PhD Disease. Gaussling’s 2nd Epistle to the Bohemians.

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As I continue to cross off yet more days behind me in the great calendar of life, I am increasingly aware of just how truly strange and perhaps artificial my station in life is. Occasionally I detach my consciousness from the abstractions of my work and intellectual life and join those who live in the “eternal now” of daily life.  It is the world of real estate, car repair, and weeds. 

Having an advanced degree in anything marks a person as a kind of freak.  Not automatically in a pathological sense, though that is possible.  A freak in that to have gotten from freshman year through PhD is unusual in the statistical sense.  Not a large fraction of the population even try to do it.  To have done this is to be relegated to the far end of the bell curve by virtue of low frequency. 

Many people seem to be overly impressed by someone with a PhD.  To be sure, there are many PhD’s who are extraordinarily bright people.  But it takes more than just smarts for most of us.  It requires focus, tenacity, and endurance.  It takes a willingness to absorb abuse as well.  Getting through grad school has a large political component and a wise player learns how to negotiate with difficult people- advisors, post docs, and other faculty. 

Speaking only for myself, I have become quite aware that my path on this adventure will not be followed by any family members. My love affair with the science of chemistry is my lone passion and the wonders and elegance of its form cannot be fully shared with loved ones. That is a shame.

This lurking sensation of strangeness is especially noticeable at parties.  Say you spent the week trying to isolate a new product; noodled through numerous GCMS fragmentation patterns; or attempted to find meaning in the oddities of phosphorus NMR.  Suddenly friday night you find yourself at a party nursing a Fat Tire in a crowd where most of the people are in construction or real estate.  All of the conversations are about, well, construction or real estate. You find a friendly group and try to fit into the conversation. 

But here is the hard part.  You’re not running a construction site and you don’t deal with construction workers.  The price of copper pipe or the vagaries of the uniform building code have no impact in your life.  You’re just a freakish white collar worker who uses vocabulary that means almost nothing to nearly everyone on earth. You worry about selectivity, isomerization, and line broadening.  It really is a bit odd.

So, after you’ve made a few wry comments and patiently listened to the conversation, someone asks the question “What do you do?”.  This is where everything can fall apart.  You want to be accurate, but concise.  You can’t use obtuse language. If you are a synthetikker, you don’t want to say merely “I’m a chemist” because it is certain that the questioner will imagine that you wear a lab coat while you pour test tubes of “toxins” into the river to mutate the poor fishes.  And, for the love of god, you can’t let them think you’re an … analyst.  Good gravy, what would the neighbors think?

No, you say something to the effect that you make some product or other and it is used for ____.  This is that fork in the road that someone will take to get another beer or suddenly recognize some lost associate across the room.  Others will notice that something is wrong with their watch and pull out the cell phone to get the time, feigning discovery of a voicemail that they have to get. There many ways to eject from a conversation gone bad.  I have seen many of them and invented a few myself.

What I hate to see is the person who wears their PhD degree on their sleeve.  The blatant insertion of this status into the mix is like a turd in a swimming pool. Once it’s spotted, nobody wants to jump in.  For myself, I only use the title of “Dr.” in official company correspondance where I have to establish some credibility to weigh in on a certain range of matters.  Otherwise, I will admit that I have this degree only if people ask. The effect of title dropping on certain groups of people is that they shut down discussion when you walk into the room.  This is bad if the goal is to brainstorm or do a debriefing and the result is that people clam up. 

It’s best to let the strength of your arguments advance your cause. I don’t have a PhD in life- just a thin slice of chemistry.  And that slice seems to get narrower all the time.

Joe “Gumby” Lieberman

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America’s latest cartoon action hero, US Senator Joe Lieberman, has publically stated that the US should strongly consider a bombing strike against Iran as push back in response to their activities in Iraq.  Lieberman cites an estimate of 200 US soldiers killed owing to direct Iranian involvement.

Obviously Iran is up to trouble in neighboring Iraq.  Iran is a state with powerful ambitions and this troubles a great many other nations. It is also a state that has designs on installing Islamic government in that part of the world.  But … bomb Iran????  Didn’t we try that in Viet Nam and Iraq? What does Foghorn Leghorn Joe Lieberman think the Iranians are going to do the day after a night of bombing? Slap their head in V-8 fashion and sheepishly admit to the error of their ways? Does he think that we will face a uniformed Iranian army with armor and close air support?

