an old book review.... Absolutely Small

Schrodinger's Quantum Cat










With the rising importance of technology related to quantum mechanics it becomes more and more important for laypeople to understand the elusive concepts behind this twentieth-century discovery. Digital cameras, CAT scans and spectroscopy of forensic science have each revolutionized their respective fields in ways that transform everyday life. If Professor Michael D Fayer’s goal is to make these technologies more understandable on a molecular level through logical explanations, he largely achieves this goal in his book Absolutely Small. He states, “The idea is to make quantum theory completely accessible to the nonscientist.” With diagrams, analogies and simple math he strives to make the subject accessible to the nonscientist. The only small problem with this claim is that his simple math and explanations seem to be geared toward a layperson at his university, Stanford, where nonscientists are likely aware of basic tenets of science.


He starts out with basic differences between fundamental principles of classical physics and quantum mechanics. Schrodinger’s cat, (superposition of state), size (observable with or without interference), waves, particles and the application of these concepts to the actual behavior of a photon/electron in various situations are all covered. He thoroughly describes the interferometer, diffraction grating, cathode ray tube, and other experimental results of the literature. Beyond these fundamentals, he applies all of this to trends of the periodic table, bonding behavior and how bonding behavior affects molecules of everyday life: carbon dioxide, trans fats, proteins, beer and water (to mention a few).

This book carries a repeating theme throughout: the fundamental building blocks of a concept are followed by a more detailed, comprehensive explanation. The first chapter is titled “Schrodinger’s Cat”. Anyone with an academic background in the physical sciences knows this is a common way to explain the concept of a superposition of state. Schrodinger’s cat is described as both dead and alive at the same time. It is 50% dead and 50% alive. Of course this is a ridiculous statement, except in a quantum mechanical context. In quantum mechanics, the superposition of states allows a photon or particle to exist in two states simultaneously before it is measured. It is the measurement itself that causes this superposition of states to collapse into one of the two possibilities. An excellent but imperfect analogy is extremely effective here to make this ridiculous concept a bit more accessible to a quantum mechanical virgin; Fayer compares it to a coin toss, a 50/50 choice between two possible choices. The difference here, as he points out, is that there are two distinct choices in the coin toss. As opposed to Schrodinger’s cat that is 50% alive and 50% dead at the same time, each side of the coin exists as a separate entity before the coin toss. This is just one of several successful analogies Fayer draws to help his reader’s relate with his subject matter.

The building block technique of explanation is used throughout the text to illustrate various complicated ideas: the particle in a box explanation of discreet energy levels of waves leads into a discussion of waves within three-dimensional molecules and absorption and reflection of color; a discussion of blackbody radiation precedes a discussion of the quantization of energy levels in a hydrogen atom. Since the principles that dictate the behavior of a subatomic particle or the “absolutely small” particle are so different from anything classical in nature, it is necessary to reveal the principles in a step-wise fashion. Toward this goal, Fayer is largely successful. If anything could make these explanations even clearer, it would be more reminders throughout the text that this behavior only applies to something “absolutely small” as Fayer titles his book- at the point at which a particle can be measured without interference it is no longer “absolutely small” and these concepts no longer apply.

Other effective real- life situations Fayer successfully draws into his book include the following: to describe wave interference he relates constructive/destructive interferences of sound waves to louder and softer regions of Davies Symphony Hall in San Francisco; he compares the overcoming of binding energy in a molecule to a children’s game of Red Rover; he relates the wave nature of light to the creation of colors on the diffraction of light of a musical CD.

Alongside these analogies designed for the quantum mechanics beginner, Fayer also includes many passages that make the text perfect for someone preparing for a medical exam, graduate school preparatory exam or other such test. At one point in the book I felt the title Quantum Mechanics and its Application to all Subspecialties of Chemistry would be much more fitting. The shapes of orbitals and the four quantum numbers are described in enough detail to help any prospective graduate student gain entrance. As Fayer elaborated on molecular orbital theory I recalled studying the very “simple” diagrams he provides as test material for my 400-level inorganic chemistry class during my senior year of college.

Many times in the latter half of this book I felt Fayer was a bit unrealistic in thinking someone newly introduced to the concepts in the first half of the book could relate. Examples include the maximum stability of molecules, oxidation states, and the desire of elements to attain the nearest noble gas configuration. I teach these concepts to beginners without even half of the introductory concepts in the first half of the book. It is not that the early material is not relevant to these concepts; it is that understanding how the fundamental concepts apply to the actual bonding behavior of molecules is abstract and probably not appropriate for the nonscientist. It would be better to start with an explanation of how elements/molecules bond together and then delve deeper into the mysteries of why it occurs in this way (quantum mechanical principles introduced earlier in the book.)

The second half introduces applications of quantum mechanics like the characteristics of hydrogen bonding that allow water to be a liquid at room temperature despite its low molecular weight. (All other molecules of similar molecular weights are gases at room temperature.) It is this type of molecular behavior that might better be introduced in introductory chapters to peak the interest of a nonscientist. The overall concept of elecronegativity/polarity that gives rise to hydrogen bonding is fundamentally quantum mechanical in nature, however, this phenomena could be described and understood outside of a quantum mechanical perspective.

Overall, if Fayer aimed to help educated scientists understand how their discipline of science is understood from a quantum mechanical perspective, this book would be perfect. If his audience is a layperson who is not even versed in principles of classical physics, then despite his real-world analogies and clear explanations, he introduces concepts with an approach that is beyond the layperson. In some cases, he includes details that are probably not necessary for the level of his readership; an example would be a discussion of Rydberg and Balmer lines for the hydrogen atom. This discussion supports the discovery of the structure of the hydrogen atom but is not critical to a fundamental understanding of how the hydrogen molecule functions.

