Everyone Gotta See This

Truth, all truth.

http://www.pbs.org/kcet/wiredscience/video/82-dangerous_science.html

This is my story as well. If this were a religious evangelical meeting I would be on my feet yelling "Testify!".

I in fact have my own first edition copy of the "Golden Book of Chemistry Experiments"!

I in fact had my own "lab space" under the basement stairs in my parents house.

TESTIFY!

Research and Ghosts

So ... it's been a long time. I was pushed into a sabbatical, worked out an agreement with the family and a regional university that has me working in a nearby city, bought a broken down Kia Rio and got it working, developed an association/collaboration with a research group and started cooking up chemicals.

Research at the bench is what it always has been. Sometimes it is a visceral delight as the reagents combine into something new. More often than not the process involves taking pure, expensive starting materials and turning them into sewerage but that's the way love goes. Sometimes it is a grind to get through routine housekeeping necessary to keep a lab working. Sometimes bench research erodes the soul with countless small stumbling blocks that can stop a research program in its tracks. I have known them all in the last month or so.

The car has worked well. The driving has been fine since the trip from home to here is in my opinion a great little drive. The weather has been "tourist weather" (hot and sunny). So I leave the unplanned, garish squat of a community by an unloved river where I live and drive to an urbane and quiet small city with a wide beautiful river where I used to live. Why did I ever leave here?

Ghosts.

The research has gone pretty much as I expected. Slow, and at times frustrating. I was fortunate to stumble into a discovery that will allow me to look at some chemistry relevant to some aspects of battery chemistry. I am currently up to my eyeballs in various forms of oils that refuse to form solids let alone crystals. But it's the colour changes that jazz up my day. I have discovered a chemical reaction between two white compounds that have been known for decades and one of which is an industrial reagent. Not only that, the reaction features the combination of two white crystalline solids with a secret solvent and I get the brightest most interesting colours and colour changes (so far ... Blue, green, yellow (lots of bright yellows), orange and red). If I can determine what the chemical species are that are responsible for the colour changes I may just get into the inorganic textbooks after all. It looks like I will be spending the balance of my sabbatical doing ESR and Raman and hopefully X-ray crystallography. Why did I ever leave here?

Ghosts.

We had a water main break in the the basement of the Chemistry building two days ago. The water filled a room so that it was about a meter deep and the doors into the room could not be opened (genius designer had them all swing INTO the room). Not only that the only access to a shut-off valve was behind a wall in the room filled with water. Needless to say the lower floor (which includes the chemical storeroom) was inundated and they had to turn off the electricity to the whole building. We suddenly discovered that the fumehoods have an important role in making it possible to breathe the air and we all bolted for the nearest exit like a bad Mexican burrito.That meant that yesterday I ended up in the Engineering Library doing some long delayed literature work. After a long day of somewhat fruitful reading I headed out of the library and wandered around looking for a bathroom.

Ghosts.

In a random corner of a random corridor I ran into this picture ...

And this picture had this small detail ...

Kevin was a friend, a good friend. We went to school together, we worked together and we enjoyed each others company. He was bright and devoted to sports. We were both raised in a rural community where feelings were mostly repressed but I knew him as a sensitive and curious brother. We sort of drifted apart in University I went into science and he went into engineering but it was a measure of his ability that in a program where the "four year degree" took everyone five years to complete ... he still finished in four. I remember meeting him in the hallway of the Chemistry building the year he graduated ... we walked by each other and simultaneously turned and realized who the other person was. For fifteen minutes it was like old times ... but time had moved on and Kevin was anxious for work so he had decided to go into the Armed Forces. We talked about wives and babies and then the tide took us apart.

About a year later we heard that Kevin and some other students were down in a hole in British Columbia learning how to wire explosives. One of those "can't-ever-happen" accidents happened and some people died including Kevin. I went to his funeral where a doddering old pastor who didn't know him said some stuff that had no meaning to a young wife and daughter. We all cried at the outright wrongness of his early death. And then our lives moved on.

So here I am in this random corner of a random building crying again. That is why I left this place ... there are too many ghosts that can bubble up from my past and rob the precious moment of the present from me while I remember old wounds, words or loves. I have gotta go home and kiss my family and commit to living in the precious gift of the present. As long as I live, I will carry the memory of that last conversation. It is precious to me and, in reality, symbolized all the friends left behind while I was off chasing electrons. Rest in peace brother ... you are not forgotten.

