solid. Tendon is polymer.

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Muscle is a composite material made of actinomycin (protein) fibers. Proteins themselves have polymer properties. Skin is even more complex than the other tissues. Again, it is a composite, with some polymer properties. 2.3.5. Phase change in a biological material does not usually occur at one specific temperature, but, rather, occurs over a range of temperatures. What do you think is the explanation for this? Phase changes are dependent on material properties. Biological materials are often mixtures, suspensions, and solutions. When a phase change begins, it doesn’t extend over the entire material at once. There may be a front demarking the boundary between one phase and another. The material becomes even more inhomogeneous due to the phase change: a solute may be left behind as the solvent changes phase, for instance. This solute concentration makes it even more difficult for the phase change to proceed. The only way it can proceed is to add or subtract energy, depending on the particular phase change. This is indicated by a temperature change. 2.3.7 Describe a gas plasma and state where gas plasmas are important in biological engineering. A gas plasma is a super-energetic fluid state full of charged particles. Gas plasmas can be very useful for sterilization of food and medical instruments. The gas plasma is very effective and leaves no residue. 2.3.6. Add to the list of Applications and Predictions. Let’s see what the students come up with. 2.4.1. What distinguishes between a path function and a function not dependent on path? Why can the value of a path function not be totally determined from its values at the start and finish? The value of a path function depends on the way one arrived at its current state. Thus, the amount of work, for example, required to compress a certain amount of material depends on whether the pressure-volume (capacity) relationship of the material is linear or nonlinear. The value of a function not dependent on path (a state function) does not depend on the particular way the present state was arrived at. The value of a state function is totally determined by its present state. Thus, a difference in state function at two different states can be obtained by finding the difference between the function values at the beginning an end of a process. Contrarily, the same means cannot be used to find the value of a difference of path function. For the path function, all states in between the beginning and end must be known.

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2.4.2. Give the difference between positive and negative work. What happens to potential energy during each of these types of work? Work is positive when the force and direction of movement are aligned and in the same direction, as in climbing up stairs. Potential energy in all likelihood increase with positive work because force is usually vertical. At least the reaction force against the foot is vertical and upwardly directed. Some friction forces are horizontal during horizontal walking, and this is positive work that doesn’t result in more potential energy. Negative work results when the force and direction of movement are aligned, but in opposite directions. Potential energy likely decreases during negative work, An example is walking down stairs, where the reaction force is the same as walking up stairs, but the motion is downward. The decrease in potential energy motivates the movement down the stairs, and requires the expenditure of energy to counteract the tendency to accelerate down the stairs. Just as with positive work, potential energy may not change during negative work. 2.4.3. Diagram the process of converting chemical potential energy in the form of food into mechanical energy in the form of running. The diagram could be something like this: Food ↓ Eat ↓ Digest (Catabolism) ↓ Distribute ↓ Form ATP (Anabolism) ↓ Muscle Movement ↓ Run 2.4.4. Does a growing plant perform mechanical work as it lengthens? Why or why not? Plants grow from the tips of their shoots. So, they do not do much mechanical work as they lengthen. The raw material that forms their structure is large carbon dioxide and water. The carbon dioxide comes from the atmosphere surrounding the leaves, meaning that the mass of carbon is not significantly raised or lowered. No significant work there. The water often originates in the ground, and must be raised to the leaf level an beyond. This process requires work.

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2.4.5. Diagram the relationship among chemical energy in food, physiological work, and mechanical work. The diagram could look something like this: Chemical energy in food → waste and heat ↓ Physiological work → heat ↓ Mechanical (Physical) work 2.4.6. What do we mean by efficiency? How would we determine the energy efficiency of a clam? Efficiency is the ratio of output energy to input energy. Both output and input must be defined. We need to know what we should be measuring. When determining energy efficiency of a clam, we would probably define the input as the energy equivalent of the food that it ingests. The output may be more difficult. We may define the output as the net locomotion of the clam. Clams aren’t known to move far, energy efficiency would zero or approximately zero. If the output is defined as the energy equivalent of opening and closing its shell, then we will get a nonzero energy efficiency. We would also need to decide if we were going to include basal life processes in the output or not. Efficiency figures for living things often depend on the definitions used. 2.4.7.

Add to the list of Applications and Predictions.

This question is intended to make the students think about biology from an engineering viewpoint. Make sure their reponses are reasonable, if not original. 2.5.1. There is a spontaneously occurring process (let’s say, for example, the oxidation of biological wastes). What does that say about the relative magnitudes of enthalpy and waste heat? Does the process result in work being done on the environment or by the environment? If the process proceeds spontaneously, then Gibb’s free energy is negative, and the environment does work on the process (energy for the process to proceed comes from the environment). That means that waste heat is larger than enthalpy. The process is exothermic. 2.5.2. Consider Figure 2.5.1. What constitutes waste, and how does it differ from heat and work?

