Chemistry Blog

Mar 03

Online Textbooks: ChemWiki Part 1

I remember buying my first O-chem books back when I was attending DVC (Diablo Valley College), a not-so-little community college here in the Bay Area. At first I checked the bookstore and lost my lunch when I saw the price of the new books. The text was $215, the lab manual was another $70, and the solutions manual was $100. Unfortunately, a new edition had been released that year, so even though the professor said that we could use older editions, many of the problem sets wouldn’t match up, so we’d have to get the problems from our classmates. In the end, the cheapest and most convenient route was to go online and buy the international editions. Even after extending the method to all my other classes, I still paid almost $500 for books that semester. Now I attended DVC before California went belly-up, so my classes were still a great bargain at $18 a unit. Since I usually took ~19 units, my total tuition cost was around $350 a semester. The cost of the books were actually greater than my cost of tuition. The sad thing is, this wasn’t an unusual case. Luckily this wasn’t too much of a hardship for me; I had a job on campus and money saved up. However, I knew a lot of students for whom the beginning of the semester meant not eating lunch in order to save up gas money.

Now students have probably been complaining about textbooks since time immemorial. Aristotle probably complained that his scribe made spelling mistakes in his copy of The Republic. Most of the time our bellyaching is justified. Not only do textbooks cost a lot, but there is often a gross amount of errors in them. Everyone knows that the first time you find a caption or answer wrong, it makes the rest of the book suspect. Also, these errors give the publishers a reason to release a next edition…that never seems to fix even half of the errors. However, they do switch around problem numbers, add a few pages of new content, and possibly even rearrange chapters. So now the professors lesson and homework plan, that goes by chapter numbers, page numbers, and problem numbers, is moot. And the student is effectively forced to buy the new edition (price “adjusted for inflation”) or suffer some inconveniences. Most choose to simply buy the new edition since tracking down the old one can be difficult and you have to be quick. Also, sometimes bookstores won’t buy back the old edition so if you had it, and an edition switch occurred before you finished your course track, you are up the creek.

Some of these issues can be addressed with online textbooks. The idea of supplementing physical texts with online modules has been around and implemented by publishers for many years. However, I’ve yet to see a good entirely online chemistry textbook. The advantages of online texts are of many: accessible anywhere you get 3G or Wi-Fi and have your mobile device, interactive learning capabilities, easy distribution, instant update/revision, and low cost publishing (server fees). Of course this won’t necessarily result the publisher make more money, but at 4 billion (yea, you read that correctly, billion) dollars a year, the industry doesn’t really need much help.

The student, however, does. We need these online textbooks, not just to save our wallet, but also to help prevent being stuck with an expensive and lousy text for a year that does a poor job of explaining the material. That expensive O-Chem book I bought really was terrible and it forced my professor to do a lot of extra work in teaching us not to follow the book’s direction of simply memorizing 500 reactions, but to see the patterns and the underlying physical explanations. In the end, we learned from his powerpoints and I paid $215 for a glorified reference book.

Well, some people are pioneering an effort to create an “Open Access Textbook”. In a perfect example of “chem 2.0”, UC Davis Professor Delmar Larsen is the project director of the ChemWiki, a truly free online textbook written by everyone, for everyone. In an absolutely Herculean effort, the developers and Larsen (Mary Obrien, Ron Rusay, Brent Krueger, Michelle McCombs) are trying to create a free and complete, as in covering all branches, chemistry textbook using a community of students, faculty, and outside experts from around the world. Of course they aren’t there yet, and there is still a long way to go but hey, their text literally gets better everyday.

Now I know you probably have a lot of questions: what about correctness and plagiarism? Could such a thing ever be considered an Authority? What do the publishers say? Does anyone actually use the thing? Well, it just so happened that a couple of weeks ago, I was at Davis for the Borge fellowship visitation and I had a chance to talk with professor Larsen who agreed to answer some of these questions for me. In a couple of days, I’ll post the interview here. For now, I suggest you go and check out and browse not just through the core, but the wikitexts and community as well.

Mar 03

Chemistry YouTube Videos – February 2010 Roundup

A student in a chicken suit gets tackled by organic chemistry lecturer Owen Priest at Northwestern University.