It would have been helpful to have more discussion of observable effects and technologies that exist as a result of quantum mechanics; quantum teleportation as shown on Star Trek and gadgets that use photoelectric effect technology would be a great place to start. Fayer briefly mentions these types of examples to illustrate his points- however, he has a tendency to select subjects like the operation of a cathode ray tube –this is beyond the layperson.

Noticeably missing from this book is the double-slit test. This experiment is usually used to illustrate the inability of scientists to differentiate between the wave and particle nature of light. Fayer uses the interferometer to describe not only this paradox but also to show how the superposition of the photon/electron collapses into one of two possible states. He is able to show more detail with the interferometer application of this experiment, however, my fear is that he loses the reader in his burdensome explanation of the mirrors and other technical aspects of the experiment.

Also noticeably missing from this book are detailed analogies that relate an entire personal experience to a larger concept of quantum mechanics. In a book written about quantum computing for a similar audience as Fayer’s, A Shortcut Through Time, New York Times science writer George Johnson includes an entire chapter about an analogy between tinker toy logic and binary logic used in computers. The chapter is clever with mention of tic-tac-toe and diagrams using childrens’ tinker toys. Johnson is not a trained scientist but rather an educated layperson himself. From this perspective, the comparison is not a fair one; however, perhaps it makes him better equipped to understand the intended target audience of his explanations. While Fayer touches on this type of approach it is not nearly as developed as the analogies/illustrations of Johnson’s book.

Fayer does include relevant applications of quantum mechanics to all varieties of chemistry. His applications include an explanation of solubility, an explanation about how global warming relates to the vibrational modes of carbon dioxide and a correlation of molecular orbitals to the subatomic processes behind electronics (semiconductors and superconductors). These chapters are excellent additions to the text and add context to the explanations. This section also includes a lot of technical jargon that might make it difficult to relate it to the fundamental concepts of quantum mechanics.

Fayer writes a comprehensive account of the history, experimental evidence and applications of quantum mechanics. His building block approach spans diagrams, math, explanations, and analogies. Overall, the text is comprehensive, complete and very clear- for people who are generally educated in the physical sciences.

An inspiring book.....

I find myself going over to Gretchen Rubin's Happiness  Project blog more and more these days. I guess I'm fascinated by the pursuit of happiness. She does such a great job of researching it.

Yesterday her blog recommended a book I would really like to ready. Alfie Kohn’s  Punished by Rewards: The Trouble with Gold Stars, Incentive Plans, A’s, Praise, and Other Bribes. The book is already on my amazon.com wish list.

I'm fascinated with the idea that rewards and gold stars really are NOT good for us and our motivation. I wonder what his argument is really? I'll just have to buy the book and find out....I wonder how he suggests that we motivate ourselves?

My most favorite toxin..... melittin

 I missed out on the fun! Last week there was a toxin carnival at Sciencegeist and I wasn't aware of it. It inspired me, however, to think of a toxin I would be interested in researching. I knew immediately what my choice would be: bee venom. (I don't think anyone covered this topic but I only perused quickly through the articles listed.)

Bee venom has always fascinated me. How is it that a  tiny, tiny creature like a bee can land on a person and create such an excruciatingly painful welt on their skin? It amazes me that such a miniscule, otherwise insignificant creature can do such a thing. So- I want to know more about the chemistry of how it happens.

It turns out that the chemical causing pain in these pesky and painful bee stings is called melittin. It would be logical to assume that, given the small amount of bee venom injected by the teeny, tiny pest that it would be 100% melittin. Wrong! Only about half of the approximately 0.1 mg of toxin is actually the toxic compound itself. The rest are other peptides which contribute to the strong Ouch! of pain but none more than the melittin itself.

Melittin has a tetramer structure. What? You might ask. What is a tetramer? I asked the same question in my 400-leve inorganic class during undergrad when we had finally graduated to naming complex compounds. A tetramer structure is a repeating structure of  four base units (in this case peptides made of amino acids). (Hence the prefix "tetra") (If you study enough chemistry you begin to realize the utmost importance of memorizing your Greek and Latin prefix and suffix terms. It is one of the many times in science that a mastery of the English language comes in very handy.)  The tetrameric structure may seem insignificant until you realize that it greatly influences the overall function of the molecule.

If you are a beginner (and I expect my readers to mostly be beginners) then I would suggest you visit my post about how soap works before you read on. This molecule has the polar/nonpolar properties in common with the soap/water/grease situation which is a simplified version of how this molecule works.

Basically, the way the alpha-helical monomers are structured, their polar outsides and nonpolar insides allow the molecule to penetrate phospholipids and interfere with critical body processes like the sodium/potassium channels that allow production of ATP.  But- just like many toxins, this capability can be used in a positive way for medicinal purposes.

Melittin is currently being researched for its ability to fight diseases like lyme disease. It is also being investigated as a possible cure for cancer. Apparently they are developing a nano-device to deliver the melittin to specific areas of the body  in order to avoid exposure of the chemical to healthy tissue.

So whether you come in contact with melittin by accident (and a small Ouch! of pain) or via the purposeful hand of a healing doctor (let's hope not) this "toxin" is versatile to say the least!

Sources:
Wikipedia
The Triple Helix Online: Sweeter than Honey by  Colleen Thurman, Dec  7, 2009
Thomas C. Terwilligert and David Eisenbergg. The Structure of Melittin. The Journal of Biological Chemistry.  1982, Vol 257 No 11, 6016-6022.

Regulatory affairs and waiting room times in medicine

I read an article last weekend in the Wall Street Journal called Long Medical Waits Prove Hard to Cure. I didn't think much about it until today when it popped into my mind as support for what has become a theme of this blog and of the situation of much of the United States: regulations pervade our lives.