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Waste isn’t always waste. It depends on the intended purpose of the process. For instance, heat generated by an internal combustion engine can be considered waste if all it does is escape to the atmosphere. If that “waste” heat is used to make the interior of the automobile more comfortable then the heat is no longer considered to be waste. Fecal matter is waste to an individual, but not to an ecosystem, where it is just another form of nutrition for other organisms. Waste in the physical sense differs from heat and work because there is no useful purpose being served by the waste. There is usefulness for heat and work in a physical sense. Taken in a large enough context, there is very little waste in the universe, just as waste output from one organism can be useful input for another in a large ecosystem. 2.5.3. Add to the list of Applications and Predictions. Students should think of original answers. Many of the Applications and Predictions in the book came originally from student answers. 2.6.1. If living things are ordered, and order requires energy, what living things are the most likely to survive the longest without additional energy? The obvious answer to this would be the most elementary entities. Some simple microbes have been known to last for years, centuries, and even millennia. Some viruses (are they living?) cannot be killed by normal means. Elementary life forms that form endospores to outlast severe environmental conditions use almost no energy in their quiescent states. 2.6.2. What types of biological processes require energy expenditure? How do these lead to maintenance of order? Any of the life processes that involve building structure or metabolism require large amounts of energy to proceed. Building structure, as in maintaining a cell membrane or forming a new cell wall for a plant cell that has just divided, increases order by becoming nonrandom. Metabolism allows all other cell processes to occur, and so keeps the cell from deteriorating to its elemental substrates. All biological processes fro the cellular level on up depend on these cellular processes. 2.6.3. Add to the list of Applications and Predictions. Once again, students can try to apply what they have learned.

2.7.1. Explain why human hands and feet feel cooler than the trunk of the body on a cold day.

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Human appendages have high surface-to-volume ratios. Thus, they tend to lose more heat (related to surface area) than to generate heat (related to volume). The consequence is that they feel cooler because they are cooler 2.7.2. How do animals manipulate their surface areas to increase or decrease heat exchange? Contrast the expected heat transfer responses by a dog and a lizard on a sunny, cold day. Animals change posture in order to conserve or lose heat. Curling their bodies exposes less surface area to the environment and conserves heat in cold weather. Stretching their bodies and limbs exposes more surface area to the environment and allows more heat loss in warm weather. On a cold, sunny day a cold-blooded lizard will expose as much area as possible to the sun, thus promoting solar warming. Because the air is cold, the lizard will flatten itself against the ground in order to minimize heat loss surface area exposed to the cold air. Once the lizard’s muscles have warmed sufficiently, it may move around enough to generate heat to sustain its body temperature in a comfortable range. A dog, on the other hand acts differently. Because it is covered in fur and generates more heat than does the lizard, the dog may actually overheat on a sunny day. The fur insulates the dog’s skin from losing too much heat to the cold air. If it is cold, the dog’s fur will stand on end, increasing the amount of insulation afforded by the fur. The dog would not be immobilized as would be the lizard, but can actively engage in other muscular activities, also increasing heat generation. 2.7.3. How does circulating blood contribute to heat exchange with the environment? Blood is a good carrier of heat. Blood carries heat from warmer parts of the body to cooler parts, and contributes to temperature uniformity in the body. Similarly, blood carries heat from the interior of the body to the skin, where it heats the skin and allows greater heat loss to the environment. If heat maintenance, rather than heat loss, is warranted, less blood is sent to the skin. The skin cools, and less heat is lost. 2.7.4. Animals living in hot climates are usually leaner than animals living in cold climates. Considering heat exchange issues, would you expect microbes adapted to hot climates to be shaped differently from those adapted to cold climates? Microbial shape is not determined by heat transfer, as is the shape of larger animals. Microbes are so small that their temperatures would be indistinguishable from their surroundings. Thus, there would not be any expected difference in shape for microbes in hot or cold environments.

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2.7.5. How does circulating blood help to maintain the correct heat balance of the body? There are several answers to this. The most obvious answer involves the transfer of heat from one part of the body to another through the heat capacity of the blood. Heat generated in regions of high metabolic activity, such as the liver or the brain, can be removed by the blood and spread to other regions of the body. Removal of excess heat from the body is enhanced by directing the warm blood to the surfaces of the appendages, where there is enough surface area to lose heat by convection. Heat maintenance is achieved by directing the blood to flow in the interiors of the same appendages. The surface temperatures thus fall and conserve heat. The blood does several other things. First, it brings oxygen and glucose to tissues and stokes the metabolic fires. Without the blood bringing metabolic substrates to tissues and removing wastes, metabolism would slow or stop, and heat would not be generated. So, the blood acts indirectly to generate heat. Another thing the blood does is to supply water so that sweat can be produced when the body is overheated. Sweat production lowers the plasma concentration of the blood. So, the blood has an indirect effect on heat loss. 2.7.6. Add to the list of Applications and Predictions. This question is meant to induce the students to consider the implications of the material that has been covered. They should submit original answers. 2.8.1. Speculate on what would happen to body size if atmospheric oxygen percentage increased to 50%. Body size is determined, in part, by the ability by oxygen to diffuse useful distances in short times to maintain metabolism. Once oxygen can no longer diffuse sufficiently unassisted, other means are necessary to distribute oxygen to different parts of the body. Thus, blood circulation systems appear. These systems are efficient oxygen distributors, and allow body size to escape the limitation that would otherwise be imposed by oxygen diffusion. Increasing oxygen percentage in the atmosphere to 50% would allow small animals and plants to be bigger than the two-cell thickness that is true with oxygen being 20% of the atmosphere. But, there would hardly be any effect on larger plants and animals because circulatory systems are so effective. With 50% oxygen in the atmosphere, other changes might be more apparent. Different metabolic pathways would be necessary and different means used to limit oxygen availability to tissues to calm the toxic nature of hyperoxia.

