Category Archives: Science

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.

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?

8th Grade Science as a Path to Madness

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So it happens that my kid is in 8th grade and is studying chemistry for the first time in earnest. As luck would have it, the kid’s teacher is of Haitian extraction and is on some kind of leave of absence either due to illness or possibly because 3 family members perished in the quake. I don’t know. This fellow seems to be a good teacher.

His replacement, however, is not very good. In fact, his replacement is … awful.

For the first time, I had a serious discussion with a principal about a teacher’s performance. The principal is apparently aware of the substitutes classroom foibles and sins of omission. The principal’s own son is a student in that class and so he has a personal interest in the matter.

So, after some time with the kid at the whiteboard in our basement last night, it dawned on me that I had completely forgotten how utterly strange atomic theory and the chemical phenomena that derive from it really are. It is all quite abstract and maybe even a little weird.

The curriculum gives some emphasis to understanding the concept of pH. Alright. But this requires some ideas about logarithms and exponents. Then there is the matter of chemical equilibrium. While kids are wrestling with the math, you are also trying to tell them that only a very small number of water molecules actually come apart into ions. But the kids need to be comfortable with the notion of ions and charge.

But, what makes hydrogen ion different from hydroxide ion, really?  And why does hydroxide ion have the negative charge? How is it that acids corrode iron to form H2, but hydroxide does not? What does it mean to be an acid? What does it mean to be a base?

You can try to use structural models of sulfuric acid rather than line formulae like H2SO4 to appeal to the idea that these are little things with attachments that do things. One could argue that it is a bit more concrete that way- little structures with parts that are detachable. But as soon as you start drawing structures, you run into a rats nest of intermeshed concepts relating to bonds and lone pairs. Then there is the bloody octet rule, covalency, and orbitals!!!

For crying out loud!! How does anybody learn this stuff?? The learner has to absorb 20 abstract concepts almost simultaneously to begin to “get” chemistry.  Even worse, if a chemist/parent teaches the kid about a concept, almost certainly it will not mesh with curriculum, leading to confusion and tears for the teacher and the student.

I taught orgo to college sophomores, but evidently 8th grade chemistry eludes me. I’m just too dense to grasp the level of abstraction they will accept. Oh!  To have an hour with Piaget!

The Passive Aggressive Opera. Act I. Reverse Delegation.

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Supervision of people is one of the things that a chemist can look forward to on the way up the ladder. The people who report to you may be called staff or report-to’s. The term “my employee” should be reserved for use by those who sign paychecks. What ever you call them, they’re your group.

I’m not going to write about how to manage people. After many years of doing it I’m not sure I really understand it yet. All I can say is that every day some people show up and expect you to keep them busy.

Okay, I’m just kidding. But I am serious about the mysteries of management of people. I think most would agree that the best way to lead people- the way most of us would prefer to be lead- is by setting a good example. It’s pulling instead of pushing. Inspired leadership by a charismatic and talented individual is preferable but, unfortunately, rather unusual. 

There are many theories of management and more management consultants than you can count out there urgently interested in telling you how to manage your staff.  All you have to do to sample the many management theories is to stroll through the business section of the local bokstore. Every one of the authors will trot out a set of polished anecdotes that outline the path to their own professional enlightenment.

Chemists on the  management track may move in many directions in a business organization. Most obvious is management of a technical activity like R&D. But there is also management opportunity in scale-up, pilot plant, production, QA/QC, and analytical services activity. Management of the production side is sure to include inventory and warehouse control, regulatory affairs, personnel issues, engineering, and maintenance. Itis not uncommon for engineers to head the production unit.

On the less technical side is sales, procurement management, and business development.  While perhaps less technical, the chemical industry needs (requires, really) chemically savvy people to handle purchasing and sales activity. It is not uncommon for sales oriented people to ascend into the upper reaches of management generally and the chemical industry is no different.

What is perhaps different in the chemical industry is that chemists are often disfavored in the track to the CEO’s office by their lack of economic training. The ability to deliver big projects on time and on budget is a key attribute and engineers are especially well positioned to do this very thing. The bigger the scale of operations the greater the likelihood that an engineer will be in charge. Or so my experience has been.

