Chemistry: The volatile profession.

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One of my department manager duties is to review resumes sent to colleagues in other departments. HR gets them and records them and distributes them for review. Earlier in the 1st quarter we had to review a large stack of resumes from well qualified people. Perhaps 4/5 of them were from people in industry who had been let go. For the most part the applicants were chemists from the pharma field. Most had quite impressive backgrounds with lots of publications, patents, and responsibilities. More than a few could have been my boss. It was a sobering experience to see so many good professionals on the street.

I have been in such a position in the past. It is disorienting and deeply distressing to be let go. It is not unlike a death in the family. When you are a highly educated specialist, your ego is unavoidably tied into your career. Your career is who you are. No professional job, no value. No worth.  Even more maddening, it is difficult to stay connected with the profession when you are unemployed. You are off the train and standing there looking at it while it rolls into the distance. And chemistry is not a field of endeavor for the unaffiliated.

I still think of my lowest point between chemistry jobs.  I was working in construction and had spent the day in a  dirt crawl space pulling wire for a remodel job. It was up high in the mountains in the winter and it was very cold.  At the end of the day I drove down the canyon into Boulder and stopped at a pharmacy to pick up some cold medicine for my kid. I had to ask the pharmacist a question, so I stood there in dirty coveralls and muddy boots and asked about the dosing of the cold med for a 2 year old.

The pharmacist seemed exasperated for a moment, but then composed herself and spoke to me slowly while enunciating her words clearly. Her, the supermarket pharmacist, standing there on the raised platform in her white smock. Speaking slowly, so I’d understand. Simple words so I wouldn’t be confused. Me, standing there in Osh-Kosh coveralls and a filthy insulated work shirt draped over my aching body after a long day of labor in the dirt. I was a 40 year old apprentice electrician with a chemistry PhD who had hit the bottom of the ego pit. Or, so I thought.

I accepted her advice politely. I paid for the med and walked out to my pickup truck. What resonated so deeply was the realization of how it is that we judge people by their appearance. My grubby appearance had caused someone to presume that I was slow witted and in need of being patronized.

I had supposed that after this dose of humility there was no where else to go but up.  But I guessed wrong. There was much more to come.  When your ego has been roughed up, it can become inflamed and hypersensitive. Your sense of proportion can be lost.

Being discharged from your place of employment is one of lifes big shit sandwiches. While most people will learn and improve from it, it will always remain a sensitive spot in your psyche. You never forget the circumstances. Being called to a conference room only to find HR there with a table full of handouts and forms to sign. The metallic tang in your mouth as it dawns on you what is happening. The grim warning that your termination “package” is valid only if you agree not to sue or publically criticize your ex-employer.  But you sit there with tunnel vision and listening impairment. You’re nervous system is electrically charged with panic and the instant, crushing worry about how you’re going to keep your family fed and in shelter. As you take the last drive home you’re mind is numb.

Behind most every resume I read is a story of long term success and a recent setback. For those freshly out of work, the contrast between the emotional high and low is staggering.  I understand somewhat of the plight and angst they are feeling. But, like someone once said, the only way out is through. You have to be willing to start over down the pecking order to recover your career. Sometimes further down than you want. The cherished notion of seniority is one that will have to be reconsidered.

I am starting to believe that this chemical unemployment wave is different. I think that we are seeing a phase change in how the chemical industry does business. The acceptability of outsourcing R&D is the reason for my pessimistic view. It has become axiomatic in many organizations now that R&D must be outsourced to countries where the overhead rate is substantially lower. And the outsourcing of R&D can only be bad for US chemists.

Euphemisms gone bad. The carrot and stick.

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Good lord. Do I have to explain everything??  It’s not “carrot or stick”. It’s “carrot AND stick”. The phrase “carrot and stick” is not meant to imply a choice between pain and pleasure. It is meant to suggest motivation by the placement of  a reward that is always just beyond reach. It’s motivation for donkeys, oxen, and the physics challenged. And the talking heads who read news in front of cameras.