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2.8.2. Would you expect a faster diffusion rate to the environment from a larger plant or a smaller plant? Diffusion rate depends directly on surface area, so larger plants and animals with more extensive surfaces would probably diffuse faster to the environment. Diffusion per unit area, however, would not change, or may even decrease. Diffusion does not depend exclusively on surface area, but depends also on concentration and diffusion coefficients. Larger plants and animals may manipulate either of these to change diffusion rate. Keep in mind, too, that diffusion to the environment is often insignificant when compared to convection. 2.8.3. Estimate the relative magnitudes of resistance to diffusion in a plant leaf, stem, and roots . Just considering the functions of each of these plant parts, it is clear that resistance to diffusion in the stem must be much less than diffusion in the leaves and roots.. Diffusion in the leaf must be high to admit carbon dioxide and oxygen. Diffusion in the root must be high to absorb water and minerals. The actual values of resistance depend on the rates of uptake of each of these substances and the concentration or pressure differences that exist inside and immediately outside the plant. 2.8.4. State the ways to enhance material movement from the environment into an organism. Material movement depends on diffusion or convection. Diffusion can be upgraded to convection. Both diffusion and convection depend on surface area and concentration differences. Each of these can be manipulated: surface area can be increased, or concentration difference can be changed either physically (say with a circulatory system) or chemically (by changing pH of the environment, for example). 2.8.5. Give a physical justification for circulating fluid in a body. There are many possible justifications that can be given. One assumes the presence of a flowing fluid that does not circulate. Instead, it begins at one point in the body and terminates somewhere else. After a short time, a great deal of material and energy would be expended to continually produce fluid. Fluid would accumulate at the other end. To solve these two problems, the fluid could be allowed to return to its starting point, or, in other words, a circulating system would be formed. We could also mention efficiency: substances carried by the fluid that are not completely used can be made available for use in a recirculating system Or, a fluid circulation allows the transport of raw materials in one direction and waste products in the other.

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2.8.6. Given the principles stated by West et al, compare circulatory systems of small and large animals. From the first principle, we would expect that small animals would have a smaller number of capillaries than would a large animal, because the space to be filled in a large animal is greater. From the second principle, we would expect no difference in the sizes of capillaries in the two different sized animals. Capillary size is determined mostly by diffusion of oxygen, carbon dioxide, and nutrients. From the third principle, we would expect that energy minimization would lead to fewer intermediate size vessels in smaller animals than in larger. 2.8.7. Describe osmosis. If water is the only molecule that can pass freely from one side of the membrane to the other, how is equilibrium achieved? Osmosis is the process of water movement through a membrane with channels large enough for water to pass freely form one side to the other, but small enough that other solutes may not pass freely (some solutes may go from one side to the other, but not easily). The concentration of water is diminished as the concentration of the solute increases. Thus, water moves by diffusion from the side with higher concentration (and lower solute concentration) to the side with lower water concentration (and thus lower solute concentration). Water continues moving through the membrane until physical (static) fluid pressure pushes water back through the membrane at exactly the same rate that diffusion pushes it forward through the membrane. 2.8.8. What types of materials are expected to move easily (without large energy expenditure) through the cell membrane? Materials with small molecules can pass freely through the small pores of the membrane. Water is one of these, as are some very small organic molecules like urea. 2.8.9. Add to the list of Applications and Predictions. Once again students are asked to wrack their brains. 2.9.1. If viscosity of water were higher, what would happen to the required size and strength of the heart? Higher viscosity of water would translate into higher blood viscosity, thus making it harder to propel the blood through the vasculature. The heart muscle would have to strengthen in order to do this. Stronger muscles require more fibers, and this would make the heart larger. A larger heart muscle has more inertia and is harder to move. Thus, its energy efficiency would suffer. A similar situation exists in congestive heart failure.

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2.9.2. Does laminar or turbulent flow occur at low fluid velocities? If it was desired to mix a hormone in blood so that it would have a reasonably constant concentration, would laminar or turbulent flow be required? Lower velocities proceed in laminar flow. Turbulent flow occurs at higher velocities. Turbulence accompanies a good deal of mixing as the fluid twists and curls. This results in homogenization of concentrations in the fluid. 2.9.3. Given that laminar flow occurs at low Reynolds numbers, if it was desired to maintain laminar flow in a channel, suggest means to promote laminar flow.