The article discusses how the methods to measure doctor's office waiting times can be manipulated for reporting purposes. For example, patients not seen within 48 hours might have to wait a really, really long time to see a doctor while other patients who called later are accommodated within 48 hours. The hospital knows that once these patients are cleared from the log their waiting time numbers will worsen.

"Any waiting-time measure can be thwarted or misrepresented," says Michael Davies, an internist and acting director of high reliability systems and consultation at the U.S. Department of Veterans Affairs.

This problem represents a larger issue in regulatory affairs; misconstruing data to match whatever regulation has been put in place.While I wouldn't go as far as to say I support the practice, I certainly am very sympathetic to businesses who have a bottom line to attend to. How can we expect them to pay the price of revamping their business practices for a regulation that may be revoked next year? This is very, very costly. And with the number of silly, nonsensical regulations out there, often this type of dishonest practice is the only option available to these businesses. Often they are just buying time to figure out if the regulation is actually a long-term one or if it is just the whim of an official who may be voted out of office next year.

Regulatory affairs is a tricky business, one I'm afraid we need more training for as a nation. Already we have certificate programs and masters programs available for people interested in studying it. I'm predicting it will become a staple career of the future like being a doctor or a lawyer. You might say something like, "I passed my RAC" in the future and people will recognize that name the way they recognize passing the bar in law or the boards in medicine.

We need some very educated, insightful people to take care of these overarching issues or a lot of time and money will go to waste. We're already seeing that with a regulation on hospital waiting rooms that just seems to cost labor, time and effort to implement- and the data is misconstrued. What a waste of everybody's time.

Book recommendation for science educators....

A few years ago I did a blog entry about a book review I found in the Wall Street Journal about a book called The Wave Watcher's Companion. That book has been sitting on my shelf since then! With all that has happened in the last two years I never took the time to follow up and actually read this wonderful book.

In the last week or so I've mustered up my ambitious spirit and started to read the book. Why now? you might ask. Well, I'm going back to work in the fall! Yes, I've been confirmed to teach at Irvine Valley College starting Aug 19. I am so excited to return to work and yet I'm also nervous. Nervous thinking perhaps my knowledge of introductory chemistry has grown rusty in my time away....

So I made it my goal to digest this book for the next week, month, or however long it takes to really take it in.  In the first thirty-one pages I already have enough anecdotal stories to fill a new class about introductory physical science. Here is my favorite part of it so far. (He is using an analogy to describe the way waves travel)

"The crests appear in the calmer water at the back of the group, travel through it and disappear again in the calmer water at the front- rather like ghosts running through the train carriages. Isn't it nice when things are so straightforward?"  (obviously sarcastic remark here)

Why does this even matter? You might ask. Waves and energy are a critical part of introductory science in general. An understanding that spans deeper than just a textbook definition is important  early  in comprehension.

Graphene shows its colors (The Economist)

This week's Economist has two science articles that seem particularly interesting. I wrote about the element 119 article the other day. Today I'd like to focus on the article about graphene and the hopes that it will propel technology to yet another new height of sophistication.

Most people might peruse through this article and not realize its connection with the digital revolution, quantum mechanics and all the ingenious technological devices we all carry around in our pockets. This is a concept that earned Albert Einstein a Nobel Prize. He articulated and illustrated the concept that had been part of experimentation, literature and science for a period of time before he really tinkered with it.  Ironic, I think, that the man famous for saying, "God does not play dice" received the majority of the credit for a discovery that largely supports the tenets of quantum mechanics.

In a nutshell, photoelectronics uses the wave/particle nature of light to transform photons of light into electricity. A photodetector is needed for this process. This article nicely explains photodetectors and their current limitations. Most are made of silicon material that isn't flexible, sensitive or cheap enough to really run electricity through anything large.

It is thought that graphene might replace silicon as the material of choice for these photodetectors. Perhaps in the future we'll see photodetectors used in high gain transistors, like those of the telecon industry. The future of electronics is now in limbo again....

Element 119 - Turning a Line (The Economist)

I flipped to the Science and Technology section of The Economist this week to find an article about the periodic table. What fun! Turning a line can be found here.

The title is appropriate because the article discusses the pending discovery of a new element on the periodic table. Unlike any other new element made in the laboratory, this element actually adds a new row to the bottom of the table. This has never happened before because there are elements in all existing rows that can be found in nature. It was not until 1940 that transuranic elements began to be added to the seventh row of the periodic table. At the time they were discovered, these elements existed only momentarily in a laboratory and would quickly radioactively decompose.

This is a pleasant article discussing the introduction of something entirely new in chemistry- another shell of electrons surrounding the nucleus at a distance never before realized. I wonder what the shape of that shell might be visually?

One comment near the end made me laugh. "That will be a feather in GSI's cap in its friendly competition with the Lawrence Berkeley National Laboratory in California..."  Friendly competition? Doesn't this author remember the 2001 fiasco with Victor Ninov and element 118? That situation illustrated that the rivalry between labs is anything BUT friendly. Victor Ninov was hired because he successfully worked at GSI and discovered 110, 111, and 112. Berkeley hired him to show up their rivals (GSI) that they were smarter, quicker and had not lost their edge. They were sheepish and ashamed they had missed out on discovery of the most recent three transuranic elements.  So they hired their rival who then forged data in an attempt to beat GSI to the discovery of element 118.

There is a book that describes the fiasco quite well. It is called The Disappearing Spoon by Sam Kean. The book was just okay overall but the chapter about Victor Ninov and element 118 made it worth reading. Fascinating story. And- something the author of this article in The Economist should really check out to be a bit more accurate next time.

A friendly competition? Anything but.....

A Celebration to End the Year.....

Today was the final potluck of the year for my music group. It was fun as always. But I missed the familiar faces that greeted me 5-10 years ago before I became really involved in the organization as a leader and performer. Catherine, my accompanist and music enthusiast was most sorely missed as she would often accompany us for the group singing at the end. She also performed much of the ritual. However, life marches on and the younger girls (they call themselves 80s babies) have taken over much of the leadership and ritual functions. I am older myself- I'm the absent mom on maternity leave right now (in some sense of thinking about it).