A link to an appropriate piece of music for my mood.

You want the Chemistry? ... You can't handle the Chemistry!

OK I guess I need to provide some detail. I was a graduate student in an inorganic fluorine chemistry research group. We were investigating Main Group compounds that had inorganic pi systems created by oxidizing electron rich molecules using Arsenic pentafluoride in liquid sulphur dioxide.

The graduate student ahead of me discovered reaction 1. S4N4 is a contact explosive prepared from one of those classic fire from God reactions that were popular in the late 19th century. So you prepare the explosive and then grind it to a fine powder (grind gently because I was in a lab in England where a small beaker of the stuff spontaneously exploded and split a lab bench from end to end). You put the fine powder and some sulphur in a vessel with lots of sulphur dioxide as solvent and then add lashings of AsF5. About a week of recrystallizations later gets you to SNSAsF6 which contains the dithianotronium cation [SNS]+ (think ONO+).

Now SNS+ is a lot of fun but I discovered rxn 2. It turns out that SNS+ does not react like ONO+. SNS+ is a propargyl-allenyl 1,3-dipole favouring reverse electron demand cycloaddition reactions with pi bonds. Thus the reaction with alkynes gives the derivatives of CAT in high yield.

The hero of this story is the 4,5-bis(trifluoromethyl)-1,3,2-dithiazolium cation. I discovered that the reduction of this cation by sodium dithionite in liquid sulphur dioxide gives the blue gas radical in reasonable yield but the reaction works the best because the products are the radical, insoluble NaAsF6 and the solvent SO2. Laborious fractional distillation of the reaction volatiles give the black liquid referred to in the previous post. And I always wondered why the preparation wasn't repeated more often.

Thanks for the interest in the chemistry.

My Small Contribution to Compounds with Pretty Colours

It was the summer of 1984. I was in the first year of my graduate work and I was cleaning up a project initiated by a previous graduate student. I had come along at the end of his run and picked up the SNS+ reactions with pi bonds and had started with alkynes. I had prepared a variety of compounds using the SNS+ / alkyne reaction and they had worked well. My supervisor decided that I should go to England to learn how to do cyclic voltametry in liquid sulphur dioxide. That brought me into the sphere of a fragile, dedicated chemist of the collegial old school. It was in Durham that I was trying to do anion exchange reactions to get rid of the fluorinated anions so that the cyclic voltametry would work better (in fact the CV never did "work"). One day, late in the afternoon, I would wash a solution of the cation into a solution of potassium iodide and to my wondering eyes the whole flask filled with a pale blue gas. In my small area I knew all that had come before me and I knew that I had discovered something new. I was seeing something important for the first time and it was important and new not only for me but for my whole discipline. My real research career had begun.

It is still unique in my area of chemistry.

The product of the reaction was a radical, traditionally an unstable, reactive family of compounds with only a fleeting existence. In this case the heterocycle was stabilized by extensive pi delocalization and the carbon atoms were shielded and electronically changed by attachment to electronegative, kinetically stable CF3 groups. This also meant that the melting point of 12 degrees C resulted in a liquid with a significant vapour pressure at room temperature. This resulted in the blue gas.

I remember when I did the melting point. I had laboriously prepared the cation salt and reduced with huge excess of sodium dithionite and then fractionally distilled the volatile products three times to remove solvent and bi-products (which I would discover later to be the result of facile photolysis reactions). Then when I had grams of pure dark green black liquid I froze it and slowly warmed the solid in a Dewar until I reached the melting point. What
I was not ready for was the high volatility of the solid near its melting point and soon I had huge shiny blue-black crystals growing perpendicular from the side of the flask. They were altogether some of the most beautiful things that I had ever seen. I would spend a whole year of my life preparing and characterizing this compound. The last problem to fall was the precipitation of the photolytic impurities using a method I had stumbled across in an early JACS paper written by Speed Marvel in which he noted that he had precipitated polysulphide impurities with a catalytic addition of amine. I found a whisper of triethyl amine did the trick just fine.

And that is my coloured compound story.