This is not such an easy question to answer because the answer depends on the conditions. Decreasing diameter of the channel decreases its Reynolds number, and should promote laminar flow. However, increasing channel diameter decreases flow rate, leading to lower Reynolds number and more laminar flow. But it can’t be true both ways. A lot depends on the source of the flow. If it is a pressure source, then flow will be determined by resistance, and that is inversely related to the fourth power of channel diameter (d-4). But volume flow rate is determined by pressure divided by resistance. So volume flow rate is proportional to d4. Fluid velocity is inversely proportional to cross-sectional area, related to d2. So, decreasing diameter increases resistance, decreases flow, and decreases Reynolds number proportional to d3. This promotes laminar flow. If the source of the flow is closer to an ideal flow source, resistance has no effect on flow, and decreasing channel diameter promotes laminar flow by decreasing Reynolds number proportional to d, not d3. 2.9.4. Describe what it would be like for us to move around if we had the same Reynolds number as a microbe. Oh my! It would be tough to move. We couldn’t walk or run as we do now because the surrounding fluid would oppose our motion so much that our feet would slip on the floor. We couldn’t swim, because the fluid would be so thick that we couldn’t push it aside. We would probably have to develop a twisting motion with our legs and corkscrew our way through the surrounding soup. 2.9.5. A bison faces into the wind of a storm. On what part of the body would you expect the fluid pressure to be the highest? Why? The part of the bison directly facing the wind will have the highest pressure because the wind velocity drops to zero at that point. All the kinetic energy represented by the flowing air transforms into potential energy, as represented by air pressure. Other spots on the bison have nonzero air velocities, and so have lower air pressures. There are probably places where the air must accelerate around the bison’s form. These spots have air pressures lower than atmospheric.

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2.9.6. Describe the engineering trade-offs involved in the design of a natural heart. Compare these with the design trade-offs for an artificial heart. A natural heart and an artificial heart have nearly the same general design trade-offs. Both must be capable of propelling the blood to meet the body’s demands. Both must be as efficient as possible, both need to use available energy sources. Both need to be able to adjust pumping volume as the demand changes. Both need to be able to fit in the space available, and both need to be reliable. There are some limitations on the natural heart that are not pertinent to the artificial heart. The natural heart must use variations of hearts evolutionarily preceding them. That is, they can’t abandon intermittent pumping. They also must use muscle tissues to perform the work, and they must use ATP as their energy source. Also important: they must be self-contained and fit entirely within the chest wall. The artificial heart has many of the same limits. Just as with the natural heart, the artificial heart must not cause blood to clot when it resides in the heart. And they both need to provide sufficient pressure to overcome resistances of the vasculature. The trade-offs for natural hearts involve the limitations described above. A heart that can deliver higher pressure, for instance, has thicker muscle tissue that has ore mass and is harder to move. A heart that uses less energy may not be powerful enough to propel sufficient blood when demand is greatest. A heart with but two chambers mixes oxygenated with spent blood, and doesn’t serve the body well. An artificial heart that is powerful enough to pump blood to meet the highest demands of the body may not be able to fit within the chest, nor will it be able to have a compact energy source. A heart that is able to adjust to demand is more complicated than a simple heart, and thus less reliable. A heart external to the body has longer connecting tubes, and is more likely to cause blood clots. There are many other tradeoffs that can be mentioned by students. 2.9.7. Why are smaller blood vessels short? short?

Why are larger blood vessels

Smaller vessels are short because they are efficient distributors of oxygen, glucose, and collectors of carbon dioxide. Longer vessels would not be any more effective than short ones because blood in the short vessels has little more supply of oxygen, etc., to yield to the tissues. Many short vessels in parallel are more efficient suppliers. The parallism takes care of the resistance problem with small vessels. Larger vessels are no longer than they need to be because they represent impedance without directly contributing to the primary purpose of the circulatory system. They do not contribute significant oxygen delivery to the tissues. For this reason, longe vessels need to be short to reduce resistance and improve system efficiency.

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2.9.8. If internal hydrostatic pressure can substitute for shell rigidity in a softshell crab, why does the shell need to harden? Good question! Why, indeed? The answer is that establishing and maintaining hydrostatic pressure takes a good deal of energy. Once the shell hardens, that energy is not required. The advantages of the shell are not free, however. As the crab grows it must invest energy in forming additional shells. 2.9.9. Of what importance is the Law of Laplace to biological organisms? How does the Law of Laplace explain shapes common in biology? The Law of Laplace is the outcome of a force balance on a shell, balancing shell tensile forces with internal or external pressures. The Law of Laplace explains why longer radii of curvature require thicker and stiffer materials to maintain shape. Most biological shapes are rounded. There are very few sharp projections in biology (and most of these have to do with defense or killing – a porcupine’s spines or and eagle’s talons, for instance). A lot of roundness has advantages of aerodynamics and stingy material usage, but the Law of Laplace also points out that maintenance of shape is easiest when the shape is round. 2.9.10. If moving bacteria had the same Reynolds Numbers as fish, how fast would they swim? Equivalent diameters of microbes are of the order of 10×10-6m. Fish have diameters on the order of 10-1m. Hence, in order to have the same Reynold’s number as fish, microbes would have to swim 100,000 times as fast as fish. A leisurely-swimming fish might swim at a rate of 0.03 m/sec . That would mean that a microbe would have to swim at 3000 m/sec to have an equivalent Reynold’s number. That’s about twice the speed of sound in water. 2.9.11. How would you outsmart the beaver? Let’s see what the students come up with. There might be many solutions. The problem is that beavers sense flowing water. Solutions can range from the physical (stop, or slow flowing water, and the Clemson pond leveler does), chemical (add a drug to the beaver’s food so that it cannot sense flowing water), or biological (train the beaver to ignore the water or distract it). 2.9.12. Give other examples of places where a circulatory system can help deliver something uniformly to various locations. Here is a real challenge to the students’ imaginations. Answers can relate to: Mass transit to carry people from one place to another Ventilation systems to deliver heat or cooling