Bombing Iran will unleash an epidemic of terrorism and anti-American fervor unlike anything we have seen in the past. And they will bring it to North America. 

Liebermans pronouncement on Face the Nation will be taken by Iranians on the street as further validation of the apocalyptic rantings of Mahmoud Ahmadinejad.  The US has been intervening in Iranian affairs for quite some time.  The US covertly engineered the overthrow of Premier Mohammed Mossadegh in 1953 and helped install Mohammed Reza Shah into power.  The Iranians know this and it has helped to instill considerable skepticism in their attitude toward all US actions, even the genuinely benevolent.

Why Joe “Gumby” Lieberman?  Because I have to believe that someone is moving his ams and legs into the pose he has taken.  Let’s hope that cooler heads prevail and that we exhaust other avenues before we fire any warshots in Persia. 

Scale-Up and the Three Pillars of Chemistry

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The practice of chemistry rests upon three pillars- Theory, Synthesis, and Analysis.  To bring a chemical product into the market place efficiently, a program of development must evolve that rests upon the three pillars.

Ostensibly, in order to rationally synthesize- that is, conceive of a new substance and design a means to bring it into being- it is advantageous to have some kind of theoretical background in order to take advantage of the orbital formalisms of bond making and bond breaking.  It is certainly possible to do chemical synthesis without even a clear notion of atomic theory.  William Perkin was able to embark on a synthesis of quinine and (end up with a synthesis of Mauve Dye) in 1856 without the benefit of molecular orbital formalism. Of course, if he had the formalisms and the analytical technology, he might have actually come up with quinine and would henceforth been known as the father of pharmaceuticals rather than the father of the synthetic dye industry.

I have been witness to numerous product development cycles in the fabulous commercial world of specialty chemicals. If there has been one underlying theme to all of this product development that I have been a part of, it is that synthesis development is typically years ahead of the analytical devlopment.  Allow me to elaborate. 

[Please note that I am not talking about pharmaceutical product development.  I do not operate in that strange universe and I do not pretend to understand it or even desire to be in it.]

Somewhere a company with lots of R&D money to spend and dash of vision will arrive at a stage-gate in its new product development.  A collection of compounds will be identified as having solid potential for use in a profit making chemical enterprise.  Project managers will have to decide on a molecule to launch the project.  The molecule can be a final product with a specific identity, or it can be a substance used to facilitate a technology platform.

The drivers of the project will invariably be synthesis chemists and engineers.  They may choose to make the molecule of interest in-house.  If the molecule or material is the product to be sold, they will almost aways make it in house to capture the economies of vertical integration and scale.  But if the molecule of interest is a reagent, catalyst, initiator, or specialized intermediate requiring some black art, the developers may choose to farm out the molecule. 

In the latter case of reagent, intermediate, etc., farming out the molecule to a specialist vendor requires that the company disclose the identity of the species and probably a synthetic pathway.  Like dogs sniffing one another, a customer and vendor will circle around each other for a short while trying to assess the merits of the relationship.  Once an agreement to move past the disclosure stage is agreed upon, the vendor will set upon the task of noodling out a process. 

I believe it is axiomatic that analytical culture is different from synthetic culture.  Analytikkers live in a world of validation, significant figures, calibration curves, error analysis, and standard test methods.  Synthetikkers live in a world of space yields, solvent effects, reagents, exotherms, hazmats, filtration, distillation, etc.  Each group looks at product development from a different angle and imperative.

Here is the point I wish to make.  Compounds that have been recently discovered and submitted for scale-up are very often “new species”. That is, molecules that are not fully understood in terms of stability, contaminant profile, and importantly, analytical signature.  It would be best to take the time to fully investigate the compound. But to fill out the data table on a species that may not actually go forward is to commit precious time in a very risky way.  Usually, it seems, a candidate for process development is minimally characterized and put on a frantically short timeline for commercialization. 

