The Squamous Chronicles. Going down the rabbit hole.

A month ago I went in for some surgery to have an enlarged lymph node removed from my neck. During the procedure a pathologist examined the excised node and determined it had cancerous squamous cells in it. So, the dissection was expanded and the ENT surgeon removed 32 more lymph nodes, all of which were clean. The lymph node was a secondary tumor with an occult primary. Thus begins my journey to find the primary.

Being new to the cancer industry, I have been trying to find a high point above the thicket to get my bearings. Here are a some early observations from down the rabbit hole.

• The cancer industry is spread over the landscape in many forms, all boasting of individual care and of powerful means of treatment.
• Cancer treatment seems to be partitioned into three domains- surgery, radiation oncology and “medical” oncology, meaning medicinal treatment. These domains are further subdivided into groupings that specialize in particular body parts or particular modalities of irradiation.
• An oncology department can consist of as few as a couple of docs and several PA’s or nuclear medicine techs.
• An oncology department can be rather large at a university hospital with docs serving in the role of professor, researcher, and clinician.
• If you have a hammer, everything looks like a nail. There seems to be a little of this inclination in medicine. This is understandable. Clinic payroll has to be met and the payment on the CT scanner has to go out.
• There is no “undo” button for a large radiation dose. The option menu is restricted for previously irradiated tissue.
• It is important for the pathologist to determine if the squamous cell cancer is of the HPV type or not. The outcomes may be different.
• “Cure” means 5 years of survival.
• CT scans are used to position the patient in the irradiation device in order to aid in precise dosing of the desired tissues.
• CT scans are superimposed over 18F PET scans to correlate metabolic hotspots with the affected anatomy. Expect a lot of CT scans.

Minutes after the PET scan was collected I walked out to the car and switched on my Geiger counter. I was hotter than blazes. Realize that with the penetrating power of 0.511 MeV gammas and 2 gammas with reciprocal trajectories per 18F decay, the GM counter was understating the activity. I watched the decay rate taper off substantially after ~20 hours. The rad tech injected 15.4 millicuries of 18F glucose into my veins. A day later I was at approximately background by the GM counter.

A person with cancer has to consider that they have a disease that they must shop around to the cancer industry. There is no substitute for background information in this arena. If you indicate to the physician in the consult that you have some rudimentary knowledge, they may be more likely to avoid poor analogies and misleading or confusing expectations.

The first doc recommended 68 Gy of radiation to a suspected hotspot in my throat. She also recommended simultaneous chemo (cisplatin) to take advantage of some kind of synergistic effect.

I’m presently working on getting a second opinion on radiation and drugs. We’ll see what happens next.

Ice stalks. A winter oddity.

Yesterday I placed clay sorbent granules on my steep, north facing driveway to add some friction so the car and visitors can negotiate the grade in the snow and ice. The clay granules are used for absorbing oil and are similar to cat litter. I used the granules because I did not have sand.

Ice stalk formation. Note that many of the clay granules have been lifted by the slender stalks of ice. Copyright 2013 Th’ Gaussling.

The granules were deposited on freshly shoveled concrete with just a thin layer of clear slush. I would estimate that, overnight, the temperature ranged between 25-32 F. In the morning, the 1-5 cm stalks of ice were observed only where the granules were deposited.

The slender stalks were capped with flat, irregular plates of ice.  Many of the stalks had lifted granules off the ground. Most appear to have arisen from the granules. Obviously, the process forming the stalks lifted some of the granules and ice vertically. Curved ice stalks appear to have extruded gradually from the granule and, under the influence of gradually shifting cover of snow or other ices, have extended produced a curved shaft of ice.

The granules are manufactured with absorbency in mind.  In this circumstance, I will hypothesize that capillary action pulling liquid water from the concrete surface is delivered to the upper surface of the granule where it freezes at the air/water interface by evaporative cooling. Why it doesn’t just stop is puzzling. Perhaps the action of freezing at the granule upper surface reduces the vapor pressure of water enough to induce a small pressure drop through the pores of the clay that draws liquid phase to the surface where is freezes continuously. The heat of fusion at the surface may be sufficient to prevent freezing of the water within the pores of the granule in the subfreezing range of the air and shutting the process down.

This is a very curious type of ice formation, one that I have observed on two separate occasions. This is another odd thing water can do.

Priestley Medal 2013

Congratulations to Professor Peter J. Stang on winning the 2013 Priestley Medal. The C&EN bio at this link reveals quite an interesting career.