This type of occasion gives me the opportunity to put into practice my resolutions formed as a result of reading The Happiness Project (by Gretchen Rubin). I remembered my friend's daughter was graduating from high school this year so I brought her a small gift. I think she appreciated it. As part of enhancing happiness overall I want to remember and recognize more occasions like graduations, baptisms, and birthdays. It is a small token of friendship but builds over time. Last Christmas we made our usual picture calendar for my 100-year-old grandma and I added all of my family birthdays to the calendar. My aunt ordered a copy for everybody this year.  This helps me remember all my extended relatives birthdays because I can see them every day on my calendar!

One of my music sister's started crying during one of the songs we sang at the end of the potluck. At first I thought it was silly (I'm not very sentimental) but soon I started to tear up as well. The song was about how friendships become nearer and dearer as time goes by. It really is true- even though we only see each other once a month (approximately) these women have become nearer and dearer to me as time flies by.

My friend with the daughter graduating from high school was about my age when I moved to San Diego. Her daughter was six or seven when I first met them. Now she's eighteen and I consider her mother a very dear friend of mine in town. We're over a decade apart in age but somehow we just connect. I'm not sure how I found this friendship except that I opened myself up to a group of women interested in the same topic as me- music. And this is how it has unfolded......

Happy Mother's Day!

This year I'm amazingly blessed to have both a mother and a grandmother to celebrate on mother's day. My grandmother is 100 years old and living with skilled nursing care. We are awaiting the fateful phone call any day now that she has passed into a better place. But, for now that phone call is still in the future and we want to celebrate every day of her life that we can cherish.
I found a book at a local card store that really made me think about the meaning of mother's day. It had the words "Grandma" on the cover and when you flip through it you find journal pages. Each journal page has a leading question for the entry. Leading quotations/questions included the following: What was your favorite memory of a time with your own mother? Describe your first transportation to school as a child. What kind of Saturday afternoon schedule did you have as a child/teenager?
The book made me want to buy one for all of my relatives as a future gift for their children. How I wish I had such a thing from my own 100-year-old grandma. She is so full of stories and wisdom. One time she told us about how she rode a horse to school when they lived out in the country because they didn't have a car to drive to school. She is not able to write anymore so I couldn't send it to her. Instead, I sent it to my own mother who is now "grandma" in her own right.
The book also made me think about how I would want to be remembered as a mother myself. If my own daughter were to write in such a book for her children what would her favorite memory of a time with me be? What would I want her to remember about her childhood?

This gets me thinking about what is important as a parent. I think the single most important thing I'd like my children to take from their childhood/adolescence is the importance of relationships. There is no greater gift in life than supportive family and friends. And to have these it takes some work. I'd like them to see me value these relationships in my own life and model that their own lives.

Buy Some Happiness..... (Gretchen Rubin)

I still haven't finished The Happiness Project. As typically happens with me, I'm reading three books all at once. Usually I'm lucky if I finish one out of the three I'm currently reading.

Anyway- I find myself putting down my other books to refocus on Gretchen Rubin's Happiness Project. In the section I'm currently reading, she spends an entire chapter on how money can contribute to happiness. Of course there are many wealthy people who are very unhappy. But, generally, people who have a certain amount of wealth report a greater level of happiness than those that do not. She goes into detail about the research she did on this subject- on a macro-level mostly- comparing wealthy countries to poorer ones. And then she  looked at it on a small scale. For example, who would report a greater level of happiness: the wealthiest person in a small town in Nebraska or someone on the lower end of an affluent New York suburb? Obviously the New Yorker is probably exponentially wealthier than the Nebraskan, however, studies show that comparative wealth actually is a better predictor of happiness than absolute wealth. Gretchen outlines all sorts of examples like this to illustrate her point. Her overall point is that money brings security and security allows for more freedom. This brings happiness.

So how can I maximize on my own situation and BUY some happiness? I'm not wealthy by any means, at least not compared to the average person in southern California. But I have enough money that I'm not on a strict budget (relatively speaking) and I can afford to stay home part time, at least for now. So, how do I BUY some happiness?

So if I were to buy any one object or group of objects to increase my happiness what would it be? This is a question I don't think about much because I am a penny pincher by nature. I am always thinking about ways to save, ways to cut spending, ways to pinch pennies for a rainy day.

If I think about enabling myself to experience happiness by purchasing an object that might guide me toward that end I remember board games. Board games? You might ask. Yes, it is a family tradition on holidays and vacations to get out guesstures (board game version of charades), balderdash, rummikub, and boggle, for example. I can remember many Thanksgiving and Christmas holiday parties with these games as the center of the entertainment. These memories bring me happiness.

Therefore, to this end, I would invest in a set of board games for our house. We have a few lying around the house but not enough to provide choices for a group of friends or family at our house on a holiday. I think I'll buy myself some happiness and invest in a set of board games for the future.

I only have three chapters left of the book to go.

Book Review for Technical Communication

Unfortunately, this review is shorter than I'd like due to space limitations. I have a 500 word limit to stick with. I'm still editing it. Please make comments if you see fit!

Writing Chemistry Patents and Intellectual Property: A Practice Guide
Francis J. Waller. 2011. Hoboken, NJ: Wiley. [ISBN 978-0-470-49740-1. 238 pages, including index. US$79.95.]