Among those I have observed, managers who have exemplary experience in controlling the big money are often the ones groomed for executive leadership. And the big money is in big projects with lots of sales volume. It is the source of life giving cash. That which makes the corporate world go ’round. The elusive spondulix.

But back to management. One of the most vexing aspects of managing people is that you have to manage people. People are complex and prone to nonlinear behavior. Everybody knows this. But the manager is tasked with using human resources to provide some kind of work product on time and on spec. How do you compel people to do this every day?

The threat of termination is a good though heavy handed tool to compel folks to do their job. But this is a tool that can also backfire. Frequent termination of people is stressful and puts the manager in the position of having to be in a more or less constant training mode. Best to hire hard working people who are self-starters.

I have not found a simple formula for management. All I can do is to support down and fight up. I fight for resources and reasonable expectations. I treat people in the most hospitable manner I can muster and in return I expect the same.

One of the most annoying behaviors is the phenomenon of “reverse delegation”. You ask your report-to to do a particular thing. In reply you are told that they can only do the thing if you first make some arrangements. You have to get this or that ready, or perhaps you have to write an SOP or work instruction, or maybe even they will need to fly to a hotel in Vegas or Orlando to take some training course. It is all push-back: a kind of passive aggressive behavior meant to deflect your attention.

What I have found is that these reverse delegators may be very concrete in their approach to the unfamiliar. They will assert that they must possess a good deal of skill to even begin some new task. Sometimes this is true. But often it is only a matter of time on task to make some good progress.  The hard part for some of us is dealing with the simple truth of the matter. Not everyone desires being collegial and operating on the give and take level of colleague. A lot of folks only respect the brusque barking of orders by a Captain Bly figure and the sight of a**holes and elbows hustling in the plant. I would have been Captain Kangaroo, not Bly. It’s just a fact.

Keeping up with the data stream

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After many years of immersion in technical work I still marvel at how an organization can become mired in raw data. Smart people can easily succumb to the notion that data equals knowledge. Especially in circumstances where data is accumulated faster than it can be assimilated.

It is relatively easy to collect data in a chemical lab. You take a set of samples and prep them for testing, load the sample vials into the sample tray, and let the automated sampling widget move through its paces. In a few minutes or hours the software has accumulated files bulging with data points.  It is even possible to construct graphs with all sorts of statistical manipulations on the data, but still not morph the data into usable knowledge. I’ve been to meetings where graphs are presented but were not backed up with interpretation. What was the presenters point in showing the graph?

Computerized chromatography stations will spew data all day long onto hard drives based on selections from a cafeteria-style menu. With hyphenated instrumentation, an innocent looking 2-dimensional chromatogram is actually just a part of a higher dimensional data set with corresponding mass spectra or UV/Vis spectra.

The task for the technical manager is to get control of this stream of data and render some of it into higher level knowledge that will help people run the organization and get product or research out the door. This is the true work product of the experimental scientist: knowledge woven from a data cross-fire and supported by accepted theory.

I do not know what others do when confronted by a data tsunami. I can only speak for myself on this. When the data flow gets ahead of me, it usually means that I am spread too thin. It indicates that I am not taking enough time to properly devise experiments for maximum impact and am skimping on the analysis in favor of other duties.

Another issue relating to managing diverse data output is the matter of storing accumulated data and knowledge for easy retrieval. It is easy to throw things into folders and file away. But in a few months, the taxonomy used for filing a given bundle of data becomes murky. Soon, one is forced to rummage through many files to find data because you’ve forgotten details on how you organized the filing system.

There are ways around this problem. Laboratory Information Systems (LIMS) are offered by numerous vendors. A good LIMS package goes a long way towards managing data and distributing knowledge. We have a homebrew LIMS system (built in MS Access) that seems to work rather well for analytcial data. However, it was not constructed with process safety information in mind.

What I have constructed for my process safety work is an Access-based application that structures various kinds of information graphically into regions on a form. Within each region is a set of data fields that are subordinate to a given heading or context. The form is devised to prompt the user to consider many types of thermokinetic experiments and provides fields that are links to specific documents. The form provides both actual data and links to source documents. It can be used to enter data or to retrieve it.

