Well, I knew I wouldn't be a big blogger. Let me update you on what has been happening (or not). In some ways, I too wonder, what the heck I have been doing.

I have been answering a lot of student questions on various web forums. This included my own. An additional word about this. My webforum was becoming heavily spammed and I wanted to cure that. I was looking for some phpBB hack that I could use. Long story short, my ISP was un-helpful, I changed my forum software twice and now operate with punBB. It hasn't been spammed yet and future is to install some hacks to moderate forum and block spammers.

Answering questions tells me two things. One, it tells me the kinds of questions or problems that students are having ... Read More...

How to Learn Organic Chemistry

I've put together a string of questions and answers in several email exchanges. You might want to skim over ... Read More...

Chemical Heresy

I have taken a momentary side track from editing "The Language of Organic Chemistry". I have created a presentation in which I have written out my thoughts on how atomic structure exists and reactions work. My next objective is to find an audience for it. It would be useful to have someone who is both critical and yet open-minded. I am interested in receiving criticism, especially where I may not have thought of something ... Read More...

Changes to AGOCM

This is what is on my mind. I was going back over the chapters and writing notes for changes, new reactions, errors, and notes that might be made.

One, in order to keep the changes orderly for owners of the book, I am going to create an update that contain only the changes. This will involve new reactions, changes to reactions, and errors corrected.

Two, I need to decide how many notes I am going to include. The book was supposed to be a workbook. It was never supposed to be an organic chemistry textbook. Read More...

Learning Organic Chemistry

I see a lot of people trying to find an easy way to learn organic chemistry. That is the main hurdle to learning, trying to find an easy way. If you wanted to learn to drive a car, but didn't want to actually get behind the wheel, it would be exactly the same. It isn't that learning to drive is so difficult, but if you never actually drove, you could logically complain about how difficult it was.

The analogy of learning a foreign language is also apt. The most effective methods ask that you ... Read More...

Update of A Guide to Organic Chemistry Mechanisms

I had created Adobe Acrobat files in December for each chapter of TLOC. When I did so, my objective was to put them in proper order and to protect them. I had begun to wonder why many people have examined the files for a few minutes and then moved on. Showing them the book is the best I can do. Why aren't they printing any pages? You really can't learn organic just be looking at a few problems. You have to do them. I don't see how people can do them without printing them.

So, tried my own site. I clicked on a page, but it wouldn't do anything. It wouldn't start Adobe Reader or anything. I went to Windows XP and it opened fine after entering my password as expected. I printed a page. Adobe Document Center logged the printing. This confirms that people are just looking at pages without doing any arrow pushing. Read More...

Future Objectives

I've been spending my time getting TLOC ready for publishing with InDesign. I've taken one part, extracted all of the graphics files, saved them in ChemDraw, exported them as EPS files, and imported the document into InDesign. I then manually replaced each low res structure with the corresponding EPS file. What really made this doable in a practical sense was to use Quickeys. I created scripts that would go through MS Word, find the structures, copy them, paste them into ChemDraw, and save them. This took about 1.5 hrs (I was away). When I came back, it was done. I created another script to open each file and then save at as the EPS file. That took about an hour. I struggled with creating a script that I could use to put the files into InDesign. I didn't really attack this with the idea of using a script. As a consequence, I partly made it more difficult than it needed to have been. (I just realized this now.). I ended up creating another script that would let me place each file where it needed to be and scaled it into the graphics box. This was part script and part manual. I did that in a few hours. So, I did most of the heavy lifting in much less time than I first imagined. More importantly, by using scripts, it save me a lot of trouble matching content. Whew.

While that task in being worked on, I really need to get back to remedying parts of my website. My Google ads aren't generating the specific click through rate I would hope for. Read More...

Skating on Lake Carnegie

We had gone out to do some errands on Feb 11. On the way out, I thought, "Wow, look at all of the skaters on Lake Carnegie." I didn't have my camera with me and I didn't want to push the patience of my wife. When we returned home, I grabbed my camera and went out and shot some photos. As usual, I didn't know what I was doing. It was bright and sunny and cold. I thought I need a wide angle lens to catch everything, wrong. This is one photo I took with a 135 mm lens. When I took it, I didn't think it was going to be what I was hoping for so it was the only shot I took like this. When I cropped it, it was just what I was looking for. To see an intermediate sized version, click here.