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Electrical distribution systems 2.9.13. Add to the list of Applications and Predictions. The students are asked to be creative. 2.10.1 Will a car traveling straight use more, less, or the same amount of fuel as the same car going the same speed along a winding track? The car traveling a winding path will use more fuel because it is accelerating every time it changes direction. Besides, the winding path is likely to be longer between any two points. Thus, fuel use would be greater just for this reason. 2.10.2 Isometric muscular exercise results in no visible movement. What is the mechanical efficiency of this exercise? What happens to the energy used? Because there is no movement, can we assume that there is no force generated by the muscles? The mechanical efficiency of isometric exercise is zero because there is no physical work done. There is physiological work done, however. All the energy developed in the muscles ends up as heat. Although there is no movement, there is, of course, force generated. 2.10.3 Is Newton’s second law theoretical or empirical? What is the difference? The difference between a theoretical and empirical law is the degree of applicability and acceptability of its results. Both start out as empirical observations generalized to make them more universal. Eventually, if they are found to be acceptable, they are accepted as fundamental. They are then considered to be theoretical. Theoretical laws do not usually account for small perturbations or exceptions. They are considered to be immutable and basic. Empirical “laws” never get that far. They include exceptions and perturbations. And they are of limited use, both in the range of usefulness and in terms of time. They are usually more complicated in form than the general theoretical laws are. Newton’s second law, F = ma, is considered to be theoretical. 2.10.4 List advantages and disadvantages of living in a world without friction. Make your list from the standpoint of a human, a worm, and a fungus. From the standpoint of a human, living without friction would mean a great deal of difficulty moving about. In order to move, one would have to do something like blow air in the direction opposite from the desired direction. It would be hard to pick up an object, and to hold it without putting a hand under it. Without friction, the heart could be smaller without having to overcome vascular resistance. Our sports would be

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much different, and so, too, would be our tools. Students can list a lot of different advantages and disadvantages. A worm would have similar advantages and disadvantages. Less energy would be spent moving through the soil, but a different means of movement would have to be employed. Moving food through the gut would be different, and there would be less friction in the circulatory system. A fungus is nearly immobile, and anchored, so would not have the advantages and disadvantages of frictionless locomotion. There would be no resistance to movement of fluids inside the fungus, and movement of gases would be similar. It can be said that living things have developed to use friction to their advantage, but have also had to develop ways to overcome friction. Without friction, a lot of changes would be necessary, but there is no doubt that means would evolve to adjust to the different conditions. 2.10.5 Speculate on the relative magnitudes of the reaction forces for a small bird and a large bird. What effects do these birds have on the surrounding air? Let’s consider reaction forces for birds in flight. In order to accelerate the bird with the larger mass, a greater reaction force is necessary. Once up to cruising speed, the larger bird would probably have more air resistance, and so needs a greater reaction force from the air. In order to generate these reaction forces, the birds must accelerate the surrounding air backwards. 2.10.6 Living organisms have unique ways to deal with large mechanical stresses. List some of them. Starting with single-celled organisms, there is usually an actin cytoskeleton inside the cell to help maintain structural integrity. The shapes of single cells also help to resist large mechanical stresses (Law of Laplace). Shape is also important for larger organisms, such as plants. Plants form cell walls composed of cellulose and lignin (in dead cells) for stiffness. Hydrostatic pressures are used in some organisms such as the soft-shelled crab. Many organisms bend and assume shapes that minimize mechical stresses, such as trees in prevailing winds. Movable organisms may just move out from under mechanical stress. 2.10.7 Why is springiness important in biology? consequences if biological materials were not elastic?

What would be the

Springiness helps to store energy that would otherwise be lost. For instance, springiness in the tendons of the legs helps to transfer energy form one step to the next, springiness in the bent backs of galloping horses helps to do the same thing, and

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springiness in the arteries helps to store energy during systole that propels the blood during diastole. Without springiness, organisms would be much less efficient. More energy would have to be expended to perform the same operations, more heat would be generated and would have to be removed, and intermittent operations, such as pumping of the blood, would need to be performed differently to assure a constant flow. Plants would break readily in strong wind. The consequences could be profound. 2.10.8 Why do you suppose most biological materials have the shape of the force-deformation curve given in Figure 2.10.2? There are many possible reasons that can be given. Most biological materials are nonlinear, and that is one reason, although that begs the question. There is advantage to the S-shaped curve because: 1. the maximum sensitivity lies in the center of the curve 2. the curve exhibits soft limits 3. catastrophic breakages are less likely than with a straight line 4. etc 2.10.9 If you were to design a device to insert a needle automatically into the liver, what mechanical considerations would you have to account for? A listing of some of these is: 1. stiffness of the liver 2. stiffness of the surrounding tissue 3. angle of insertion 4. strength of the needle 5. size, especially diameter, of the needle 6. size of the liver, and how far the needle is to be inserted 7. locations of major blood vessels 8. suction of fluids 9. location of the liver 10. expected wear on the needle 2.10.10Add to the list of Applications and Predictions.

