Friday, June 22, 2012

Periodic Table of Videos

I just discovered this rendition of the periodic table:  click here

It is a perfect way to slowly learn about each element on the periodic table. You click on each element and hear a simple tutorial about that element. It would be ideal to listen to 3 a day, for example, and then realize that at the end of 7 days you had learned about 21 elements.

I think I'll make this my summer goal. By fall I will be well versed in ALL elements on the periodic table.

Wednesday, June 20, 2012

How To Stop Science Alienation Syndrome - Deborah Blum on k-12 education (Slate)

Today there is an article on the Slate website by Deborah Blum about k-12 science education. The article can be found here.

Instead of leaving a comment at the end of the list of 102 comments I decided to blog about this entry. (This, by the way, delays publication of my blog about infant nutrition that I was going to do today.)

Blum's idea is to create tracks for K-12 students so that everybody is required to take four years of science education. There would be a track for future scientists, a track for college-bound poets and perhaps a track for noncollege bound, vocational-type people. (Or something like that- details to be worked out as needed.) Overall, I think this is a good idea, however, I have a few hesitations when it comes to "tracking" people.

The problem with creating tracks in science is the same as the problem with creating an "honors" program in the humanities. While I agree that we need to accommodate more science education into our schools,I'm not sure this is the place to start. Here is why:

The tracking system creates cliques of people. It is exclusive. It leaves out people that were erroneously placed in the wrong "track" and have forever been bored out of their minds. Sometimes it even creates situations where higher level work is going on in a "lower" track. I can say this from personal experience.

I started my high school honors program in the 7th grade and completed every year of it through my senior year in high school. Except one semester, I was in it all the way. Yes, we read more books, generally produced more papers and generally worked harder than the regular classes did. But we were also left out of a lot. During the semester that I spent in the regular classrooms, I saw the variety of people and socioeconomic classes at my high school. I met people I'd never met before and worked with people I never knew were interested at all in school. I saw some discipline problems in those classes as well.

Did that experience make me work less hard? No, it didn't. It made me appreciate my own love of literature, history and the arts. It made me appreciate that I care and some of them don't. But- most of all it taught me that I really wasn't that different from the people in the lower track. There were times when I felt the discussion was more lively, more engaging and more intellectual in the classrooms of the lower track. So all this leads to the question of what the upper track was doing that was really all that special?

We did have more required coursework than the lower classes. But- I think that in the end a lot of the higher track was just a reputation, a group of exclusive people who thought we were better than the average student. And in some cases we really weren't.

My current experience at the local junior college has taught me that it is very helpful to teach chemistry "warmup" classes to students who want to take college-level chemistry (for whatever career track be it science or medicine). For three semesters I have taught various renditions of a chem 100 class. For one school it is strictly for nurses. For one school it is for all prescience majors (premed, prenursing, preengineering mostly).  I have observed one important thing about the course description and how it makes people feel.

The students who take a class that has a label of being for beginners, nonmajors, nonscientists, etc are generally labeled as less intelligent. They have less confidence and generally perform more poorly.  But I'm not always confident that they have less ability or even interest. In this section of my chem 100 class I cover more chapters of the textbook, give more tests, and expect the students to do more experiments than those in my section that is geared toward engineering and medical school students. Its almost as if someone overcompensated the standards and decided that the nursing majors really need to prove themselves in chemistry to get their degree. In some cases, I feel the content is not really fair- it is a lot of information that is cherry-picked from a diverse area of the field. It's not well covered in the text. For this reason, I include extra handouts on my blackboard site. (I do not have those handouts in my premed class because we don't cover that topic.)

The point is that the designated levels that these chem 100 courses are supposed to fulfill are not consistent across schools and disciplines. It is luck of the draw to know how difficult of a chem 100 course you are going to get. It depends on which teacher you get, which school you take it at and during what time period you take the class.

Does this type of tracking make me confident that we can successfully "track" k-12 students? No, it doesn't.  It is too subjective as to what the people in charge feel are the standards at any given time.

I can confidently say, however, that having a chem 100- style class that students take prior to taking college-level chemistry is very helpful. Sheepishly, after teaching this class I actually understand the concepts on a deeper level because the class is presented strictly from a conceptual point of view. So often in general chemistry it is the manipulations of formulas, getting the right answer and the math that everybody gets so hung up on. While this is an important part of introductory chemistry, the more important part is getting people to understand the large concepts behind the math and the details.

The textbooks that I've worked with in this class include Bauer, Tro and Zumdahl. Each has its positive and negative points but all three have something in common: a focus on concepts.

So here is my proposal for updating science education in the future: Regardless of what the career goals of any individual are at any given time, students should be allowed to focus on concepts. This means professors and teachers will administer essay tests in the sciences. People need to be able to explain the behavior of an electron rather than just plugging numbers into an equation for an answer. I also propose more integrated programs of sciences with humanities, literature and the arts. Perhaps if we studied the lifestyle and literature of Richard Feynman in English class while we poured over the atomic bomb physics in science and studied the socio-political climate of Europe and America during this time in history then so much more of the science would be relevant.