Oh, by the way.  Am I the only one to notice some faint resemblance between the Medal winner and Ambassador Sarek from Star Trek? Face it. Being a JACS editor is about the same status as an ambassador.

Well, it depends …

Getting technical people to offer insight and advice can range from simple to vexing. Following a recent purchase of an unusual type of spectrometer we found ourselves in need of advice regarding consumables and sample preparation. Going into this installation I believed, naively, that our set up to operate the new instrument would be eased by patient advice from the seller.  I was mistaken.

I could whine on about deficiencies in this or that, but instead I’ll get to my point. Consider the following exchange-

Q:  What sort of electrode should we use to run this mineral sample?

A:  Well, that depends.

Q:  It depends upon what?

A:  Well, it depends on the type of matrix you have and the concentration of the desired metals.

Q:  How do we decide on what kind of electrode to use?

A:  We do not have experience with that element or that matrix. And there are many kinds of graphite widgets, many for specific uses. The widget company did not return your email because they are small and would prefer to talk to their customers.

Q:  So, how do we get started?

A:  You’ll have to prepare bracketing calibration standards that match your matrix as closely as possible.

Q:  What can you tell us about buying or the preparation of calibration standards? Are there any special materials we can use as diluents or any preferred methods?

A:  There are no manufacturers of these solid calibration standards anymore. We bought out the inventory of the last one.

Q:  So we can compound our own standards at concentrations close to the spec of the inventory you hoarded bought out?

A:  Well, yes, I suppose. It depends on your capabilities ….

And on it went.  Eventually we extracted the information we needed and are moving forward.

Here is my point. Everything “depends”.  A little louder.  EVERYTHING DEPENDS. For crying out loud!  This is one of the fundamental theorems of life. We technical people have to get past this barrier when a questioner asks for help.

A few sentences of advice-

On the assumption that everything depends, offer a hint to the questioner in the form of a range of possibilities. Open with insightful examples or a recitation of common practices. Do not sit there, Sphinx-like, while the questioner sputters and struggles with finding the best questions. Offer some guidance by way of general performance boundaries.

The technical service folks we spoke with were very much in the quandary of Buridan’s Ass. In this fable, a donkey was in between two identically appealing piles of hay. In the end he starved to death because there was no good reason to pick one over the other.

In the case of the tech service folks, one pile of hay was to offer zero advice and make no errors. The other pile of hay was to offer frank advice and satisfy the customer. Having been in this position, I know that offering advice has it’s appeal, but it may be fraught with liability. Telling people how to run their equipment can have negative consequences- thus the reluctance to speak. But sellers are there to service their customers. They should use words and pictures to help their customers get started.

The thin blue line

I had the opportunity to take a ride in a CT scanner yesterday. It was my first such experience. It’s a great opportunity to pick up a few milliSieverts if you find yourself short in the ionizing radiation department. The particular device I refer to spins a helical beam of x-rays through you as the platform moves you through the big donut with its rotating source and detector.  Through the magic of the integrated circuit and millions of lines of software code the computer reconstructs images based on extinction of the x-ray beam as it careens through your tissues.

During this wierd little Roentgen ride I had a peculiar experience. After the iodinated tracer injection the radiologista trots around the shielded wall, clicks “go” and the sequence takes off. As the beam was scanning from head to chest I had the distinct sensation of a horizontal thin blue line in my visual field for just a beat. Because my eyelids were closed I was not seeing a focused image through the lenses of my eyes. Against the backdrop of latent images slowly fading from consciousness there appeared the line. I was not thinking about this at the time- I was focused on obeying the breathing instructions.

My theory is that the visual stimulus was the result of the x-ray beam inducing a bit of fluorescence acreoss the width of my retina.  There are plenty of pigment molecules in the retina as well as the tracer compound coursing through the retinal vasculature.

Question- Has anyone else had or heard of such a phenomenon?

A splendid iridescent grime

While sitting at a stop light this morning, facing south and bathed in the low morning sun, I happened to notice an interesting thing. The sun was a palm width above the horizon and admittedly a bit of a driving nuisance. As the radio droned on I absently squinted toward the east. Just then I became aware of a thin layer of mist-deposited road grime clinging to my driver’s side window. It was alive with thousand’s of faint but unmistakable points of diffracted sunlight. The thin gray layer had an overall iridescent aspect to it that I had never taken note of before.