Another axiom: If there is a hole, someone will fall in it.  Scale-up is often the beginning of the period I refer to as FMD, or “Failure Mode Discovery”.  During this FMD period up to and including pilot scale processing, it invariably transpires that in-process checks and analyses of intermediates is complicated by the improper choice of analytical method and failure to characterize side products. 

In their frenzy to meet deadlines and goals, synthetikkers may not be able to complete a crucial aspect of their job.  That would be to form a complete understanding of the process.  It includes the identification of side products and the fullest characterization of the product as possible.  It is crucial to find in-process markers that indicate that a reaction is proceeding swimmingly or that it is going afoul.  I believe it is squarely the responsibility of the synthesis chemist to survey the composition of critical intermediates and the final product mixture. 

While the preceeding seems obvious and even pedantic, the cost pressures on new product development are often severe and accordingly, processes are rushed out of R&D without much attention to the analytical issues.  I have seen new products from some of the world’s greatest R&D groups hit with severe quality issues in commercialization because analysts weren’t brought in to help with the characterization.

Analysts frequently need input with the development of quality control test methods for new substrates.  This is where the synthetikker can provide the crucial input.  Synthetic chemists must be well versed in the Three Pillars of Chemistry.  We acquire a theoretical background to support our synthetic activity, but we have the critical responsibility of knowing a variety of analytical techniques to validate our assertions that we have made a particular molecule.

Many times in our haste to get a project wrapped up, we rely on NMR for primary analytical data. Very often, NMR is perfectly satisfactory as a stand alone spec, as long as you do not need reliable data below 0.1 %. 

But NMR doesn’t always tell the whole story.  In fact, I have often seen fellow chemists throw up their hands in a gesture of complete frustration and give up when NMR fails to afford a clue to a process or product problem.  Basically, NMR is fast and affords structural details that are unavailable any other way.  Everything else is a science project.  

Having served in business development and product management, I can testify that unforseen quality issues can become show stoppers. It is not unusual to spend as much R&D time trying to noodle out unanticipated quality issues as it took to develop the product in the first place.

It is good to have two or three ways to quantitate purity. I’ve found it useful to have a good relationship with the analytikkers- one that allows for brainstorming and problem solving. 

Contrarian Views on Corn-Based Ethanol

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If you travel through the American midwest, you cannot help but notice that corn-based ethanol is in the news. Over at the Oil Drum blog there is a good post on the merits of corn-derived ethanol (EtOH).  One of the important points that was made is that EtOH will be replacing MTBE as an oxygenating additive. This is an important point. For the near term, as MTBE is phased out EtOH is taking its place.  Therefore, the net effect on imported oil volumes may be nil. 

Then there is the matter of the energy balance for EtOH production.  There is no clear consensus on whether or not corn EtOH production is a net gain in BTU’s.  And then there is the matter of unintended consequences in shunting large mass flows of corn into energy production.

Modern agriculture has been characterized as the process of converting diesel fuel into food. High yield crop production also requires large machinery for efficient cultivation, soil amendments, advanced corn breeding, crop rotation, and specialized pesticides.  And this is just the farming part. Modern grain production requires substantial distribution infrastructure as well as financing for the upfront seed and fuel costs.

By unintended consequences the writer of the Oil Drum post means the possibility of ecological insult resulting from intensification of corn production.  Intensified corn production may result in reduced soybean production in the US, resulting in increased production in Brazil. US farmers may simply choose to grow fewer soybean acres. Increased soybean production in Brazil could result in accelerated deforestation to meet the demand uptick. 

What the writer did not mention is that reduced US soybean production could mean reduced crop rotation, placing increased demand on synthetic ammonia (NH3) production to make up the demand for fixed nitrogen.  Ammonia production uses natural gas (CH4) as the source of hydrogen, and the carbon is lost as CO2.  Increased nitrogen fertilizer use may result in greater run-off into the watershed, placing the aquatic ecosystem under increased stress and polluting drinking water supplies. 

Increased ammonia demand will stress the natural gas market to some extent and result in increased greenhouse gas emissions. 