A Distraction

I went out and shot some photos of people ice skating on frozen Lake Carnegie in Princeton, NJ. You can find some of the photos here. (If you are interested in any or want to see a larger version, or know who is in them, contact me.)

Website Progress

                Ice skating on Lake Carnegie
How long ago did that happen before this year?
The back side of marketing "The Language of Organic Chemistry" is to convince visitors of its value. In order to do that, the website needs to rank reasonably high on Google's "organic" index. (This rates a combination of links, hits, and ??. Academic sites are rated more highly than commercial sites due to their greater gratis.) I have been checking this periodically and still find my website fairly low on their organic index. The path to improvement is to improve my content. As content can attract visitors and links, so will the organic index.

I have screen shots of nearly every page of "The Language or Organic Chemistry". My current project is to link those screen shots with the Table of Contents and the Index. The other side of this is to place metadata also into the pages (or perhaps to create individual .pdf pages) so Google can link directly to individual pages. In that way, if someone wants to find the mechanism for the Swern Oxidation, the link could take them directly to it. It is interesting that the Swern oxidation has the highest click through rate of my keywords. It doesn't provide the most impressions, but it does give the most hits.

I need to provide more opportunities to link to mechanisms (good content) in order to improve my Google organic rating.


A link to my ideas on electronegativity.


Publishing objective

      Nassau Street in Princeton
I stopped at the Princeton University bookstore. This is the reality they expressed. They only order books through the major distributors. If I want my book accessible on a large scale, I must register with one of these distributors. I had planned this, but this note makes it rather more imperative than I otherwise thought.
I have been experimenting with Adobe InDesign. I have a bit of a learning curve for using it, but I also have a problem with reformatting the chemistry files. InDesign requires an additional step. In contemplating how the book will appear, I need to determine the best way to do this. I have numerous smaller files in MS Word that print directly. This method was good because MS Word took care of some of the accounting, formatting, etc. To the negative, it was also true that MS Word limited some aspects of formatting. InDesign is different and can provide different solutions to those problems.

A third option is to use iWork Pages. Pages is in between MS Word and InDesign. It has a number of formatting options similar to InDesign and is more compatible with the ChemDraw files without creating an intermediary structure.

I'm currently experimenting.

How to learn organic chemistry

Ducks in Millstone River near Canal in Kingston
Why is organic chemistry hard? Your professor shows you a reaction and the product. Why not just memorize it? It is fast and easy. You know what the product is.

Does it matter if you don't know everything about the reaction? Let's say you are in a strange place and you ask for directions. The person giving them doesn't speak English very well. He knows the terms 'left' and 'right' are the directions he needs to use, but isn't sure which one is correct. Does it matter? Do you really have to know every word? I learned that while traveling to ask the person to also point in the general direction I had to travel. If you want to understand, you must know the meaning of every word. Just because you know the destination, does not mean you know how to get there. What if you don't know the exact destination?

Here is the problem. Organic Chemistry is like a language. It is easy to learn a number of phrases that one must use. Because it does not contain the complexity of other languages, students do not realize the importance of how reactions take place (the mechanisms). Furthermore, for a number of reactions, the mechanism may not be known. Therefore, the importance of having and using a mechanism is left out of many reactions.

As students progress, the number and variety of problems increase. Again, like learning a language, the phrases that were statements are now questions and mixed in tense. You need to know how words are used and varied. That is the difference between memorizing phrases and understanding the words. To understand the words is to understand the logic of the language. What is the equivalent in organic chemistry? That is how mechanisms are useful. They are the meaning for organic chemistry. They are the explanations of how and why electrons move.