This is what is meant by "carrot and stick"

Phosphate the Wonder Anion

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I thought it would be good to start the week by highlighting a particularly praiseworthy anion. That anion is phosphate, sometimes called orthophosphate, (PO4)3-.

So, you ask, what is so bloody interesting about phosphate? Isn’t every atom, ion, and molecule special in some way?  Well, yes, but phosphate is uniquely constituted to provide services in the critical area of genetic information keeping and functional group transformation (without Pd and boronic acids).

Here is the curious thing: Biochemical systems use phosphorylation and hydrolysis as a means of executing molecular transformation. Remember oxidative phosphorylation?  So, how is it that a phosphate moiety that is so useful as a leaving group or activator is also able to hold together DNA with such high fidelity?

Phosphate Backbone on RNA and DNA

In his much-referenced 1987 paper entitled “Why Nature Chose Phosphates” (1), Frank Westheimer observed that phosphate diesters have a very useful property as a linking group for nucleic acids. The charged oxygen on (RO)2P(=O)O- serves several purposes.  The presence of a charged linker renders DNA and RNA compatible with the hydrophilic environment inside the cell. The charge prevents the nucleic acid polymers from migrating to more hydrophobic environments found inside of cell membranes. And equally important, the monobasic anion serves as a kinetic barrier protecting the millions of phosphate linkages in a DNA strand from cleavage under neutral or basic hydrolytic conditions over the lifetime of the organism.

The hydrolytic stability of phosphate diesters is not to be underestimated. Westheimer points out that dimethylphosphate anion has a half-life of 1 day at 110 C in 1 N base. He cites the rate constants at 35 C for the saponification of (CH3O)2PO2- is 2.0 E-9 (1/mol sec);  (CH3O)3P=O is 3.4 E-4 (1/mol sec); and for ethyl acetate 1.0 E-2 (1/mol sec).

However, the very simplicity and current prevalence of phosphate ion in the environment does not go far in explaining how phosphate might have found its way into metabolic and structural use.  In prebiotic times, the occurence of phosphate is in doubt (2).  But not just the occurrence of phosphate is in doubt. The relative abiotic inertness of phosphate towards esterification and the formation of other metabolically useful species raises the question of the original oxidation state of phosphorus during the onset of early life.

While phosphate is found in certain meteorites, Pasek suggests that a more ubiquitous meteoric phosphide mineral species such as schreibersite, (Fe, Ni)3P, found in iron meteorites may have provided the necessary reactive precursors for metabolic evolution (2). Pasek cites growing evidence of a late meteoric bombardment period at 3.8-3.9 GA.

Schreibersite hydrolyzes to a variety of oxidized species including phosphite. Phosphite has the advantage of being substantially more water soluble than phosphate, providing a larger molar concentration in seawater.  Schreibersite reacts with acetate to form acetylphosphonate. In fact, a variety of organophosphorus compounds may be formed on exposure of schreibersite and its hydrolysis products with organic materials.

Lowly phosphate isn’t sexy like the newer anions triflate and BArF. But its seemingly mundane properties are key to the function of metabolism and genetics.

(1)  F.H. Westheimer, Science, 1987, 235(4793), 1173-1178.  (2) Pasek, M.A. PNAS, January 22, 2008, vol 105, no. 3, 853-858.

The Disappointment Locker

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Never have so many voted so overwhelmingly for so little as the members Academy of Motion Picture Arts and Sciences did for The Hurt Locker, this years Best Motion Picture.

Th’ Gaussling sat through a screening of The Hurt Locker last weekend. I must say that it was competently produced and directed. Without a doubt, the cast and crew did a fine bit of journeyman film making. However, an outstanding bit of film making it was not. It should have been titled Opportunities Lost.

What is so tragic about this movie is that all of the elements of an outstanding motion picture were there. An action packed setting, the threat of explosive death, flawed characters, intrigue, and comraderie. But somehow the director was unable to pull it together. Despite all of the raw materials available for a cliff hanger, director Kathryn Bigelow managed to patch together a picture that utterly lacks the fizz and crackle of a thriller. It’s as emotionally flat as a pancake.