Chemistry Labs and Teaching

It is a truth accepted by everyone that especially in Science principles and concepts taught in lectures are best understood by the student when coupled to a laboratory experience where the student not only has a "hands-on" experience with the experiment but also must grapple with recording and analysing the lab in the context of what was taught in the course. So we believe.

The horrible truth is that for the most part the link between lecture and lab is tenuous at best. In many places the labs are so de-linked from the lectures that the lab are offered as a separate course (although perversely in such institutions the number of credit hours required to graduate is increased for science students to the amount of lab courses). It takes a student with a vast memory and a strong desire to make the link to actually benefit from the lab in the manner which was intended.

And then there are the microlab enthusiasts.

Some time in the 1990's micro scale lab procedures swept the discipline. It was everywhere and the rationales were many. Smaller amounts of reagents meant less risk and the same pedagogical goals were attained. In my opinion the same goals were attained because the intent of the lab experience was lost prior to the change to microscale and its popularity was simply the result of pragmatic lab management and prescient students falling somewhere between mind reading and "Clever Hans". We who love chemistry all remember the astonishment and glee that we knew in our synthetic labs when the procedures "worked" and gave us handfulls of product with crystals that you could kill aliens with. Conversely we also knew the hot acrid taste of crystal envy or the shame of prep-TLC inadequacy. Not possible when you have a mini centrifuge tube and the positive sign of reaction is a decrease in transparency. No, it requires bulk, it requires amounts where static cling from the vessel does not retain more of the product that you can recover.

But, it is almost over and it will be soon. We could see it coming and those of us of a certain age will remember our chemical youth with nostalgia. This story has been making the rounds (first to my eyes by a citation from Derek Lowe of "In the Pipeline" commenting on this link).

In my opinion the liabilities, poor link with pedagogical goals and cost (of teaching, maintaining and disposing) of chemistry labs will bring their demise. There will be a transition period where we will rejig our labs to run on nothing but consumer chemicals and ethanol but that as well will pass because the waste will just cost too much to deal with (because the safety officer will not see how bleach in the lab could be handled like bleach at home). The bell will also begin to toll for university research chemistry labs as well. It may take longer but it will have to happen as environmental concerns and the power of safety officers approaches an absolute level. At least some of us were around for the golden age of teaching chemistry both in learning and teaching.

"Pull out the projector Tommy we are going to watch a video of a chemistry laboratory."

F. A. Cotton RIP and Textbook Selections

In the academic world there are three seasons. The teaching season is followed by the testing season which is then followed by the textbook season in an eternal hamster wheel of learning. Yeah I know, what about research? Research is not a season but a constant state of mind. Right now, it is textbook season and full colour encyclopedic texts with an average mass of 2.5 kilos are falling on my desk with the steady thump - thump - thump of the artillery rounds from Charlie that haunt my dreamless sleep. The organic texts are the worst. I can understand that general chemistry textbooks have to be generic clones of each other with an almost Bataan Death March one-chapter-a-week broad spectrum coverage of our ever widening discipline. But Organic Chemistry? Is it really necessary to show your typical 18 year old University student 1500 pages of organic chemistry, hike up our elasticized waistbands and proclaim (as if we are some latter day Hemingway) that since we were taught (somewhat indifferently) by I. B. A. Famouschemist that they as well would be best served by eating the whole banquet of organic chemistry as we did? Holy moly, no wonder they bolt for the nearest exit like a bad Mexican meal.

With that in mind I heard with deep regret that F. A. Cotton had passed away this past week. He was prolific, a generous and kind scientist that was not awarded the Nobel Prize in Chemistry because we were too busy awarding it to biologists. Some 27 years ago F. A. Cotton became Gandalf to my Frodo when the awe inspiring copy of his "Advanced Inorganic Chemistry" landed on my desk as the text for my second year Inorganic Chemistry Course. I was stunned. Not only that, Cotton was not the only required text. We also had to have a copy of Huheey "Inorganic Chemistry". It was felt that Cotton and Wilkinson was "too systematic" and Huheey was too "topical" so that a balanced diet of the two texts was required. To make us feel better it was noted that we would not be required to purchase any more texts for Inorganic Chemistry until we graduated after we had self sacrificially gotten through Moria, crossed the river, climbed the mountain, slain the monster and destroyed the ring (all metaphorically of course). I have to admit that having been through that system, my internal compasses all point me in that direction as well. I would love to choose completist and exhaustive texts for my students that would work for many courses. I remember, however, that I am teaching the average student, not the geniuses and the deadheads (they have their own fates independent of what I do). I select my texts for the student that needs the eat the elephant one bite at a time. It is my policy as well to carefully select my texts and follow them so that the student gets the maximum use out of their investment. Well I remember the horror of a course when the professor was forced to select a new textbook (because the one he carried with him on the Santa Maria had gone out of print). He made us all buy the new text but it was only half way through the course that we realised that he was lecturing and testing us as if we had his old textbook. Promises made in the crucible of that type of experience are what shape us as professors.