As I pondered the spectral beauty of this I became aware of an alarming noise. The driver of the white Ford F-250 behind me was waving his hands and honking without the slightest consideration for the unlikely phenomenon I was enjoying. The enchantment vanished as quickly as it appeared as I motored into the intersection and the beginning of the day.

The Company Joules

We will soon have a new HEL Phi-TEC Adiabatic Reaction Calorimeter up and running. Hopefully this will help solve some nagging questions I have about the thermal stability of certain compounds. Time to maximum rate (TMR) is a useful parameter and ARC testing helps to find this value.

I have spent  a good deal of time with the Mettler-Toledo RC1 and have found it to be very useful in process development. There is a tendency for chemists to design exothermic reactions to start at low temperature and at perhaps some point raise the temperature to take the reaction to completion. The RC1 will indicate accumulation of energy in a vessel following a charge. By varying the temperature of the reaction mass and modulating the dosing rate it is possible to find a reaction temperature and feed rate that affords a steady state (or manageable, at least) output of power with minimal energy accumulation.

With the reactions I have been studying it has become apparent that sometimes a preference for low temperature (-30 C to 0 C) by the chemist may in fact be based on habit rather than need.

Naturally, the thermal picture is not the entirety of the problem. Product stability in the reaction mass and residence time at temperature play a role in how the process is configured. But a reaction calorimeter can help find threshold temperatures below which the reaction substantially shuts down.

The RC1 measures heat of reaction in Joules and power in Watts. After some time on the instrument one comes to view a reaction mass as a power generator or an absorber. Power is reported in Watts and is indicated by the magnitude of the deflection of the power curve from baseline.  Joules of energy are calculated from the area under the power curve.

The instrument has a calibration routine where it determines the Cp of the vessel contents. If you have the reaction mass, heat of reaction, and Cp, you can calculate the adiabatic temperature rise for a given dose of reactant. This is an extremely useful element in sketching out the safe operating parameter space of a reaction.

Safety is a political concept. Safety has no basis in physics. It is an artifact of anthropology. It is a fuzzy construct defined by a magnitude of ”likelihood” and type of consequence individuals and organizations are willing to absorb to obtain a particular outcome.  But when you sit down in a meeting with thermokinetic data and solid interpretation, all of the stakeholders in a plant can brainstorm and home in on a fairly rational and agreed upon process profile. This is politics at its finest- data driven and substantially rational.

Is lifting combat restrictions on women the achievement we need?

I am torn on the matter of Defense Secretary Panetta lifting restrictions on combat duties for women. I understand the rationale for greater upward mobility for women in the military. And I grasp that women are already operating in combat areas.

The point I want to offer is this:  rather than broadening the range of the population who may be exposed to combat, perhaps we should put as much energy into demilitarizing just a little bit. If bringing women fully into combat is a solution, then maybe we do not understand the problem.

As an advanced society the USA should be striving to avoid the production of disabled combat veterans. Could it be that we should engage in less combat? Isn’t that the solution we should be seeking?

Right now the USA is so heavily armed with kill-at-a-distance lethality that we have become at ease with radio-controlled diplomacy.  When you have the US arsenal in your pocket, everything looks like a helicopter landing zone.

There is so much money to be made in plundering petroleum resources abroad and in military armaments and materiel that a persistent and refractory global sub-economy of state-protected mineral extraction has frozen in place. With every kilowatt of new load connected to the power grid and with every clever new military toy that is invented we tighten the spiral toward a global energy war.

Where does this new load come from? All of the microprocessed consumer devices certainly contribute. All of the wall-wart chargers for cell phones, iPads, laptops, etc., put stress on the power distribution system and in due course create demand for fossil fuels. This demand is manifested in several ways- 1) electric current to power the devices, and 2) all of the upstream power needed from mine or wellhead to produce ultrapure gallium, arsenic, tellurium, silicon, aluminum, titanium, boron, polyethylene, polypropylene, organic semiconductor materials, etc.

If we take the view that exposing women in our volunteer military to the horrors of combat represents some kind of progress, then I beg to differ. I would like to suggest that the folks in the DoD, the administration, and the congress have salved over a civil service inequity in exchange for equal opportunity for a spectrum of life altering traumas. In regard to military matters, our government and military elites are swept up in a food web of moral corruption so systematically ossified that I do not see how we can steer civilization away from a Malthusian step change.