This is what Access is designed to do, so I have described absolutely nothing conceptually new. Access allows me to aggregate related kinds of experimental results, reports (the knowledge part), and source documents in one field of view so as to allow the users visual processing capability the chance to browse more efficiently.

An example of “related kinds of experimental data” would be DSC, TGA, ARC, and RC1 reports. What connects these fields is the domain of thermal sensitivity of a compound or reaction mixture.

Another aggregation of fields would be the conditions related to an incident. I like to select key descriptors to an incident so as to aid in incident type studies at a  later date. It is useful to be able to sort incidents resulting from a blown rupture disk or a spill, fire, triangulated drum, etc.

A database is rather like a garden. In order to be useful it must be planted and then cultivated. Ignore it and it will lose its comprehensiveness, casting into doubt its continued use.

Next up is the development of an in-house Wikipedia style browser application for aggregating product, process, and safety information. This offers the best opportunity yet for making information and diverse data available to employees. It can be written in narrative form so as to impart knowledge and history. Why was a particular vendor chosen or how did we decide on that specification? What was the rationale for the process change in step 4.2?  The ability to explain and link to in-house source documents from a familiar and single point of access is key to potential success.

Phase Change for Chemistry?

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Disclaimer: Combichem or HTE is definitely not my area of expertise. It is, therefore, inevitable that I’ll say something blindingly ignorant about it. Despite my admitted ignorance, is appears to me that there is something happening, some kind of phase shift, in the small molecule discovery marketplace that is of general interest to the chemical R&D community. In fact, it may just be part of an overall change in how we do chemistry in general.

I’ve been hearing no small amount of buzz from chemists in the job market about the flattening or even downturn of US pharma R&D in general and of combichem or High Throughput Experimentation (HTE) in particular.  It is not that HTE is in any particular danger of extinction, but rather certain companies who offer the equipment platforms and tech packages seem to be evolving away from supplying equipment as a core business activity. Many of the big customers who could afford the initial cash outlay for HTE technology are doing their work in-house, dampening the demand for discovery services by HTE players at their aggressive prices.

One company I know has evidently shifted emphasis into the drug discovery field rather than try to continue marketing HTE equipment.  Near as I can tell, they are betting that having their own drug candidates in the pipeline is a better strategy than being strictly a technology or R&D services supplier. Time will tell the tale.

What the honchos in the board rooms of America’s big corporations forget is that the art they export so profitably was in all likelihood developed by people educated in US taxpayer subsidized institutions with US government grants. American citizens subsidize the university research complex in this country and by extension, supply a brain subsidy to industry. To export chemical R&D is to subsidize the establishment of a similar R&D capacity in other nations.  I think if you poll most US citizens, they’ll say that this is not the outcome they expected.

Software for HTE has become a derivative product that, for at least one HTE player, is proving to be rather successful. It isn’t enough to have the wet chemical equipment to make hundreds and thousands of compounds. You must be able to deal with the data storm that follows.

The business of HTE technology is evolving to a mature stage as the market comes to understand how to make and lose money with it.  There is always a tension between “technology push” and “market pull”.  It is often easier to respond to concrete demand with existing tools that to get new adopters to invest in leading edge tools to discover risky drug or catalyst candidates.

The extent to which the US chemical industry (all areas, including pharma and specialties) is outsourcing its R&D or simply moving it offshore is distressing. R&D is our magic. And promoting its execution offshore is to accelerate the de-industrialization of the USA.  It is folly to train the workers of authoritarian nations like China to execute your high art. American companies must learn to perform R&D in an economically accessible way and keep the art in-house. 

What makes R&D so expensive in the USA? Well, labor for one thing. In the end, our dependence on expensive PhD’s to do synthesis lab work may be a big part of our undoing. But there is much more to it than that. Look at the kinds of facilities that are built for chemical R&D. In the US and EU they are usually very expensive to build and maintain. Regulations and litigation avoidance are trending industry in the direction of ever more complex and high-overhead facilities in which to handle chemicals and conduct research. 