Sleep well, F. A. Cotton friend and guide of my youth. Your legacy and legend will continue, especially since we as a discipline have discovered the importance of branding. We will bring in ghost writers to revise your texts just as we have the other great, dead chemistry textbook authors. You may writhe in your grave with what they will write in your name but your name will go on.

Testing Cumulative Knowledge

"Education is what survives
when what has been learned
has been forgotten"

B. F. Skinner, Behaviourist

In the liberal arts it is assumed that the intent of both the student and the institution is the development of an educated worldview. A worldview that will be useful to the student in developing an attitude towards new knowledge and contextualizing life experiences. There is also an expectation that the education will be "useful" right out of the box. That expresses the hope that a graduate will have developed a mastery both of content (direct knowledge) and process (how to learn and teach).

In chemistry, knowledge is cumulative. Just as in a language, progress can only occur when the student has remembered the previous lesson(s). In fact, the language of science is mathematics (or more correctly the mystical symbols that we use to capture our thoughts about mathematical truths). In math, knowledge and content and progress are intimately linked in an upward spiral. As we fall way from the maths into the physical sciences and then the natural sciences or more observational sciences we begin to see the disciplines becoming so chopped up that it is possible to develop courses that are completely self-contained and there are no expectations of knowledge prior to the course and indeed no consequences to forgetting, after the course.

Into this tension between the global goals of the liberal arts education, usefulness and continuity of knowledge comes the physical sciences professor. When I started out, I taught at three different universities in four years and at each university they had me attend their "Teaching Essentials for New University Professors" full day symposium thingy. I went for the brownie points, free lunch and the chance to escape diaper duty for a full Saturday. Anyhoo, in all of the presentations it was made clear to us that a fair test only tested topics that had been clearly covered in the course and were completely covered in the supporting readings for the course.

In my courses, where there is a clear link to the content of a previous course (for example second year organic chemistry and first year general chemistry) it is my habit to have a mid-term test in the second week of classes. This mid-term will only test material from the previous course that is directly related to topics that will be taught in this course). In my opinion it gets all the students walking in the same direction, cleans up any differences between in-house and transfer students and it forces them to realize that there are some principles so fundamental that they form connections between prior knowledge and the current course.

For this I am constantly harassed by the students and my fellow faculty. In response, I voice the ideals that I used to begin this post. We have enough of a liberal arts tradition in our university that the ability to invoke the ideals means that I have thought this through and people will leave me alone. The only concession that I have made over the years is that I will have three mid-tern tests and will allow the student to have the lowest test mark dropped. Personally I think I caved on the ideal but there is a direct link between how a student does on the first mid-term and the final exam.

Teaching Female Students

The physical science blogosphere has been humming recently about the role of female students and faculty in the physical sciences.

It is an ongoing (and somewhat defining) issue with the blogs at FSP [Link] and Propter Doc [Link] but a recent confessional at a popular chemistry blog (The Chem Blog [Link]) initiated a wider discussion.

My history with female students and professors goes all the way back to when I started University in 1979. I was fortunate to fall into a group of students that was more than 50% female and while the larger fraction of my professors were male ex patriot Brits there was a significant and constant presence of female instructors and faculty in my academic life. It is true that in the Chemistry building I was there when the space crunch was so bad that they renovated a women's washroom for the office of a new male faculty member. In all my years as a male student in contact with female students it was my overall impression (from both observation and discussion with my fellow students) that the issue from their perspective had both positive and negative aspects. Chemistry, as I knew it, was enough of a meritocracy that intelligent, motivated women were encouraged by the same system that encouraged me.