When I graduated with a master’s degree in chemistry ten years ago, I knew nothing about intellectual property or anything else about the legal side of science. After joining the local Association for Women in Science (AWIS) chapter, I began to understand the large role that intellectual property and law plays in the vast world of scientific research. I also discovered a wealth of opportunity for women in the development and approval of patents in science. Much of this opportunity remains hidden at the academic level because of the omission of the field from formal tracks of education in the sciences.
This is one of the main reasons that Francis J Waller wrote and published this book, Writing Chemistry Patents and Intellectual Property. He makes it clear in his narrative that access to information about intellectual property is not readily available. For this reason, The American Chemical Society has had Waller teach a class every year since 2006 on this subject at their national meeting. Because scientists leave their graduate programs without any formal training or knowledge of the subject, Waller attempts to fill this knowledge gap with his all-encompassing, dense, one-stop shop approach in describing his 35-plus years of real-life experience.
Waller’s knowledge and the sheer amount of information necessary to convey in a short book make organization a challenge. Overall, the book is logical in its design: a broad overview of intellectual property followed by vocabulary definitions and a discussion of patent versus trade secrets lead into the meat of the book about patents. The chapters become more focused on the individual aspects of a patent—writing it, formatting it, and filing it—the further into the book that you get. Waller has written some of the book strictly for PhD-level chemists who are looking for answers to questions about real patents. There are, however, some helpful chapters written for anyone who has concerns over general intellectual property questions. An example is his discussion of copyright and trademarks in chapter 11, where he discusses the concept of fair use—a topic that is becoming more relevant to all disciplines, especially on the Internet. One improvement Waller could make is to provide a brief mention of critical definitions in the overview chapter. I found myself flipping ahead to the vocabulary section so I could better understand the general overview.
Chapter 7 is most specific to chemists working on actual patents. In his discussion of specific patents, he cites examples that are included in a special appendix. This is where he really dissects each patent of its components and the issues surrounding these components.
Waller presents a dense topic in a clear manner in only 238 pages. Perhaps he should devote a longer book to the subject for people who could glean from his expertise. For now, this one-stop shop approach will suffice.




Julie Kinyoun
Julie Kinyoun teaches chemistry at local community colleges in southern California. As a freelance writer, she writes about biological, physical and chemical sciences for local and national publications. Julie holds an MA in chemistry from San Diego State University.

Cancer's Epicentre- The Economist

There is an article in The Economist this week that helps me understand a bit more about why Carl Zimmer made the error that I pointed out in a previous post.

The article outlines a new explanation for cancer's mysterious genesis and proliferation throughout the human body. Its a similar article to the book review Carl wrote about epigenetics. I don't recall his book review focused specifically on cancer as a disease- it was more of a discussion about how gene therapy and epigenetics could combat a variety of conditions (I would need to reread it to be sure).

The article in The Economist mentions that genes are switched on and off by plastering the DNA or surrounding proteins with chromosomes containing clusters of acetyl and methyl groups. This would explain why Carl mentioned methylation as carbon, hydrogen and oxygen. He merely forgot to mention that the methylation can also sometimes be acetylation. Acetylation does, in fact, include oxygen. So- instead of getting the definition of methyl group wrong perhaps he forgot to include the additional functional group (acetyl). Then, carbon, hydrogen and oxygen would all be involved, as correctly noted in the article.

 Glad I got this ironed out. Didn't think Carl was prone to errors.

Surfactants: How does simple soap work?

I am currently reviewing a book about intellectual property for a trade publication. It specifically focuses on chemistry patents which I know very little about outside of my master's level knowledge of basic chemistry. Interestingly, I have learned about scientific patents in general from my involvement in The Association for Women in Science (AWIS). Several PhD level female scientists have taken the patent agent exam and worked for law firms as patent agents. It seems to be a logical, lucrative and practical solution to the problem of an educated woman in the business world. For some reason the patent/law world is able to accommodate women much better than academia or even industry science is able to do.

Partly for this reason, I volunteered to read and review the book for Technical Communication. This brings me to the focus of this post- surfactants. Apparently surfactants are used to solve a nanotechnology/quantum problem. This is fascinating to me because the two areas of science seem so distant from each other, yet apparently in this case, someone wrote a patent using surfactants for their more electricity/nano oriented problem. (This also gives you an idea of where I get ideas for these posts. Usually I'm reading about something that sparks my interest into writing about a related topic.)

Surfactants help make something intermix with something else. The most obvious example of this is when you are washing your dishes. (Believe me, I'm the queen of DLD right now as a stay-at-home mom- this is coined as DLD or "dinner, laundry, dishes") You have a stack of plates covered in greasy, leftover food. Hopefully, you remove the excess food before you place them in hot, soapy water to wash. Why not just hot water? In most cases, some of the grease is still left if you just wash them in hot water. On a molecular level, here is why:

The grease on the plates is full of hydrogen/carbon chains that have the properties of something  "hydrophobic." Generally, the chemical properties of carbon/hydrogen don't mix with the properties of water (made of hydrogen and oxygen). This is related to the concept of polarity/electronegativity that is discussed here in my other blog.Generally, polar compounds mix evenly with other polar compounds and nonpolar compounds (pure covalent compounds) mix with other nonpolar compounds. Water is extremely polar while any kind of grease or fat is extremely nonpolar.

The detergent molecules (surfactants) create an interface between the polar and nonpolar so that the grease molecules can be removed from the place.  The detergent generally has a polar head that will "stick" to the polar water molecules while it has a nonpolar carbon/hydrogen tail which will "stick" to the grease molecules. By intermixing with both polar and nonpolar components of the grease/water mixture the soap is able to engulf the grease and send it down the sink.

 As you can see in the picture, the left side of the soap molecule is a carbon/hydrogen chain while the right side (the head) has oxygen-containing functional groups. It is these oxygen functional groups that will intermix with the water while the greasy tail (left side) will combine with the grease on your plates.

Here is a picture of nonpolar greasy molecules in the same container with polar molecules:

My book likens it to a mixture of magnetic and nonmagnetic particles. Can you think of anything else that behaves this way?