Here is my primary beef with The Hurt Locker. It lacks application of the fundamentals of storytelling. While there is a lead character, the emotional hook that connects a viewer with the character is missing.  The viewers emotional connection to the lead character, Sergeant First Class William James, is lost through a series of missed opportunities. The director tries to paint this character as a man of steel or a “wildman”. But never convincingly. Even the attempt to hook you in with his half-hearted try to befriend a camp rat (an Iraqi kid) was botched.

The film makers tried to give this picture a documentary feel with the handheld photography. But it doesn’t catch. There are movies out there that use this method successfully- District 9, Cloverfield, and especially Saving Private Ryan.  But to do this successfully, in my opinion, the director must focus on a the characters.  One of the characters in The Hurt Locker was, by default, Iraq. But the development of even this “character” was poor.

To be compelling, the director must use some narrative trick to put the viewer on the spot with the characters. Either through a first person presence by a principle character as with Private Ryan, Cloverfield, District 9, or Apocalypse Now, or some other storytelling device like good character development on sympathetic characters. View the  Blackhawk Down and look at the difference.  In Blackhawk Down, there was better development of Somalia as a kind of character. It was not a sympathetic character, but it certainly had more depth.

OK. They did a few things right. They did not fall into the ridiculous cliche about the trick detonators. You know the scenario, there are many wires around the bomb and if the wrong one is cut, the detonator fires immediately. This is a regrettable dramatic device introduced foisted generations ago on ignorant audiences to raise the suspense level during the bomb defusing scene. Well guess what, audiences are still ignorant but at least the writer & film makers had some integrity this time. The EOD guy was portrayed doing the proper thing- looking for the initiator. That is where the drama is.

All in all, I would recommend viewing this movie if you have NetFlix so the financial investment is low. But I wouldn”t spend $19.95 on a DVD.

Zoning and Hard Times

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Many have written about the essential fragility of the economic situation of most American workers. We save too little and accumulate too much high interest debt.  Our consumption in every context seems unsustainable. The fragility of the monetary system with its lack of dependence on gold and the cosmic-scale debt that our country has racked up has many people worked into an existential lather.

The hard reality is that a worker can lose his/her job and all of the forms of stability that comes with it. We have become absolutely dependent on the economic system of the “employment” by people and organizations. We exchange our labor for payment on an hourly or salary basis and hope to sustain a stable and predictable lifestyle therefrom.

When a person loses their job, the reality of maintaining shelter and keeping everyone fed and clothed pops straight up into view. Because we have structured our culture and economic system on sustenance by employment, our ability to improvise is weak. Our ability to get another cashflow stream going is limited and most people pursue solutions that consist of finding other employment.

What workers in America lack is something that is available in much poorer countries. When an American worker loses their job, either they must find another job or start a business to sustain a living income. But if an American worker wants to start a business making something or retailing, chances are that local zoning codes will bar them from operating out of their home.

There are certain kinds of business activity that people can do out of their residence. Many people do office type work like accounting, consulting, writing, and other information intensive services out of a home office. Baby sitting, daycare, sewing, and small scale construction contracting are commonly based in a residence.

But if you want to repair cars, retail specialty parts of all kinds, or manufacture widgets at the microscale, chances are that your activity will be banned either by municipal ordinance or by a home owners association.

If you visit a city in a poorer country- say, Thailand- what you will see are large sections of housing where people combine their occupation with their residence. I recall being lost on foot somewhere in Bangkok a few years ago, wandering through neighborhoods where families lived in small shops that had a metal overhead door for street access by potential customers. At sundown, the shop activity ceased and the stove came out and a pot of soup was put on the heat. Fans, televisions, and music would blare into the sweltering streets along with the aroma of food.

Poor as these folks might be, they have something that American city dwellers absolutely lack. They have the ability to consolidate their resources to provide shelter and an income. By day a family might sell parts for small gas engines or some particular range of plumbing fittings. By night they repair to the back room for supper and relaxation.

An American facing the prospects of no job and left with only industrial skills is in a bit of a pickle.  While they might have very valuable skills, chances are that these skills are not readily transferable to common home-based activities. Someone with retail experience, on the other hand, might be able to put together a small shop.