How do you learn mechanisms? I found this to be easy for me. I knew I was going to be asked to solve a problem that used the mechanism that was being taught on a new problem. It was clear to me that before I could use that mechanism on a new problem that I had to be able to write it for an old problem first. Therefore, I memorized the mechanisms. I also found that as I memorized more mechanisms, they were similar to mechanisms I already knew. I started from a blank sheet of paper and wrote them out over and over until I could write them without any notes.

While I could encourage students to do as I had done, I quickly learned that my approach and abilities did not work for other students. What I learned that I needed to do was to go back to how a language is learned. You don't teach English to a child by reading the New York Times to him or her. If you did, there would be no context to the words and therefore no meaning would be acquired. In college, I learned French. In the class, they took phrases and gave us translations so we could grasp the meanings of the words. However, they also made us use the words in class. They varied the sentences so that new connections were created in our brains that allowed us to use the words in meaningful ways.

What "The Language of Organic Chemistry" does is to reproduce that process. The mechanisms are broken down into meaningful phrases. The different parts contain portions of the problems. Mechanisms are learned bit by bit. This is to teach the patterns of reactions because our brains are efficient at learning patterns. Finally, the book is laid out so you can make copies of pages because you cannot learn a reaction by writing the solution a single time. (On this last item, that was how initial versions of the book were created. However, it is difficult for me to predict whether I can or should maintain that format given the practicality of the publishing process. Furthermore, I had anticipated that an electronic version of the book would allow students to easily make copies of any page. However, if the book were released as an unprotected version, there would not be a book, but things change. Adobe has created a mechanism that allows me to retain control of the .pdf files. In that case, do we need the hard copy or does the hard copy need to be in a format that can be easily photocopied?)

Make individual chapter pdf files available for A Guide to Organic Chemistry Mechanisms

   Bridge over Millstone River in Kingston
Slowly, I am learning. I was experimenting with the Adobe Document Center yesterday. I can control the .pdf files individually. That is, I can specify who can see and print each file. That means that I can make individual chapter files available. So, anyone interested, look for the ability to access an individual chapter real soon now.

The marketing advice I found on the net suggests that I also start advertising on Google in addition to or rather than Yahoo. That, and to sign on with Lightning Sources, Inc., re-write the book in InDesign, possibly change page sizes (??), increase my organic forum contributions, I guess my work is cut out for me.

Update of A Guide to Organic Chemistry Mechanisms

I think I am arriving at acceptable web content. I did receive a question about putting some sample pages up. I had started doing that around Christmas, but I had wanted a more sophisticated way of doing it than just a string of pages. Read More...

Continued changes in website

Using RapidWeaver, I have succeeded in creating a basic website. I have two linked sites, one at CurvedArrow.com which has a sub-site phpBB forum dedicated to an organic chemistry forum. Read More...

Changes in website

Using RapidWeaver, I have succeeded in creating a basic website. I have two linked sites, one at CurvedArrow.com which has a sub-site phpBB forum dedicated to an organic chemistry forum. Read More...

How our brains work?

I was listening to Carla Shatz on http://www.twit.tv/fib10?p=0 . She was discussing her work on how the brain works.
Carla J. Shatz, Ph.D.
Department Chair and
Nathan Marsh Pusey Professor of Neurobiology
Harvard Medical School
“The human brain is the most complex computational machine imaginable. There are well over a hundred billion nerve cells and even more connections. It is this complexity of connectivity, and its precision that determines how the brain works. But how does this wiring happen during development? How do nerve cells know where to grow their connections? To what extent does the brain have to function in order to achieve its adult precision of connectivity? The major aim of research in my laboratory is to elucidate the cellular and molecular mechanisms that establish this precision during neuronal development.”
The above is from her website. She was talking about control of brain growth and development. About two distinct portions, one fixed and the other malleable. The fixed part is connections between the eye and the brain. It always happens. The other is influence by environment and changes with age. There are molecules that act as signals for connections and others that slow or stop growth. She was suggesting that if the brakes could be turned off, then functions lost through injury, a stroke, might be returned. (Not the memory contained in dead cells, but the ability of the brain to learn again.)
I have continued to feel that you and I, everyone needs to know how the brain works in order to find strategies that are best suited to using it.