In addition to ecological insult, there will be a shift of wealth associated with increased diversion of corn to fuels.  If corn yields and acreage cannot be increased to make up for increased fuels demand on corn supplies, the food product chain could be subject to greater scarcity with an increase cost to consumers for everything associated with corn- corn oil, high fructose corn syrup, starch, beer production (!!) with corn starch, cereal products, animal feeds and the associated price uptick that would cause for meat products. 

It is worth remembering that corn is one of the major inputs to our food manufacturing complex. It enters directly as whole corn or as separated corn germ and corn starch, and indirectly as food for hogs, cattle, and poultry.

Many of the choices we have in the supermarket are largely based on what you can do cheaply and on a continuous process basis with grain products.  Stress on this supply will be passed along to the consumer.

One fresh approach is from a start-up company called Zeachem who aims to produce cellulosic ethanol from biomass other than just the corn kernel.  In this process, all fermentable sugars as well as cellulosic hydrolyzates can be converted to acetic acid by fermentation and the lignin sidestream can be processed to yield hydrogen.  Esterification with process ethanol to afford ethyl acetate followed by hydrogenation yields EtOH.  This process is currently in scaleup and may prove to be a major improvement in the otherwise anemic economics of EtOH. 

Adventures with Chemical Customer Service

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For novelty I like to do raw material sourcing from time to time.  Trying to find exotic materials, equipment, or services is a sort of treasure hunt.  Like everyone else, I enjoy the thrill of the hunt and the satisfaction of finding a good buy.  What is striking is the great variation in helpfulness among customer service people.  Just today I encountered a customer service rep who was most helpful (Company W), and one who was, how shall I say, a miserable and unhelpful little snit (Company A). 

I’ll do a compare and contrast.  The helpful rep from Company W listened to my recitation of requirements and offered the best fit from their extensive collection of products.  We discussed the parameters and came to a conclusion. The rep offered to send a free test sample of product which will arrive by mail in a few days.  I’ll do a benchtop test and we’ll see if it works.

The insufferable snit from Company A listened to my requirements and, because I didn’t have a specific particle size to offer, just a SWAG (Scientific Wild-Assed Guess), was unable to make any kind of suggestion at all.  Because I did not input exact information so this person could go to an specific location in the table, the entire collection of products from Company A were made unavailable to me. 

I was shopping for filter media.  I’m interested in coarse, medium, or fine.  Because Company A offered 20 products specified to the nearest 0.1 micron, and because I could not offer an exact match, the Company A snit rep was unwilling (unable, perhaps) to help me make some educated guesses as to which product was most satisfactory.  What really irritated me was that there was not a smidgeon of help.  Just silence interrupted with staccato bursts of “I can’t help you if I don’t know the particle size…” from the other end.  Sigh.

You know, I have been filtering things since the early Disco Epoch, and until just today I did not know that ignorance of particle size was a show stopper.  

Thus begins the take-home lesson. I’ve spent many hours doing customer service, so here are some observations.  Very often a potential customer does not know what they really need.  Remember, there are wants and there are needs. They’ll call with some vague notion of what they want, but it might be very superficial.  They’ll pose and swagger like they know what they want, but chances are that they are fishing for clues from you, the customer service rep.

A good customer service rep has to know a great deal about the products and their typical use. A good rep will ask probing questions that drill into the customers knowledge and begin to find patterns and show stoppers. the good rep helps the customer sort between wants and needs. 

A customer service rep is also a sales person, whether that is openly acknowledged or not. The rep should try to find the best fit for the customer from the company selection of products. But now and then, the company may not be able to offer exactly what the customer needs and should just say so at that point.  The customer will leave with a good impression of the company and may return one day with a spec that matches your products. 

The rep from Company A did a disservice to his/her company by prematurely cutting off the shopping phase of my query.  It boils down to simple ignorance and the lack of basic curiosity.  There was no offer to ask someone else nor was there an offer of a reasonable substitute. They will miss out on a sale and will never know that their loss was self imposed.

Manson Impact Structure

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Visited the town of Manson, Iowa, today.  This is a farm community nestled in the flat, corn-carpeted central Iowa countryside. Manson is situated over an extraordinary geological formation that is completely invisible from the surface.  Also called the “Manson Anomaly”, this location is the site of a meteor impact ca 74 million years ago. The Manson site was originally thought to be the source of the K-T boundary, but now it is recognized to have been formed ca 9 million years prior to the K-T event. Approximately 130 distinct impact craters have been identified.