What would stop an American city dweller from starting a home retail business is the issue of zoning and code compliance.  If an unemplyed person wanted to sell articles of clothing in a converted garage shop, there would be a long list of problems with the town board and the neighborhood. There would be applications and appeals, neighborhood input, and public hearings for a variance to the code. Zoning, parking, fire codes, and handicap access are just the start.

Then there is the matter of neighbors and their firm theories on property value. US culture has long been aloft on an arc of gentrification. People invest heavily in their homes and view their shelter not just as something that keeps out the weather. We festoon them from a vast array of manufactured decorative goods. We slather them with paint and adorn them with “accessories”.  

We have come to rely on our homes as repositories of personal wealth. And this notion, evolved from countless proposals before countless town boards, has become a complex web of building codes and ordinances controlling seemingly every degree of freedom to act that you can imagine.

Go to a town board meeting anywhere and look for those who seek to influence the board. Much of the time they are people related to real estate and development. Much of the gentrification we see has its roots with developers seeking to provide a sense of exclusivity. 

The result is that wealth creation by the appreciation of residential property value has been given a privileged position over wealth creation by the productive use of that property.

Our ability to sustain ourselves through hard times is constrained by rules to meant to protect property value and provide a basis for notions of the residential ideal. Americans are poorly prepared to be poor. We have an infrastructure that is not well adapted to allowing the unfortunate unemployed the option to scratch out a living from their homes. So pervasive is the residential ideal that the options for shelter are few in gentrified areas of the country. We have zoned ourselves into a corner based on bourgeois notions of aesthetic tidiness.

Gravity Anomaly Along the Colorado Mineral Belt

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The Colorado mineral belt (CMB) is a swath of metalliferous mineral veins and faults spanning 15 to 30 miles in width and running ~250 miles in length between Dolores and Jamestown, Colorado. This NE trending zone encloses most, but not all, of the significant occurrences of gold and silver deposits found to date in Colorado.

Significant finds like the Cripple Creek district have been found outside the CMB, but these are exceptions to the trend. The large gold/silver/tellurium lode in the Cripple Creek diatreme is the result of a volcanic past that stands somewhat apart from the vein deposition processes that produced the CMB lodes.

What is especially intriguing about the CMB is that it is coincident with a significant gravity anomaly. It turns out that a particularly deep negative gravity anomaly exists in the Colorado Rocky Mountains. A few papers on this effect can be found on the web. In particular, a paper (ref 1) by Mousumi Roy at the University of New Mexico offers some details on the  extent of the gravity anomaly and some possible reasons for the effect.

At first blush it might seem odd that a negative gravity anomaly should coincide with a region known for heavy metal deposits. After all, dense matter has greater mass per unit volume, and if there is a lot of volume, then one might expect the acceleration of gravity to be a tiny bit greater than some reference value.

While this line of reasoning has merit, it turns out that despite the presence of thin metalliferous veins in the region, the overall density of rock below the CMB formation is somewhat low. A density contrast exists in the CMB formation and the surrounding rock. A large, low density formation in the crust and/or upper mantle would cause the local acceleration of gravity to be slightly below that of the reference geoid value.  The structure of the density contrast is the subject of some scrutiny and has been addressed by Roy and others.

A large low density mass below the surface is expected to have some buoyancy. A buoyant mass is one that would exert an upward distortion on the crust. The Colorado Rocky Mountains are part of a region characterized by numerous past episodes of mountain building. Whether mountain building was the result of large scale tectonic interactions or more localized effects of density contrasts, the fact remains that a gravity anomaly exists coincident with the CMB.

The mechanical effect of the upthrust of the lower members of the crust to form the Colorado Rocky Mountains has been that a series of faults and fractures have formed. These void spaces have provided networks for the flow of mineral rich hydrothermal fluids over geological time.

High pressure, high temperature aqueous fluids are prone to cooling and depressuriation as they work their way upwards into cooler and less constricted formations. At some point these fluids throw down their solutes and suspensions in the form of solids that occupy the void network. Eventually the flows become self-sealing and circulation halts leaving veins filled with chemical species that were selectively extracted and transported from other formations.