When it came time for me to get a faculty position the difference became stark and clear. I came into the system when the hiring cycle was at a low and in all of Canada there were only eight positions advertised for my sub-discipline. In the competition that I won there were 56 applicants. It was clearly explained to me that up to the time that the Board of Governors signed my contract my job offer could be withdrawn if any equivalent female applicant from any country applied for the position that I won. The hiring pendulum was swinging strongly with a bias against my gender.

In that faculty position I found that the student evaluations were rather elaborate and involved a self description by the student. It was in this way that I found that I in fact had a significant communication problem with below average female students. I attended special professional development weekend seminars and presentations and eventually came to understand that the communication problem was due to my difficulty with stupidity. It turned out that the weak male students were used to being bluntly told in the public school system that they were going to fail if they did not change. The weak female students were not used to this message. Indeed, in conversations with some of them it came out that I was the first person in their entire life that seemed willing to fail them for not meeting a standard. Their interpretation of this situation was almost universally that I was going to fail them because I did not like them (not that they had not mastered 51% of the material covered). I was never able to bridge that communication divide.

My research group at that same time consisted mostly of undergraduate and graduate students with the post-doc du jour (I was never able to afford 2 at the same time). I always had a significant female % of my research group. What was very, very, very aggravating was that the female honours students I supervised all said they wanted careers in science and I cultivated them and published their work only for them all, yes all, to fly off the medical school at the first opportunity. Now all-in-all these women were vibrant, bright young women (I remember one that travelled with my research group to a conference and the night before she was to present her poster she "discovered" something called Electric Jello and she spent the morning wearing sunglasses and leaning on her poster ... she still got second prize for the best undergraduate poster ... remember that Chemistry is a meritocracy) and they are probably good medical doctors. My problem was that the most important thing I needed from my undergraduate students was not publishable research but for them to go from my group to the research group of one of my senior colleagues and thus build up my credit in the academic community. I will not say that I wasted my money but the benefits to my research were minimal.

I walked away from that faculty position (ironically the same year that I was granted tenure and promoted) to help start a new Science program at a small liberal arts and science University. The demographics here are probably typical for our type of institution (about 60+% female). It was my experience here that lead me to make the following comment on The Chem Blog when the women in science issue was broached.

"This issue needs to be addressed for more than just academic reasons of fairness of opportunity. Look at the demographics of your undergraduate programs our university undergraduate populations have become predominantly female (in some cases up to 60%).

It is not overstating the case that the modern University has got to be able to understand the 17 year old female student (to retain her until graduation). The modern university needs to create a learning environment that is welcoming to the young female scientist.

What your post in fact is addressing (somewhat obliquely) is a belief that academic environments and learning environments promote male OR female participation. I think that to an extent you are mistaken. There is enough of a meritocracy in what we do (that in my experience is gender blind) to allow anyone to succeed. It seems however that success is coupled to personality traits (ambition, stubbornness and self confidence) which some people (male or female) for one reason or another simply do not have. Every chemistry department that I have been in has the “Failed Genius Professor” that is so clearly more intelligent than anyone else in the department but for one reason or another the potential was never realized. We either have to change our definition of what it means to be a successful university academic or we change the system.
" [Link]

Distribution of Intelligence and Demographics

There is an interesting debate going on right now in the blogosphere over the writings of Charles Murray (famous for writing "The Bell Curve"). It is mentioned in "Confessions of a Community College Dean" (LINK) and in "Uncertain Principles" (Link).

Charles Murray claims the intellectual highground of the objective academic reporting the numerical results and deducing the rational consequences. By design or by mis-chance his writings come across as "stealth racism" and the intuitive hackles of many academics have been raised.

Murray has more recently been writings essays for the New York Times:

Murray Link 1
Murray Link 2
Murray Link 3

There is summary of Murray's position by Eric Johnson in the comments for the post in Uncertain Principles that to my eyes seems a rather dispassionate distillation:

"There is such a thing as absolute, objective, quantifiable intelligence (whether what we call IQ measures it or not, and whether it can even be described by a scalar period)

That intelligence is a relatively fixed quantity in any individual

That the distribution of intelligence is described by a normal distribution curve.

That the current political/cultural climate mandates an egalitarian approach to education that ill-serves all but the 40% or so around the middle of the curve.