This is for the students to use their imaginations. 2.11.1 Give instances where ionic charges can help or hinder an engineering design. Students can use their imaginations to answer this question. Some students have answered that ionic charges in a timing circuit can change currents and thus change

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timing of the circuit. Ionic charges that repel other ions may hinder the proper working of certain measuring devices. If the engineering design is akin to electrophoresis then ionic charges are necessary for the circuit to work. 2.11.2 How is gel electrophoresis used to identify genetic matches or mismatches? First, a restriction enzyme is used to break apart DNA strands into short pieces. These can differ by mass and charge from one DNA sample to another. The short pieces are then placed in a gel to impede their movement when placed in an electric field. After a certain length of time in the field, various pieces will have moved certain distances. If a fluorescent marker has been attached to the short pieces, they will be visible. They can then be compared to a known standard DNA sample that has previously undergone electrophoresis, The samples are compared side-by-side to see if the bands of fluorescence are in the same positions and have the same intensities. 2.11.3 How are electrophoresis and dielectrophoresis different? Electrophoresis is used to separate protein or DNA snippets by mass and charge when the snippets are suspended in a gel matrix. Electrophoresis forms a composite of many such snippets at ant one time. Dielectrophoresis usually works at a larger scale, separating single cells as they locate at different locations in an electric field. With dielectrophoresis the intention is to separate individual components rather than to identify the composite of all the components taken together. 2.11.4 List effects of electrical current flow in a living body. What kinds of charged particles carry the flow? Electrical current has two main effects in the body. The first is stimulation of nerves and muscles. Stimulation of nerves can cause tingling and pain. Stimulation of muscles causes contraction. This is especially important if the muscle being stimulated is the myocardium because then the heart can no longer pump blood efficiently. If electrical current density is high enough, then it can cause ohmic heating. Burning of tissue can result. Electrical current in the body is carried largely by ions. There may be some naked electrons carrying current, but, for the most part, they ionize atoms and molecules. 2.11.5 If electrical currents are much less dangerous at high frequencies, why is electrical power transmitted at 50 or 60 cps?

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These frequencies were determined in the days before it was known that they were particularly dangerous. They continue to be used because of political and historical reasons. In the early days of electrical power transmission there was a controversy and heated disagreement between Thomas Edison, who advocated transmission of DC electrical power and George Westinghouse, who championed AC power. AC finally was chosen as the standard because it was easier than DC to convert from one voltage to another with transformers. This is important because the same amount of power can be transmitted at high voltage and low current as with high current and low voltage. Low current means less resistive power loss in transmission. There are, however, effects of capacitance and inductance that are not present with DC power transmission. Before AC power was chosen as the standard, there was a death sentence to be carried out by electric chair (the first). Edison wanted the electric chair to be powered with AC; Westinghouse wanted DC to be used. Each wanted his rival to be seen backing the most dangerous type of electric power. AC was used, and despite that, was chosen as the standard because of its other advantages. The prisoner was killed in the chair anyway. Once a standard such as 50-60 cps AC is established, it cannot be undone without much turmoil. 2.11.6 At what intensity does electrical current become lethal? Justify your answer. There is no exact answer to this. Factors that it depends on include the path the current takes through the body, resistances in the pathway, and individual sensitivity to nerve and muscle stimulation. A few microamps may be lethal if introduced through a catheter under the skin. On the other hand, it may take several amps to kill the person. Students have a large range of answers that they can give, but they must submit cogent explanations for their answers. 2.11.7 What things limit the use of focused electrical power for removal of unwanted bodily tissue? This is a case of inputs and outputs. To get sufficient power in, the source must first be powerful enough. Then, the power must be focused correctly so that it doesn’t diffuse. On the output side, electrical power that cooks tissue can be dissipated if the surrounding tissue has a too great thermal conductance, or if the blood supply carries heat away too fast. Other limitations are the size of the target tissue (too large, and a large amount of power is required; too small, and the power may not be able to be focused well enough), the sensitivity of the surrounding tissue (loss of neural tissue in the brain can

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cause disability), and the type of tissue (bone tissue is harder to kill than is soft tissue). 2.11.8 Propose a means to deliver sufficient electrical power to a small volume in the pancreas to kill cancer cells. There are several ways that can be proposed, and the students proposing them must have reasonable explanations. Just proposing an impossible or impractical solution is not sufficient. One possibility would be to focus electrical energy from outside the body. However, some thought must be given to the focusing mechanism, because the pancreas is very sensitive tissue that, if destroyed, can be very bad. Another possibility might be to implant electrodes and deliver current that way. That is an invasive approach. Some student may propose a means to generate electrical current in the pancreas or surrounding tissue. The proposal has to be realizable. 2.11.9 How does electroporation work? Electroporation describes a process where an electrical current passed through the cell membrane disrupts the membrane, allowing hydrophilic (and large) molecules to pass through the phospholipid bilayer. This is used as one means to introduce foreign genetic material into cells. Soon after the current ceases the membrane spontaneously reassembles. 2.11.10 Add to the list of Applications and Predictions. Students can think of some new things. 2.12.1 If the viscosity of blood decreases with temperature, would you expect the work of the heart to increase or decrease as environmental temperature increased? Be sure to examine thoroughly the changes that occur at high temperatures. This is a misleading question, for a reason. Yes, blood would be slightly thinner as temperature increases. So, one might expect the work of the heart to decrease at higher environmental temperatures. However, the work of the heart actually increases because it must pump more blood just to facilitate bodily heat loss. Don’t let one fact mislead you! 2.12.2 Would flagellated microbes find it easier or harder to move within cooler liquids? Why?