The formation contains many of the classic features attributed to an impact crater and it has been studied at length.  Fortunately, the library in Manson has a collection of literature on the formation as well as a collection of core samples from about 10 bore locations. 

The impactor is thought to be a stoney meteor approximately 2 km in diameter.  According to the Iowa Geologic Survey, the crater structure is 37 km in diameter and sits under 20 to 70 m of glacial till.  It is believed that the terrain was covered by seawater at the time of impact and that the crater was filled with water fairly soon after the impact. 

What is interesting for this writer is that the Manson Crater is directly under the place I lived as a child.  Who knew that under the plain, flat, farmland were the remains of a large-scale calamity.  Things are never as they seem.  That’s what I really dig about science.

Rootin’ Tootin’ Putin

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We’re approaching full circle from cold war to Perestrioka and collapse of the Soviet Union to re-ignition of cold war fires.  News sources are reporting bluster of the most serious kind issuing from Vlad Putin in response to plans by the US to place ballistic missile interceptors in eastern Europe. 

What motivates the Bush II administration to place anti-ballistic missiles and radar near the eastern frontier of Russia is a perceived ballistic missile threat from so-called rogue states.  The reality of ballistic flight is that missiles launched from the region of Iran will fly over southwestern states of the former Soviet Union (FSU).  In order to best detect and intercept such missiles heading for the EU, equipment would optimally be set up along the trajectory.  Within the logic of strategic planning, the site placement seems consistent with the goal. 

What is less than clear is the excuse for our ham fisted diplomacy with Russia.  Yes, obviously Putin is escalating the bluster and the tensions in a manner that is less than rational. But the decision makers in the Bush administration appear to have been asleep during the cold war.  Evidently the Bush administration didn’t consult with Russia in the run-up to missile site selection.  It was felt that as members of the EU, Poland and the Czech Republic were no longer part of the eastern bloc and therefore Russia’s input was irrelevent.  This was a whopper of a blunder.

The predictable result is that Russia is behaving like Russia, and, outwardly at least, the Bush people seemed slow to pick up on this.  Finally, Bush Jr. is getting some on-the-job-training in eastern bloc politics.

The confrontation with Putin and Russia has begun to spin into something that will force Russia to vigorously protect and promote its interests.  Putin is a lame duck and has to make some kind of stand to satisfy the quiet power brokers behind him.  They can’t accept the placement of ABM systems in Poland anymore than we could allow it in Cuba or Alberta. Doesn’t matter if the initial placement consists of “smart rocks”.  Any missile site can be quietly modified quickly.

There has been a disturbing lack of cultural and economic engagement between the United States and the FSU following the dissolution of the CCCP and the communist party.  This is unfortunate.  Western states should have made a more concerted effort to engage the FSU economically and socially.   

For its part, the US has been curiously lacking in interaction with or even simple curiosity in regard to the progress of the FSU states in their difficult period of reconstruction.  But I think that Russia has been characteristically distrustful of western intentions as well.  Historians will ponder this transition period in world political history and wonder how it could be that even though a society got to push the reset button, the best it could come up with was Putin and the best that the other states could muster was benign neglect.

Gaussling Off-line for a spell

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Th’ Gaussling will be spending a few days in a midwestern flyover state bounded in longitude by two rivers beginning with the letter M and in latitude by two states beginning with the letter M. This state’s name derives from the Ioway Indian word for “corn-fed” and produced a president named after a dam.   

J.Org. Chem. Git ‘er done!

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Citations taken from JOC, 2007, 72, 3981-3987, by Bruce Ganem and Roland R. Franke.

Where observation is concerned, chance favors only the prepared mind.  -Louis Pasteur

Necessity is the mother of invention.  -Anonymous Latin saying

Git ‘er done!  -Southern country male expression (recently popularized by Larry, the Cable Guy)

That’s hilarious!  I’m not sure, but this may be the first reference to a Comedy Central character in an ACS publication.  Well, I’m fairly sure.