Chem Haiku

Mighty exotherm
Sleeping in reaction mass
Please stay home today

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Crystalline needles
Growing from amber liquor
Wistful as hoar frost

—

Give it a try and post your lines on the ACS Chem Haiku website.  化学俳句

Flame and Ash

Fire is something that we are all familiar with. Everyone has experienced the simple fact that certain things can burn and in doing so are irrevocably changed. For mankind, fire has been an agent of change from the beginning of its use. A simple campfire can be thought of as a crucible where organic matter is destructively distilled and oxidized to carbon dioxide and water and inorganic matter is consolidated to metal oxides, carbonates, and phosphates.

The flame of a campfire sits in place over the fuel source, appearing to be stationary. But really, a flame consists of hot flowing gas. It is the combustion process that is stationary.  A campfire is a kind of air pump pulling air in from the sides and lifting it upwards due to the buoyancy of hot combustion gases. As the gases rise, microscopic particles of glowing carbon are lifted above the wood giving the appearance of an envelope of glowing gas.  Properly mixed propane or natural gas give a flame that has a bluish appearance with much less luminosity. Reading is possible by the light of a campfire. It is not so good by the blue flame of a camp stove.

A wood campfire will consume the wood down to ash. But before the wood becomes ash it can be observed to change from a fibrous solid to a glowing ember of black carbon. The early phase of burning is characterized by the evolution of abundant volatiles that distill into and energize the flame. Early gas lighting used the flammable gases distilled from coal to provide flame lighting for streetlights and home lighting. The problem with coal gas was that it was free of particulates so the brightness of the flame was poor. The problem of poor gas flame luminosity lead to invention of the limelight and the lantern mantle.

The lantern mantle was developed to overcome the problem of poor gas flame luminosity. A fabric bag soaked in thorium nitrate solution (with 1 % cerium) was dried and then attached to a burner. The gas ignition process burned the fabric and caused the thorium to calcine in place, forming a gossamer webbing of thoria ceramic. The heat capacity (Cp) of thoria is relatively low and the melting point is exceptionally high. Low heat capacity materials require less heat to raise the temperature to a given point relative to high heat capacity materials. The result is that a flame of ordinary heat can raise the temperature of the low Cp thoria to produce high luminosity. The ceria in the mantle dampened the green tinge of glowing thoria to produce a relatively natural light.

Thoroughly burned wood produces an ash that is largely inorganic in nature and at one time was considered valuable. Wood ash was used to provide potassium (potash) for early gunpowder formulations.  In the early days of gunpowder, nitre (saltpeter or nitrate) was extracted from various sources and used with mixed results. Some nitre is found in wood ashes. Elsewhere, nitre would appear in damp patches of organic-rich earth as a whitish solid clinging to twigs and plant matter on the ground looking much like hoar frost. Caverns have long been a rich source of nitre. Mammoth Caves in Kentucky and Carlsbad Caverns in New Mexico were mined for their nitrate rich sediments long before tourists began tramping through them.

In 15^th and 16^th century England, nitre was systematically cultivated and extracted on nitre farms.  A nitre farm had deep beds of manure and plant matter covered to shield them from rain.  After a period of time, the nitre beds were transferred to a large basin and leached with water. The leaching solution was then boiled to dryness to give crude nitre. This crude material was carefully recrystallized to produce a white crystalline nitrate salt.

Nitre is actually a nitrate salt comprised of nitrate anion and a counter-ion like potassium, sodium, calcium, etc. In the early days of gunpowder, quality and reliability of the powder was highly variable. One of the variables was the extent to which gunpowder attracted moisture. Powder makers eventually learned that gun powders made from potassium nitre were much less likely to be passivated by humidity than those made from sodium nitre. It became common practice to combine wood ash with nitre extracts to produce what we now know to be potassium nitrate.

Nitre from the guano beds of Chile were rich in sodium nitrate while material from the great nitre deposits along the Ganges river in India were substantially potassium nitrate. Indian saltpeter was an important commodity of the East India Company and strategic material for the British Crown.  Until the invention of the Haber-Bosch process of synthetic nitrogen fixation in 1909 and subsequent oxidation of ammonia to nitrate, the world’s guano beds and saltpeter veins were the major source of nitrates.

The first World War has been called the chemist’s war in part because of the tremendous casualty counts due to the mass implementation of nitroaromatic and nitroester explosives. Haber is notorious for his part in the use of war gases, but the production of nitrates from his process was of no less consequence.