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Flagellated microbes would find it harder to move through cooler water for two reasons: 1. the viscosity of the water is higher, and 2. metabolic rate at lower temperature is lower, so less useful energy is generated. Biological engineers should not forget about the second reason. 2.12.3 What kinds of stresses on aquatic life forms are changed as the water around them is heated? Are the changes greater or less? One of the most profound changes is the reduction in the solubility of oxygen at higher temperatures. Thus, some aquatic life forms can suffocate at higher temperatures. If they don’t suffocate, the lack of oxygen could lead to a build-up of metabolic wastes (mainly blood lactate due to anaerobic glucose metabolism). Heating the water affects body heat loss, and can cause overheating. This results in damage to essential body biochemicals, such as enzymes. They may die. Changes in physical properties of the water will have minimal effect.

2.12.4 Your neighbor calls to warn you that the temperature during the night is supposed to drop to -1°C. He urges you to pick the remaining apples from your apple tree before they freeze. You say that you are not concerned that they will freeze. Why do you say that? You realize that biological materials are not pure water, but have many different kinds of solutes and suspended particles in them. As the concentration of solutes increase, the freezing point of the solution decreases. Even when they do begin freezing, solutions left unfrozen become more concentrated, lowering their freezing points even more. One of the problems with freezing of biological materials is that the solute concentration can become great enough to draw water from surrounding volumes. The unfrozen portion can become irreversibly dessicated. You are not worried about freezing at -1°C because you know that serious freezing will not occur until at least -3°C. 2.12.5 Distinguish between effects of low temperature and negative heat flow. Temperature is only a manifestation of the energy of particles in matter. If particle energies are low, the particles have low kinetic energies, and a thermometer measures low temperature. But, if the particle density is low, then there is not much opportunity for higher temperature matter to lose energy to the lower temperature matter.

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This situation can happen in the upper atmosphere, where the air is rarified, and the temperature can be low. Very little heat flow can take place because there is little contact between atmospheric particles and another piece of matter located there. This points out that temperature is an effort variable and heat is a flow variable. Although there must be a temperature difference for heat to flow, the mere presence of a temperature difference is not enough to cause heat to flow if there is no pathway for it to follow. 2.12.6 Add to the list of Applications and Predictions. Again, it is up to the students to see the implications of their readings.

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QUESTIONS Chapter 3 3.0.1

Distinguish among the different subdisciplines of chemistry.

General chemistry is the study of properties of elements and compounds and of formation of chemical compounds. Organic chemistry studies compounds of carbon, whether they occur in life or not. Biochemistry is the study of chemicals important for life. Physical chemistry is the study of the effects of the physical environment (temperature, pressure, humidity, etc) on different chemical compounds. There may be other subdivisions that students may wish to mention. There so protein chemistry, enzyme chemistry, and others. 3.0.2 a. b. c. d. e.

In which branch of chemistry would you expect to study the following: proteins arsenic ionic bonds osmosis properties of cell membranes

Proteins – biochemistry Arsenic – general chemistry Ionic bonds – general chemistry Osmosis – physical chemistry Properties of cell membranes – biochemistry, maybe 3.0.3 Physical, chemical, and biological components of the environment interact with living things. Give examples of the chemical environment of organisms. Examples may include, but are not in any way limited to: 1. dissolved oxygen in surrounding water 2. biochemicals in rivers 3. pollutants in the air 4. hormones in tissues 5. digestive enzymes in the stomach 6. toxic materials in tissue implants 7. antibiotics 8. fertilizers in the soil 9. carbon sources in bioreactors 10. pheromones in the air 11. etc 3.0.4

Why is the study of chemistry important for biological engineers?

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Much of what happens in biology is understood by studying the elements, compounds, and their properties. This is especially true for simpler organisms, where the presence or absence of critical biochemicals can have profound consequences. Chemistry is largely descriptive, with some overlay of quantification. So, knowing which chemical families are important, and differences among elements or compounds in these families, can lead to better prediction of consequences. Better prediction leads to better control. Incidentally, higher level organisms, being much more complex, behave in ways not as easily tied directly to specific chemicals. 3.0.5 Explain why the study of chemistry is necessary to understand the workings of biological systems. Many sources of behavior in biology are tied directly to chemicals and their effects. All, or nearly all of the energy sources for living things at least pass through some chemical storage step. Toxic chemicals can interfere with metabolism and kill or severely damage organisms. Control of organismal actions is through chemical actions. Indeed, the competition at the basis for natural selection comes down to attempting to control the most chemicals in the environment. The information legacy of life, the genetic code, is chemical in nature. And, there is the interactive chemistry among species in an ecological system that forms the basis for ecological relationships. There are so many aspects of biology that relate directly back to chemistry that one cannot understand biology without first understanding chemistry. 3.0.6 Someone has said that the study of biology is the same as the study of chemistry. Why is this statement both true and false? The basis for much of biology at a very elemental level is chemistry. Actions of single cells are governed by the presence or absence of certain biochemicals, elements, or ions. It is the combination of these chemical constituents, and their effects on one another that give cells their complex behaviors that we associate with life itself. This is why chemistry and life are nearly the same. On the other hand, higher level organisms have behaviors dependent on more than just the actions of single cells. Emergent behavior of higher level life cannot easily (at least) be explained only by chemistry. At least, we like to think of it tat way. 3.0.7 Describe in your own words differences among different branches of chemistry and how they relate to biology. This is up to the students to answer in their own ways. Make sure they don’t copy from the book.