I have discussed polarity and dipole moments in other posts. Here are links:
Electronegativity
Ionic and Covalent Bonding
VSEPR Shapes

The Future of Nuclear Energy in the World

Recently there have been some intriguing articles in a variety of publications about renewable and alternative energy sources. I subscribe to both The Economist and The Wall Street Journal and took note of articles in both focused on the future of nuclear energy. This topic is particularly relevant to me as a science educator as I have seen it as a topic of study in my classes.

By now it's no news to anybody that finding alternative energy sources is essential to our health as a planet. Not only do we have carbon dioxide levels rising to dangerous levels but we have political problems gaining access to the world's supply of fossil fuels so desperately needed to maintain our energy demands in the United States. (Believe it or not when I was a child the concept of global climate change was a liberal notion of crazy, out-of-touch people.)

One thing I have only become familiar with in recent years is the theoretical amount of energy that can be harvested from nuclear sources. I had no idea that, theoretically, nuclear energy should be able to provide for all of our energy needs, and them some more after that. This is probably why people like Bill Gates bring up nuclear power as the key to energy demands of the future. Bill Gates, the entrepreneur turned business man who achieved the impossible with his power-buster software company of the 1980's that came to dominate the marketplace in the decades that followed. Bill Gates, one of the richest men in the world. Bill Gates who can afford to take risks, dream big and think in theory. It's just that theory, in this case, could also mean the end of the planet.

In theory nuclear energy is very appealing. If properly developed, a nuclear plant could solve all of our energy problems. But the realities are discussed very nicely in a recent focus-section of The Economist on nuclear energy. In reality, nuclear energy is too expensive, takes too long to develop and is too risky to really be a viable solution to our energy problems. While it looks viable on paper, nobody has been able to develop a really safe, inexpensive nuclear facility that unleashes this theoretical energy is a usable form. The risks are too high and the payoff, so far, has been too low.

There are political concerns as well. The proliferation of nuclear energy has caused international dissent about how and where nuclear energy is developed and used. Iran, for example, is developing its nuclear capabilities, and for all we know, those capabilities are to make a dangerous bomb. From reading The Economist I gather the majority of the dispute is over exactly how much of Iran's nuclear capability is energy related and how much is in the actual development of a bomb. The difference is subtle. It doesn't say this in the article(s) but I'm figuring that the only way to really tell would be to inspect the nuclear plants very, very carefully. And I suspect Iran does not allow us to do this. So we really don't know exactly how far along they are in unleashing a bomb. For all we know they are creating nuclear power to power the electricity of their citizens. We can't tell the difference from afar.

So as we march forward in our quest to develop renewable energy sources and other ways to replace fossil fuels, we know that we are not meeting our goals fast enough. The Economist outlined the rate that we are currently replacing fossil fuels as compared to what we would need to do to keep carbon emissions under check. With current progress we are falling short. This is disturbing considering the consequences to continued fossil fuel use and carbon dioxide production. But- nuclear energy, according to them, is not the answer.

Maybe they should talk to Bill Gates for some inspiration.

A Children's Book on the Elements

I was envisioning what a children's book on the elements might look like:

-   A cross between the Sesame Street version of Law and Order and something like Dr. Seuss with a bunch of funny word combinations. (In SS Law and Order the detectives go on a quest to find a delinquent letter of the alphabet on the run)
-  A narrative in which carbon walks around in chains a bit like Marley when he haunts Scrooge in A Christmas Carol (Carbon has a tendency to form chains and this illustrates this basic characteristic)
-  A narrative in which an oxygen-hydrogen structure sucks everything else to stick to it (like hydrogen bonding)
-  A narrative with a nosy and busybody fluorine molecule that buries itself deep in everybody's business/lives. It buries itself in people's lives and then creates deep damage.


There are so many other character traits that could be developed from the elements chemical behaviors. It would be fun (and challenging) to create such a story with all of this information. And- hopefully it would make the element characteristics more fun to learn and remember for children.

High School and College Textbooks in the Sciences

I was just reading  a book review on a new e-book for biology students and it reminded me of some of the challenges I've had referring my students to a helpful textbook for introductory chemistry.

The problem is very nicely explained by this writer (a professor) who basically likes the electronic videos and other gimmicks of the e-book and agrees that these tools add dimensionality to the learning environment. However, the particular ones included in this book don't strike him as resonating with sixteen-year-olds.

So, basically there are a bunch of videos that show cool stuff to people who already know what it is. 

This same problem applies to old fashioned textbooks.  Either the textbook is very clear and straightforward (appealing to a typical introductory student), but lacks depth and completeness or is very thorough and complete (appealing to the professor)  but lacks clarity and a sense of logic. How do you effectively teach a class with this problem?

Often many students in an introductory class just want the bare information needed to get whatever grade they need on the test. Chemistry is usually required for whatever career path they have chosen and they know they need the coveted A to get to their next step. For this reason,although introducing extra videos and illustrations from multi-media often seems appealing to the instructor for better understanding from the students, often the students' themselves are frustrated by it. It broadens the number of materials they are required to study for their exam and they usually can't see how it fits into the material presented by the textbook. So while it is possible these extra tools help their long-term understanding of the material, they don't help them perform on the exam.  Many students find this very, very frustrating.

A real-life example of this would be use of the Tro texts for introductory chemistry versus use of the Zumdahl texts. I've used both. The Tro text is wonderful for a step-by-step, logical explanation of each topic in chemistry. Of the three textbooks I've taught introductory chemistry from, it is the only one that explains the topic of Lewis dot structures, VSEPR shapes and bond angles from start to finish and concludes with a very helpful discussion of polarity based on shape. I had never seen such an amazingly clear discussion of the topic before in my education. For this reason, I take diagrams and other tools from this chapter when I'm explaining this to other classes at other junior colleges. Yes, the approved textbook is one by a different author but the chapter on this topic is so good I tack it onto their required reading.  (If someone knows the proper publishing procedure I need to take then please leave a comment after this post. I've tried to contact the publisher without success on this issue.)