Tracks can be helpful but the coordination of too many people is involved. I vote to streamline the classes into one big group of people. Then, propose honors/AP level projects that each student can take on as they have the time and interest. This allows anybody who wants to be involved  to perform at this level. Enough of exclusivity in education. We have enough of that already.

Tuesday, June 19, 2012

Best of Science Writing Online 2012- my comments

I downloaded the galleys for this and took a peek. Unfortunately, I am still somewhat averse to reading a complete book online.  This may turn out to be a problem in the future if all books are strictly electronic, so I better get used to it now!

Time is limited for me right now so I just wanted to make a few comments about it. Overall it looks good. A  variety of topics are covered and a wide variety of educational/writing backgrounds included.

The one main criticism that I have is that it would seem to make more business sense to make the entries shorter and include more of them. In this competitive world of science writing, including more people means building a team of colleagues. With the science reporting industry quickly dying and the the newspaper industry as a whole becoming obsolete, this publication of online writing seems to be the perfect place to create opportunities.

I write this blog strictly to connect with students and provide a perspective in the chemistry world that isn't mainstream. Let's face it- there are very few research professors out there in chemistry who are women with children. I'd like to be a face of change in that perception. Although I am not in research, I have a master's degree and I teach at the junior college level.

For people out there who are unable to teach or have no other way of making a living, perhaps a publication in Best of Science Writing Online (or something similar) might be just the opportunity they need to launch their career.

So to the editors and people in charge of this publication I ask the question: Are you making editorial decisions in the best interest of the field as a whole?

Thursday, June 07, 2012

This Week's Economist: Technology Quarterly

This week's Economist contains a section that all introductory chemistry students should read. So much of the time introductory students can't see the big-picture applications of all of the jargon and vocabulary they are learning. I know this because I felt this way when I took introductory chemistry. (Many of my friends felt the same way.) It all seemed like a foreign language to me and I couldn't see the bigger picture of why I would ever need to know any of it.

The Economist addresses just that problem this week. In this 24-page special report about new technology numerous chemicals are mentioned both in a healthy and positive way and also within the context of poisonous toxins for which we should all be concerned.

A few of the articles that were of particular interest to chemists include:

Dribbles and Bits: I happen to have a personal interest in this one. My family owns a farm in Nebraska and my father has recently purchased some pivots to increase the crop production on some of the fields. This technology could directly affect my family's farm finances- let's hope for the better. In order to more efficiently water fertile areas of ground while conserving water (and fertilizer) in less fertile areas, farmers submit topographical data into a software program. That program feeds the information to a GPS-type system that monitors the location and water usage of each pivot. This has the potential to allow farmers to conserve resources where they are currently wasted while expending extra resources in areas where crops are imminent. This has environmental consequences -the reduction in fertilizer means fewer nitrates and other nasty compounds running into the ecological web of life. I can't wait to see this unfold- before my eyes really- within the context of our family farm.

Please Rinse and Return: This article has practical consequences for all of us because it changes the way we do laundry. Yes, laundry.
Scientists are attempting to make some of the compounds used to make our clothes clean in a reusable form. This means we would wash our clothes with soap and some kind of additive that is removed and reused from the laundry machine after every load. Most likely this will be some form of plastic bead.
In bench science, enzymes are reused in reaction after reaction. A group of scientists wondered why the enzymes in laundry detergent couldn't act the same way so they tested their idea. And.... results show that this is feasible.
Ten years from now we could all have a bucket of laundry beads in our cupboards and spend a fraction of what we currently spend on soap.
I find the most interesting part of this experiment the PVC material they used to attach their enzymes in the experimental stage. I first encountered PVC pipe when I judged the San Diego Science Olympiad a number of years ago. The students used it to build musical instruments like a small tuba, flute and other wind-like contraptions. It is the plastic piping used under your bathroom and kitchen sinks. So there is yet another use for PVC pipe- in our laundry machines. (Actually this is not entirely true as the PVC pipe was just used for experimental work and they would likely come up with another material for the everyday product. Still, I find it fascinating that PVC pipe seems to be so versatile in its uses.)

Pipecleaner: In this technology, scientists are trying to find a compound that makes pipes explosion-proof by repelling water molecules from the surface of the pipe. Developing water-repelling compounds sounds a little like the chemistry behind surfactants and simple soaps (polar, nonpolar concepts)

Talking Trash: This article touts incineration as the way to cut down on landfills and recycling costs. The author claims the previous dangers of chemical release into the environment (dioxins, furans, volatile metals) are gone because of advancements in technology in the process of incineration. The author concludes with a powerful statement about the real problem: American consumption. Americans create 4.5-7 lbs a day of garbage while other countries create 2-3 lbs a day per person.

This special report is a must-read for anyone wondering why the concepts of introductory chemistry are relevant to people's lives. All students should go peruse this site for interesting applications. Use it as inspiration!

Wednesday, June 06, 2012

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.

Tuesday, June 05, 2012

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 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?

Friday, June 01, 2012

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!

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.