That those on the lower end of the intelligence spectrum would be better served by an educational system that was less disparaging of 'practical' (i.e. 'vocational') learning

That the economic, cultural, and intellectual 'health' is in the hands of the relative few in the rightmost tail of the curve and that we should be doing more to ensure the vitality of this population in particular

That an egalitarian approach to choosing what to teach is detrimental. This seems to be a stab at the so-called multi-cultural, morally relativist, academic left's (straw-man) view that diversity is strength"

This is all a long set-up for my comment. The financial and political reality of the modern University is that in order to pay the bills all universities must enroll far more students than they expect to graduate. To my eyes the ratio of students capable of graduation to students that have been mis-lead into hoping to get a university diploma is about 1 : 1. This academic cannon fodder has the important role of keeping the numbers up in the University so that the students capable of graduation do not bear the financial burden alone. Until the system changes (and the only change that would address this issue would be the creation of an intellectual elitist University system where the education was free but the student would have to matriculate in) we have to realize that an important part of our jobs will continue to be:

a) accepting the intellectual tension of having a student body with a wide spectrum of intellectual abilities.
b) accepting the responsibility of respecting the weaker student but faithfully and gently failing them.
c) realizing that the time spent with a student that is failing and may drop your course is not "wasted" or "lost" but showing respect for the money they spent for their education and hoping that some knowledge will remain so that the general population will understand what we do.

Syllabi

There was a cogent post over on FemaleScienceProfessor a while back about the crafting of course syllabi.

Link to post on FSP

In our little school we are currently dealing with the issue of wireless devices and at this point the University is allowing each professor to set their own policy as long as it is clearly stated in the syllabus."

I was indifferent to the whole issue except as an avenue for cheating until I had occasion to sit in a large undergraduate class during a lecture where a significant number of students were "taking notes" on their laptops. I realized two things:

1) For the most part the students with computers were not using them to take notes but were engaged in email exchanges and surfing the internet. Several students were playing games.

2) It was not just the students with the computers that were missing the point of the lectures but there was a clear "Cone of Distraction" that spread out behind each student using a computer in class.

If you have students using computers in your class I strongly recommend that you simply place a monitoring camera at the back of the room to see if there is a problem. On a certain level I could care less about the deadhead student that chooses to ignore my lecture (although I honestly do not understand why such a student would bother to come to class where the attendance is not recorded). My concern is the weak to average student that is easily distracted by the computers.

I know that this will place me in the Luddite / dinosaur class of professors but this is what I have in my syllabi now:

"Course Policy on Wireless Devices: The nature of the course content and the evaluation of the individual students knowledge requires that this course have a strict policy on wireless devices (laptops, cell phones, PDAs, handheld computers, pagers and all similar devices). In general, students should not bring wireless devices to any class, tutorial, laboratory or examination. Students found to be in possession of a wireless device during a quiz, test or examination will be given an automatic mark of 0% on the quiz, test or examination even if the device is turned off and a subsequent examination of the devices connection log reveals that the device was not used during the quiz, test or examination. This policy will extend to all students in a group that include a student found in possession of such a device (where they are being evaluated in a group activity). Exemptions from this policy may only be given to students that have a documented reason for requiring the device. Such exemptions MUST be granted before any device is brought to a course evaluation event."

The Problem of the Modern Science Student

"Education is what remains when what has been learned has been forgotten"
B. F. Skinner


Students that are the product of the modern education systems almost all suffer from the same problem that continues through their educational career up through University. They have all been carefully taught that there are no consequences to forgetting material that they have learned.

Almost all the public education models build up the student as a person by affirming that what they have learned is sufficient and that large concepts can be broken down to testable smaller concepts. Such education models have effectively produced legions of students that are like computers with huge RAM memory but tiny hard drives. The consequence is that they can memorize huge amounts of information for short periods of time but they can also completely forget the information when they "turn off the computer".

Thus, any topic in which knowledge is truly accumulative, where the degree depends on a sequence of courses that require intimate knowledge of material previously taught, will be left only to the naturally adept. These programs, such as the languages, mathematics, engineering and the physical sciences will all suffer (and are suffering) not because they have somehow failed to adjust their programs to fit the new students but because the actual nature of what graduates must know cannot be negotiated.

It is my opinion that interest in Chemistry has not decreased but the disciplined / trained ability of students to accumulate content / knowledge has eroded. This more than anything else results the in the dramatic drop - fail rates in our introductory courses.