As useful as the Tro text is for preparing my students to perform on tests, it does not provide some of the excellent examples of complex items from nature that my Bauer text provides. For example, the post that I wrote about carbon monoxide poisoning was adapted from a diagram/excerpt from my Bauer textbook about the importance of understanding shape/function of molecules. This kind of discussion cannot be found in Tro. It's a bit of a tangent really- only peripherally related to the main topic of the chapter. While I found it fascinating, I doubt most of my students know enough about science to appreciate its relevance to what they are learning.

I keep a very detailed blackboard site of all of the resources I provide for my students. I'm always hesitant to add extra items to it for fear the students will get bogged down in a swamp of information. I'm just fearful that the meandering explanations of Zumdahl and the unclear examples in the text actually confuse them more than educate them. However, their required homework is from Zumdahl (a very educated and accomplished chemist- just not all that clear for beginners.) Therefore, I must teach from Zumdahl and any additional materials I feel explain thoroughly and clearly the material on which I want to test.

It's really hard. Sometimes I think the students don't really know what they are supposed to study because I present so many different ideas from different resources.

More on Happiness.....

Gretchen Rubin would be someone I would have a really good time with as a friend. Our most obvious common interest is LM Montgomery. Apparently, when she identified children's literature as an interest of hers, she read everything written by LM Montgomery (among numerous other children's books). This caused me to think about my own interests: am I also interested in children's literature or just LM Montgomery's writing? I think the answer is that I am interested in children's literature but probably not enough to join a weekly club. I am also not a Harry Potter fanatic. For example, I own the first four books and have never touched the fourth one. All of the movies after the fourth or fifth one are films I will have to watch in their TV versions. But- I have read five out of the seven Narnia books and A Wrinkle in Time.  Gretchen obviously seems to have more time (or interest) in reading than I do. My adult nonfiction stack seems to grow larger and larger with books I want to read but haven't found the time for yet. I can't also add a bunch of children's books I read long ago and admired but would need to reread for a book group. I'll let her have that one for herself.

However, Gretchen's children's literature group reminded me of something about myself. It actually made me pat myself on the back somewhat. Some of the changes she describes are changes I made consciously after college without thinking exactly of my happiness, per say, but my sanity. I really needed a break and some outlets of lowering my stress after college. To this end I made an effort to get involved in some activities I had enjoyed as a child. This is the exact advice she gives herself- and one of the reason's she starts the children's literature club. My outlet of happiness was to join a music club. During my senior year in college I joined the Sigma Alpha Iota women's music fraternity. My hope was to have performance opportunities as an alumnus. Here we are fifteen/sixteen years later and that is exactly what that organization did for me. But- it also did much more than that (without my knowledge). Through my involvement in SAI here in San Diego I've formed a group of lasting friendships that are priceless. In some cases I have nothing else in common with my fellow club members other than our  interest in music. However, in some cases, the friendships have expanded beyond the group into outside friendships. Joining a group with people who have a common interest really is a way to create more happiness- whether it's the enjoyed activity itself or the contact with others, I have experienced first-hand Gretchen's notion that happiness can be found in a club.

All of this fit into her chapter on learning how to play. Another fun idea she had was to start a collection. Hers was a bluebird collection. I wondered if I should take up my old collection of stamps or if I should start something new. The more I thought about it the more I thought renewing my interest in stamps would bring me the most happiness.  Part of happiness is recalling happy times. And working on my stamp collection as a child was a very happy experience for me.  It wasn't really me that started the collection. Sure- I took the stamps off their backs and arranged them in books but I didn't actually obtain them myself. My father brought them home from work. He and his colleagues received correspondence from people all over the world - remember this is during the 1980's before email and the Internet. All communication was via snail mail. This was a good thing for me- once word spread that my father's young daughter collected stamps I received all kinds of stamps for my collection. More important than the actual collection, however, were the connections made with people through the exchange of the stamps. Just by tearing a small square off of an envelope and handing it to my dad at work I grew to recognize people's names and job titles. Unfortunately, much of this was also possible because of the use of secretarial staff in hospitals back in the 1980's. This was back when a real person actually answered the phone and they had people to dictate and type manuscripts and other correspondence. With the changes in health care, I doubt such a collection would be possible for a young daughter of a doctor today.

The collection was so much more than a collection. It was a conversation piece, reason to connect with others in my father's office and a community building activity. It brought happiness.

I'm eager to explore more of Gretchen's ideas about happiness.

My Search for a Nanny.....

So the latest news on this is the amount of money that it costs to hire a separate company to hire/fire and pay my nanny.

And the conclusion is that this is way too expensive. It is twenty-one dollars an hour to hire a temporary nanny who is covered by social security and unemployment through an agency. That is absolutely ridiculous. I could end up paying more for childcare than I make as a salary. Add gas for the commute on top of that (I drive up to Irvine) and the costs associated with working could easily surpass my income.

It's too bad the law doesn't allow honest people to hire a nanny without making them reach so far into their pocketbook that they decide it is more cost-effective to stay home.