The earths hydrothermal fluid system is continuously extracting soluble components and transporting them to distant locations where solubility properties force their deposition. But this process does not always produce solid, compacted veins. Void spaces can be left behind at all scales, from microscopic size to large chambers. These spaces are called “vugs”. Rock with a large fraction of void spaces is referred to as “vuggy”. It is possible to walk up to a mine dump in the CMB and find hand samples of vuggy rock. It is not unusual to find crystals of pyrite or other minerals lining the internal spaces of the vugs.

1.  McCoy, A., Roy, M., L. Trevino and R. Keller, Gravity models of the Colorado Mineral Belt, in The Rocky Mountain Region – An Evolving Lithosphere: Tectonics, Geochemistry, and Geophysics: American Geophysical Union Geophysical Monograph 154 (eds. Karlstrom, K.E. and Keller, G.R.), 2005.

[Note to the reader: Th’ Gaussling is just a chemist, not a geophysicist. But like many others, I have the ability to read and learn. When I learn something new and interesting, I like to write about it. It reinforces the learning.]

SF ACS Meeting, Not

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It has been 4 or 5 years since I have given a talk at a national ACS meeting. It was with great enthusiasm then that I registered and submitted my abstract last fall. There is not a lot we industrial guys can get up and talk about.  A few weeks ago I confidently decided to follow up on the disposition of my talk and was dismayed to learn that it was declined.

D’oh!!!

I am very disappointed. To my knowledge I followed all of the rules and chose a section that fit the topic.  While the ACS registration website does a good job of collecting your information, it is rather lacking in providing a means of feedback or status to speakers.

Since I have not yet been contacted by a human being, or an automated notification for that matter, I can only surmise that the theme of the section was a mismatch with my topic. Oh yes, I received a limp email “sorry” from somebody at the online help desk.

I wanted to talk about the unexpected energetic decomposition of a class of compounds and some DSC and TGA studies I have done.

Okay, I’m dismayed with certain organs of the Nat’l ACS and their inscrutable ways. But I am willing to admit that I missed some cue or other stagegate that kept me off the boat. But for cryin’ out loud! What was it?? Whose shoes do you have to shine to get an answer?

So, I’ll use the time to get more data and aim for the Boston meeting. A friend was helping with some Hartree-Fock calculations. I was able to correlate onset temperatures with certain periodic trends experimentally. Perhaps we’ll have a better theoretical understanding of the bonding issues by the next meeting.

Update.  Made contact with a person. The sections website is a bit lacking in detail, but with persistant surfing names and email addresses can be found elsewhere.

Antimatter Storage

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We had an ACS local section meeting recently in the clubhouse of the Air Force Academy golf course.  The featured speaker, a DoD chemist, gave an interesting talk on his work on some of the basic issues relating to the storage of positrons or anti-electrons. In the interest of fairness, since I am writing under a pseudonym, I’ll not wave his name about.

The speakers background is P-Chem and in particular, spectroscopy of isolated species in cryogenic matrices. He pointed out that an atom or molecule or cluster in an inert cryogenic matrix is in a dissipative environment and thus isolated from solvent interactions that might otherwise mask other kinds of phenomena.  So it is possible to spectroscopically examine the solid phase environment of the cryo matrix. In other words, an imbedded subject  molecule might find itself in an isotropic or ansiotropic environment, depending on the matrix. Infrared spectroscopy could give clues as to the symmetry of the local environment.

It turns out that ortho-hydrogen is an interesting matrix in which to study an important aspect of antimatter storage technology.  In order to collect positrons, one has to first find a source of them. While they can be supplied by some kind of nucleosynthesis, an easier route experimentally is to find a radioisotope that emits positrons.

It does not take too long for the would-be keeper of antimatter to move to the problem of storage. If you’re going to have anti-matter, you must think carefully about where you’re going to store it.  But there is another issue.  The challenge in collecting positrons from nuclear decay begins with slowing them down. As they are emitted they are travelling at relativistic velocities. Positrons, like “regular” beta particles are emitted in a fairly broad band of energies, so slowing them down via some kind of electromagnetic trap would result in very high losses. Instead, a moderator is envisioned to bleed off speed.