Then there is the cost of every widget and substance associated with chemistry. Look at the pricing in the Aldrich catalog or get a quote from Agilent. Have a look at the actual invoice from your latest Aldrich order and look at the shipping cost. High isn’t it? We’ve accelerated our demand for ready-made raw materials and hyphenated instrumentation. To what extent are we gladly buying excess capacity? Who doesn’t have an instrument with functions and capabilities that have never been understood or used?

It is possible to conduct R&D under lean conditions. But it can’t be done cheaply in existing industrial R&D campuses. Cost effective R&D will require a recalibration for most chemists in terms of the kinds of working conditions and administrative services they expect. But business leaders will have to recalibrate as well. Prestige can be manifested in product quality and a sense of adventure and conviviality rather than in an edifice. There are companies all over the world doing this every day. They set up shop in a commercial condo or old industrial building with used office furniture and grubby floors. What matters in chemistry is what is happening (safely) in the reactor. Everything else is secondary.

Mole Day Thoughts on Lab Life

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I have come to the realization that, after a career of avoiding it, I really dig physical organic chemistry. While I do have the synthetikkers love for developing a synthesis, I really enjoy taking the rare opportunity to do a focused study on a single transformation or compound.  It is a stylized form of play that any developmental psychologist would recognize. Discovery is about learning, just like play, and many of the exploratory behaviors observed in play apply just as well to discovery (well, except for hitting and crying).

One way a scientist learns is by doing a search for boundary conditions. Where or how in parameter space does a thing change? What is the best solvent for the desired outcome? What effect does stoichiometry have? Does dry, inert atmosphere really make a difference? What are the best leaving groups? Yes, it’s just research. But there is more.

In order to claim that you have expertise with a substance or process, you must have an understanding of how a process or substance behaves under a variety of conditions. If faced with a product that is off spec and the prospect of having to rework or remake, it is very helpful to understand what conditions lead to the off-normal outcome. Either the chemist sleuths each upset for a cause, or the chemist goes in the lab and purposely exposes the process to off-normal parameters and analyzes the outcome, or both. After a while, patterns begin to arise and trends become apparent. This is play.

Seems bloody obvious. But in a production environment the opportunity to explore  parameter space is often not possible. Favor almost always finds the more practical, though short term, fixes. Production managers are not always chosen for their focus on the long term. They are short term oriented- a necessary predilection for timely delivery of product on a tight timeline.

Part of a good process development program is a study of how the process behaves in various upset conditions. This is important for understanding the thermal safety issues, but it also is a good time to take snapshots of how the composition of the process system behaves when it is out of whack.  A reaction profile under conditions of reagent mischarges or off-temperature can give many clues as to the operating window of the process. It can also tell you something about the best way to do an in-process check and define flags for particular types of upsets.

Many companies do this, but a good many find a way to gloss over such work.

2009 Nobel Prize in Chemistry. The Winner is …

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I don’t have a clue who is in serious contention for the 2009 Nobel prize in Chemistry. Yeah, there are a bunch of old guys out there who deserve it. But who are the contenders this year? I have all but stopped reading C&EN and JACS, so I am unaware of who this years darlings of chemistry really are.

I’d really like to see Harry Gray share it. I’d like to see Whitesides and Bergman get a trip to Sweden as well. But I’ll admit that I’m well out of the loop. Any thoughts out there? I’m sure that I’ve slept through the discovery, development, and implementation of  several new disciplines, each with it’s own journal and series of conferences. It’s inevitable.

10/4/09.   OK, I’ll guess Craig Venter for Chemistry and Stephen Hawking for Physics.

10/7/09.  Wrong Again!!!! See later post for update.

California is on fire (again)

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The western wildfires currently in progress are having a huge effect on the clarity of the atmosphere here in the greater Denver area. The California wildfire in particular is discharging vast quantities of smoke into the atmosphere. Here, one thousand miles downwind, we are enjoying hazy days and spectacular sunrises and sunsets owing to the smoke in the air. Last night as the moon reached the meridian, it resembled a moon in partial eclipse in terms of the reddish aspect of its appearance. The long carbon footprint of California is casting a shadow upon us.