An excellent video on methane by the Periodic Table of Videos crew last month.
Safety Note: Samantha “Pants!” Tang is not wearing a lab coat, gloves, and her hair is not fully pulled back.

Also from the Periodic Table of Videos, Sam shows us the Traffic Lights reaction.
Safety Note: Sam does not wear gloves even while working with NaOH powder.
EH&S Note: Throws the solution down the sink.


Feb 26

Astrobiology: The Search for Life on Mars


(for other entries in the Chemistry in Space series, click here)

This doesn’t exactly fit in with the direction I was planning on taking with the posts on space science, but a story on on Wednesday got my attention.  The story discusses NASA’s long endeavor into the search for life outside of Earth.  It used to be called exobiology (which I find to be an awesome name), but is now referred to as astrobiology.

NASA has previously attempted to find life on Mars with the Viking program in the 1970s.  Probes were sent to Mars to look for life… Earth life, that is.  The tests the probes ran attempted to find life that would exist at physiological conditions on Earth, a supposition that perhaps seems silly in hindsight.

An option in line with NASA’s recent change in direction could have the potential to bring Martian samples back to Earth for another attempt to find life on Mars.  The program – still in theoretical infancy – would last some 3-4 years and could begin in 2018 with sending a joint US/European rover to Mars to collect samples.  In 2020, a return vessel would go to Mars, get the samples, and return.

The story talks about the potential hazards of bring unknown astrobiological samples to Earth and the need to handle them in the equivalent of a Biosafety Level 4 Lab.

Anyway, my point in bringing this up is to share with you a short story – a commentary, really – by one of my favorite science fiction writers ever: Isaac Asmiov.  Asimov (also a former biochemist at Boston University) developed the Three Laws of Robotics and is the author of the original robot series that inspired movies such as I, Robot and Bicentennial Man.  If you haven’t read any of his work, I highly recommend one of his collections of short stories, such as The Complete Robot.

The commentary you should read is titled “Not as We Know It: The Chemistry of Life” and outlines what NASA scientists should keep in mind: life outside of Earth probably won’t look like life on Earth.

(in talking about life on Jupiter): An objection that might, however, be raised against the whole concept of an ammonia background for life, rests on the fact that living organisms are made up of unstable compounds that react quickly, subtly and variously. The proteins that are so characteristic of life-as-we-know-it must consequently be on the edge of instability. A slight rise in temperature and they break down.

A drop in temperature, on the other hand, might make protein molecules too stable. At temperatures near the freezing point of water, many forms of non-warm-blooded life become sluggish indeed. In an ammonia environment with temperatures that are a hundred or so Centigrade degrees lower than the freezing point of water, would not chemical reactions become too slow to support life?

The answer is twofold. In the first place, why is “slow” to be considered “too slow?” Why might there not be forms of life that live at slow motion compared to ourselves? Plants do.

He continues on to describe, in his opinion, what life might look like under the natural conditions of the various planets.  What the background medium would have to be and what the life-sustaining molecules would have to look like.  A fascinating read and a must read, in my opinion.

Feb 25

Peer review and the new media

I attended a Macintosh Users Group recently. (Yes, I am a Mac user.) This meeting was unusual. Natali Del Conte, a tech writer for CNet and CBS, was the featured speaker. She talked about being authentic, social networking, and how technology has changed how we get information. She argued that gone are the days that information is simply pushed to us and that Walter Cronkite is the most trusted name in news.

A detail I have come to think more about is what we know. I remember that stomach acid was thought to cause ulcers, but Marshall and Warren have received a Nobel prize for their discovery of the role of Heliobacter pylori and its role in peptic ulcers.

Mitch (Feb 08) and azmanam (Feb 02) have posted on congressional misunderstanding of science and false or poor science reporting, respectively, but I don’t think chemists are as cognizant of the accuracy or correctness of textbooks or peer reviewed papers. There have been a few cases in which errors have entered the chemistry world.

I wrote the the archivist at the Oregon State University Library inquiring about whether there was any correspondence regarding a paper Pauling published (there wasn’t). I wondered what the referees may have said.  Now, I have been thinking how this is like the comments to a blog post. One of the really interesting things about the new media, is errors can be pointed out. They can be argued and open to everyone.