Positrons do not automatically annhilate with the first electron cloud they encounter. In fact, positrons were observed early on by the tracks of ionization they left in bubble and cloud chambers. So positrons can move through matter some distance without annhilation.

Electrons and positrons can pair up to give a transient neutral form of matter called positronium. There are two forms of positronium- singlet and triplet- with the difference being the relative alignment of their spins in either a parallel (triplet) or an antiparallel (singlet) arrangement.  Singlet positronium has the shortest lifetime at 125 picoseconds and triplet at a relatively long lived 145 nanoseconds.

Back to ortho-hydrogen. Positrons can interact with lattice defects in a solid, resulting in early annhilation losses. It turns out that ortho-hydrogen at 2.3 K can be warmed to 5 K and be annealed to a single crystal structure, largely free of defects. Therefore it is possible to prepare a solid moderator free of positron quenching defects.

This is where the speakers research stands at present. The have uncovered a potential positron moderator that would be part of a collection and storage system.  The speaker freely admitted that practical antimatter storage in a container is 100 years in the future. But given the high energy densities available from antimatter, the Air Force is committing modest funds to exploring the issues.

There is work being done to study the positronium Bose-Einstein condensate. It is complicated by the short lifetime of positronium. But fortunately there are ways of storing positrons in storage rings. The annhilation of positronium as a BE condensate would afford coherent 511 keV gamma rays. This would be the basis of a gamma ray laser.

Agilentus, Angry God of the Quadrupole

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I’m going home now.  Just spent a few hours trying to make a parameter change its state on the GC side of  my spiffy new Agilent GC/MS.  Modern instruments are a confederation of subsystems that must give a thumbs up before a software magistrate will allow the instrument to initiate a run. If it is a hyphenated instrument, then all the more so.  All of the flow rates and temperatures and dozens of software settings must be in the proper state before the method can be executed. 

One of the first things you learn after acquiring a complex piece of apparatus is that the help menu is limited in scope.  The mere definition of a mode or a key or a parameter is hardly enough when an annunciator declares that the boat won’t move because the flippin’ gas saver mode is on. The gas saver feature is meant to reduce helium losses from the splitter when the instrument is idle.  What is especially irksome is when an obscure  feature declares that it suddenly can’t  play ball on the (N+1)th run.

My assistant is a truly gifted chromatographer.  She learned analytical lab management in pharmaceutical cGMP and EPA lab settings. What she can do with GC or HPLC is a thing of beauty.  I, on the other hand, have become a grumpy instrument Luddite. It’s not that I don’t like chromatography. In fact I really dig it.  What I get grumpy and dispeptic about is having to claw up the learning curve of yet another software package and then use it enough to retain some kind of fluency.

So, in order to save face with my staff, I have to figure this thing out myself.  Modern chromatographic instrumentation is now configured around the needs of documentation requirements. Creeping featurism. Long gone are the days of sauntering up to the instrument and jamming a sample in it without having to answer a lot of irksome questions about method names and directory gymnastics. Software packages are designed to provide a robust paper trail on the results of all samples injected. It’s all gotten very “Old Testament”.

What is needed is a simplified mode of operation for boneheads like myself. For my process development work I just want resolved peaks, a peak report, and – please god- mass spectra of the components. I do not need a fancy schmancy report. I just need some numbers to scribble in my notebook and report in order to understand what happened in the reactor.

So there it is. A lamentation on chemistry.

Amine Question of the Day

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Here is an interesting question. What fraction of the organic nitrogen in your body is ultimately from the Haber-Bosch Process?  Any guesses?  This question arose during dinner discussion following a rousing seminar on frustrated Lewis pairs. There is no connection to frustrated Lewis pairs, but the speaker raised the question.

Oh, I don’t have an answer. This happens in science.  I’m guessing ~50 %, depending on the extent of protein containing corn products consumed. Any meat science people out there?