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3.1.1 Discuss the advantages to knowledge of families of elements with similar features. Knowing how families of elements relate can be important to appreciation of metabolic roles that each plays, in which tissues they would be stored, relative toxicities of members, propensity to substitute, and means to form variations of compounds with somewhat similar but yet somewhat different properties. 3.1.2

Estimate the number of electrons in a wart hog.

This is an interesting question, no? We must start by estimating the composition of a wart hog. There are a number of ways to do this, but what we do here is to turn to the Box in Section 3.6.4, entitled “Microbial Stoichiometry”. There it says that aerobic microbes have a composition equivalent to a molecule of: C106H263O110N16P1 Wart hogs have, in addition, considerable amounts of sodium (Na+), potassium (K+), chloride (Cl-), calcium (Ca+), and bicarbonate (HCO3-) ions in their bodily fluids. A wart hog may have a slightly different composition, but the one for microbes is a start. The mass of this molecule is (106×12.01+263×1.01+110×16.00+16×14.01+1×30.97 ) = 3553.82 kg/kg-mol. This value was obtained by looking up the masses of each element and multiplying each mass by the number of atoms of that element in the molecule given above. From Table A1a, we find that a pig (swine) has a mass of 102 kg. The masses of wart hogs do not appear in the Table, and the mass of a wart hog is probably less than the 102 kg, but we’ll use that value anyway in our estimate. From these last two figures, we find that a wart hog contains 102 kg/ 3553.82 kg/kg-mol = 2.87×10-2 kg-mol of the molecule above. Each molecule has this many electrons: (106×6+ 263×1+110×8+16×7+1×15) = 1906 electrons/molecule This was obtained by looking up the number of electrons for each element and multiplying by the number of atoms of that element in each molecule. From the Box in Section 3.1, entitled “The Mole”, we find that there is an Avagadro’s number (6.0235×1026) of molecules in a kg-mol. There are thus (2.87×10-2 kg-mol/wart hog)×(6.0235×1026) = 1.7288×1025 molecules in a wart hog. Multiplying this number by 1906 electrons per molecule gives 3.4×1026 electrons in a wart hog.

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Remember that this is an estimate. Don’t accept too many significant figures in the answer. I rounded my answer to two significant figures. That still doesn’t completely express the uncertainty associated with the answer. 3.1.3 Will an atom of Barium (element number 56) combine most readily with Bismuth (Bi, no. 83), Polonium (Po, no. 84), Astatine (At, no. 85), or Radon (Rn, no. 86)? Barium, with 2 outer shell electrons, and forming ions with +2 charge, combines most readily with an element with 6 outer shell electrons forming ions with -2 charge. From the list of elements given, Polonium is the element of choice. Note that Radon forms no chemical compounds. 3.1.4

Is carbon an alkaline or acidic element? Why?

Carbon is smack in the middle of the Periodic Chart of Elements. It has an outer shell of 4 electrons, and can form ions with +4 charge as readily as -4 charge (and other combinations as well). It is neither alkaline nor acidic, or, better yet, it can be either. 3.1.5 What is the heaviest element with a clear function in living things? Does this mean that heavier elements are not found in living things? Iodine is that element (see Table 6.3.1). However, heavier elements can be substituted for lighter elements if the lighter ones are not as abundant as the heavier ones. 3.1.6

Add to the list of Applications and Predictions.

Require tha the students think of some original ideas. 3.2.1 Rank the following bonding types in terms of stability of bonds: covalent bonds hydrogen bonds ionic bonds metallic bonds Van der Waals bonds In order of stability (another way of saying strength), they are: 1. 2. 3. 4. 5.

ionic covalent metallic hydrogen Van der Waals

There may be some difference of opinion about metallic bond strength.

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3.2.2 Compare chemical ionic bonding to covalent bonding. Is there a clear distinction between the two? Ionic bonding involves the complete transfer of electrons from one atom to another. Covalent bonds are formed when both atoms share electrons. Ionic bonds are extreme forms of covalent bonds. 3.2.3 The element nitrogen forms combinations with many other elements. The charges on nitrogen range from –3 to +5, inclusive. Give examples of as many compounds as you can illustrating different charges on the nitrogen atom. The students have many choices of compounds. Among them are: 1. NO 2. NO2 3. HCN

(charge = +2) (charge = +4) (charge = +3)

3.2.4 What biological functions would you expect to be performed by compounds composed of elements with high electronegativity? Low electronegativity? This question needs some clarification. Compounds can be expected to be formed from elements with both high and low electronegativity at one time. However, we can interpret this question to mean compounds dominated by elements with high or low electronegativity. With that in mind, compounds with high electronegativity appear on the right of the periodic chart. These compounds are basic in nature (pH>7). We might expect these compounds to be used as biological weapons, for instance, or for counteracting highly acidic environments. Compounds dominated by low electronegativity elements are acidic (pH