I have been thinking about how our ideas of atomic theory have evolved. In doing so, I have been reading a fascinating series of transcripts from recordings deposited at the Center for History of Physics of the American Institute of Physics.

It was interesting that some people thought Niels Bohr had confused the literature with his papers. However, overall, what I liked was how these transcripts contained the personalities of the scientists, their interests, and in some cases their ideas (or biases) about topics being discussed. I felt these transcripts from leading scientists were like our modern internet (although generally without the details of the science).

Our modern internet has no rules. It can be difficult to sort out the wheat from the chaff. We need to learn who to follow and who to ignore. Peer reviewed journals only give the filtered result. The referees reports are confidential. Comments are not published except in blogs. Now that science is moving toward electronic publication, would a new model for scientific publication improve the scientific world?

Just to note that this is not unusual in chemistry. Organic Synthesis has long provided a kind of review for a select set of procedures. I don’t foresee H.C. Brown’s papers becoming ignored, but independent reports could prove useful. Similarly, critical steps to improving yields  would be helpful. You can find examples of this in the Organic Chemistry Forums.

Should online journals allow comments? Would it be useful? How could it be done? Would it be science?

Feb 23

Eating Carbon Nanotubes

Fathi Moussa

Lon Wilson

Last year I covered Khodakovskaya et al.’s paper regarding the benefits of growing tomatoes in carbon nanotubes (CNT).[CB] At the time I was concerned with the potential health risks associated from eating carbon nanotubes, but today in ACS Nano my concerns are alleviated. A paper from Lon Wilson’s and Fathi Moussa’s research groups discusses the effects from administering oral doses of carbon nanotubes (concentrations as high as 1g of CNT per kg body weight) to Swiss mice.[ACS Nano] The authors summarize their work the best.

CNT materials did not induce any abnormalities in the pathological examination. Thus, under these conditions, the lowest lethal dose (LDLo) is greater than 1000 mg/kg b.w. in Swiss mice.

So feel free to eat all the CNTs you want in lab, assuming they are not functionalized, you do it only once, and you limit yourself to single walled carbon nanotubes. I think partly because the results of the oral administration of CNTs went without any interesting side effects to present, the authors also looked into what happens when you inject CNTs into the peritoneal cavity of mice.

The image on the left is the control while the image on the right is 14 days after injecting mice with CNTs at a concentration of 1g CNT per kg of mouse. Although it looks sickly, the mice injected with the high concentration of CNTs did not die. Well…, not from the CNTs anyways.

Link to paper: In Vivo Behavior of Large Doses of Ultrashort and Full-Length Single-Walled Carbon Nanotubes after Oral and Intraperitoneal Administration to Swiss Mice (ACS Nano)


Feb 18

Wisconsin-Madison Lab Fire

A graduate student at the University of Wisconsin-Madison suffered burns and the loss of their favorite chair due to a fire that was started in the lab. A small lab fire usually wouldn’t make for interesting news, but see if you can spot something strange in the redacted narrative from the Madison Fire Department.

E4 found dry chem extinguisher activated, smoke, dry chem created haze on fire floor. found burned cushion chair in stairwell that was pushed there from room where reportedly students were working with chemicals that were spilled on to a chair that then started on fire. students came up with the idea to use a dry chem extinguisher as well as push the burning chair down the hallway to the stair well. It was reported to us that (deleted) was one of the students who was already at the UW hosp being treated for burns to his hand. E4 saw no one on the fire floor upon arrival.

The student took a burning item out of the laboratory and put it in the stairwell. A follow up revealed the student was worried about other chemicals in the lab catching on fire, but to the best of my knowledge most laboratories are designed to contain a lab fire. If the fire had gotten further out of control and caught the hallway and stairwell on fire, Madison might be missing a building today.

For future reference young graduate students the correct method for dealing with a burning chair in lab is the following. Rush to the safety shower and turn the flow of water on, then with a non-flammable object push the chair under the shower. Do not transport flaming objects outside the lab!

The chemical that started the fire was ethanol. Apparently the student was cleaning a pipette with an open flame nearby. As the student was shaking the pipette dry, a few drops of ethanol landed onto the chair and caught on fire.

The fire department received the call at 11:17 pm.

More media coverage: UW student burned in lab fire (The Cap Times)


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