I'm thinking I hope one of John's relatives volunteers to do childcare for my daughter. This seems so much easier than formal nanny/childcare. How do people do it? I honestly don't know.

looking for a nanny

I saw an article in the Wall Street Journal yesterday comparing Mitt Romney and Obama in terms of their corporate tax reform policy. I thought to myself, "Could we make those corporate tax reforms apply to moms please?" Here is the reason I wondered such a thing:

I will need to hire a part-time nanny if I am going to go back to teaching in the fall. My husband feels much more comfortable with this option than any kind of group daycare or home daycare. However, it also is more expensive, if done according to the law. Most people actually break the law on this one and there is a good reason why (although I do not agree with breaking the law). A nanny is considered a domestic employee in your home and, therefore, regardless of whether the person is part-time or full-time, they are considered a W2 employee. It is illegal to 1099 your nanny. Apparently the IRS has a specific section of the code related to this regulation. Therefore, if you hire a nanny and  for some reason the arrangement doesn't work out, you are responsible for unemployment, medical and social security. My sister had this experience when she hired a nanny for her infant daughter about five years ago. The nanny was a great caregiver but insisted on creating her own schedule and dictating policy in the home. For this reason, my sister had to fire her. And- because she is a W2 employee my sister was obligated to pay her unemployment insurance. On top of that, if my sister wanted to rehire a different person to fill her shoes, her unemployment tax would increase about four times the previous rate. My sister was treated as a business and every business has a hire/fire ratio. Since she only employed one person, her hire/fire ratio was 100% and, therefore, she was obligated to pay more into unemployment insurance.

Now- how many people can afford to hire a nanny under these conditions? It doesn't make sense. Especially if you only need someone ten to fifteen hours a week as I will need in the fall. The majority of people simply break the law and either pay cash under the table or create a 1099 situation where they are not responsible for the extra government fees. I would like to be a good citizen and follow the law and so I intend to find a company that will create the W2 for me so the nanny is their employee instead of mine. Apparently, there is only one such company in the entire city of San Diego.  (There is only one such company in Bellingham, Washington where my sister lives but that is a much, much smaller city.)

Only one such company? This is an immigration issue. The reason that only one company like this exists is because of illegal immigrants who come from Mexico. Today I spoke with the owner of a nanny company in San Diego and she explained the situation to me. Nobody can afford to W2 their employees for temporary work because there is not enough demand for them. It is too expensive and not enough people use the service. Everybody employs undereducated, illegal immigrants from Mexico and pays them under the table.

How is that for a law that doesn't make sense? (Read my previous entries about regulations and the importance of relevance and enforceability) In this case, people who follow the law (like me) pay huge fees that cut into their profits while those who break the law and employ illegals pay less money and are not responsible for social security and unemployment insurance. Why can't we modify the law to benefit American nannies and create a more level playing field in this industry?

What a nonsensical system. And, once again, we are back to the concept that you can't get away from regulatory.

Joseph James Kinyoun- Founder of National Institutes of Health

https://www.nih.gov/about-nih/what-we-do/nih-almanac/joseph-james-kinyoun-md

Every family needs a genealogist. For the good of the family and for the good of the public it is critical to keep careful family records of all birth/death dates as well as complete family names of parents and children in each generation. Here is why:

Especially since the advent of the Internet my father has received numerous inquiries about his family connection to Joseph James Kinyoun, the man often credited for founding the National Institutes of Health (NIH).  It is an easy association to assume my father is related to him- his name is James Kinyoun (spelled the same way) and he is also a doctor. People type in "Joseph James Kinyoun"and come up with my father's profile as their top google hit, "James Kinyoun."

For this reason I had been looking for a number of years for a family connection between Joseph James Kinyoun and our family. It took me nearly ten years to find the connection. It is so distant that one mistake on a document or misinformation entered on a web site could have deterred me forever from knowing the real truth.

In my possession I have a recount of the family history of my father's family. It came from dear Aunt Dorothy Kinyoun, late aunt of my grandfather. She used to show up at family events when I was a kid. I could never figure out exactly who she was and why she always sent me homemade scarves and hats for Christmas. She and Claude (Mike) Kinyoun had never had any children and she had apparently adopted her nephew's (my grandfather Robert Kinyoun) children as her own. I always thought it was a bit strange she had no other family other than her in-laws children and grandchildren but I never said anything about it. We had no idea how blessed we were.

Dorothy took meticulous records of her knowledge of the Kinyouns. It is because of her that I have birth/death dates for James Edward Kinyoun and a bit of information about his children. Here is what I know:

James Edward Kinyoun came to Nebraska to raise his family. He had a daughter Jessie and a son Lem who both died. He had two sons who both lived to have children: Robert Edward Kinyoun I and John Wesley Kinyoun. (The Wesley Kinyoun family lives in Superior Nebraska today.)

This information (along with some other narrative about his life) matches the information about James Edward Kinyoun that I found on ancestry.com during a family Christmas celebration in Nebraska in 2007. My husband was playing pool with my uncle and cousins and it gave me a good excuse to duck into the study for some research.

James Edward Kinyoun (born and died on ancestry.com the same years as my Aunt Dorothy's records indicate) is the son of James Lemuel Kinyoun. James Lemuel Kinyoun was the son of Joel Kinyoun, assistant paymaster in George Washington's colonial army. Joel Kinyoun came from England to settle in America, according to text in a book written by Joseph Kinyoun Houts about John Hendricks Kinyoun (father of Joseph James).

Here is the complicated part of the story that is confusing because the records are not clear: Joel Kinyoun must have had two wives that both had a son named "James Kinyoun" within about two years of each other. So "James Kinyoun"and "James Lemuel Kinyoun" were half brothers, I think. James Lemuel (known as Lemuel) was the father of James Edward Kinyoun (my relative) while James Kinyoun (his half brother) was the father of John Hendricks Kinyoun, surgeon in the civil war for the south. John Hendricks Kinyoun is the father of Joseph James Kinyoun, founder of NIH.

Whewwww..... you say. Yes, that is complicated. So- to summarize: Joseph James Kinyoun is the second cousin of my great-great grandfather Robert Edward Kinyoun I. Their fathers (John Hendricks and James Edward) were first cousins. And their fathers were brothers. Except- it is not a full brotherhood- they were half brothers (I think). So- we are only half related to that side of the family.

Always, always, always keep meticulous records. You never know when you might want to trace the history of your family.