The Squamous Chronicles: A flea market of side effects.

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So, here I am wide awake trying to recall what the Ambien molecule looks like. I’ll probably have to look it up.

Later this morning is my 3rd chemo treatment of 6. Something is knocking me down. The x- radiation plainly has been doing what it does best- giving a 3-D sunburn. The throat is developing mucositis and Is crazy sore. Blistering should start soon.

I’m using magic mouthwash, comprised of lidocaine, benedryl, and Maalox. This pharmacy concoction has the snotty rheology of melted ice cream.  The throat issue is definitely interfering with getting enough calories for body weight maintenance. Have lost ca 10 lbs to date. I’m gonna get a talkin’ to from the dietitian today.

Other than sore throat, the next unpleasant drug side effects are those from the anti-nausea meds. The anti-emetic meds prevent one from hurling through a sore throat. They are also very effective at constipation. So, one gets to know the offerings at Walgreens.

The Squamous Chronicles. I am a platinum ligand.

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This afternoon I’ll get my 7th dose of 1.8 Gy of x-rays on the way to 54 Gy. The machine doing the deed is a Varian IMRT. It is a very impressive bit of technology. It has a continuously variable aperture and intensity. The rad tech opened the access panels up for me yesterday and showed me the innards. There is a rather large microwave generator inside with waveguides piping energy … somewhere. She said this TrueBeam system could also do electron beam therapy. The machine has a built-in CT scanner to verify that the sorry sod strapped in is aligned properly.

Last Monday I officially became a ligand for platinum. Got the first dose of cis-platin. Somewhere I have molecules- DNA- that are ligated as Pt complexes. The first dose hasn’t been much of an issue. The anti-nausea meds definitely have side effects though.

Five more weeks and 5 more cis-platin doses to go. Week one was without serious side effects thanks to Dulcolax.

Heap Big Stinkum

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The current movie “The Lone Ranger” is a real stinker. The buffoons who produce pictures like this should not be encouraged with good attendance figures. You can’t build a movie solely on a sight gag consisting of Johnny Depp with a dead crow on his head. In fact, I’d rather not invest anymore heartbeats on the topic. <end>

The Squamous Chronicles, part deux: Into the beam we go.

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My adventure with Head and Neck Squamous Cell Carcinoma, HNSCC, soon enters a third phase.  A week from this writing I’ll don my custom prepared plastic mesh mask and they’ll strap me onto an x-ray machine. Oh yes, one other thing. There’ll be a weekly dose of cis-platin coincident with irradiation. Turns out that there is a synergistic effect with radiation and platinum poisoning cis-platin chemotherapy. No doubt it is related to the fact that platinum is a heavy atom with a lot of electron density ripe for scattering. Platinum ligated to DNA during irradiation is a bonus as well I suppose. Your own DNA as a ligand for platinum. A funny thought for someone in the catalyst business.

The first phase was the identification of a swollen lymph node and its subsequent removal from its cozy perch on my right carotid artery. Here I learned first hand why cancer is destructive. Mutant squamous cells from some molecular-genetic train wreck are washed away from their birthplace to lodge in distant locations. In my case, the aloof cells got hung up in a lymph node. There, they invaded the node and proliferated to the point where much of the lymphatic tissue became necrotic, likely from blood starvation. The node was not especially painful. Well, until the biopsy needle went in. Then it became very, very angry. But I digress.

The second phase, post surgery, was the adventure of finding suitable oncologists. This is a little bewildering. It is easy to get overwhelmed by information. I went for a second opinion and soon thereafter chose the Anschutz Cancer Center at the University of Colorado in Aurora. I’ve already had medical students and residents sitting in on consultations and exams.  The medical oncologist is a research professor specializing in head and neck cancer. He sees patients on Fridays too. The radiation oncologist sees a lot of HNSCC and seems knowledgeable and confident.

More to follow.

Comments on Edward Snowdon

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I have to say that I am tickled to death over what young Edward Snowdon has done in regard to his leaking of the NSA PRISM project. Funding and compelling otherwise well intentioned civil servants to sift through the transmissions of US citizens and allies under the false idol of “national security” represents a sort of cancer of civil society. The future is not for the faint hearted. Unfortunately, the faint hearted are in charge.

The assertion that X number of terrorist attacks were prevented by internal espionage activity is patronizing rhetoric uttered by functionaries who are powerless to actually prove it. Obviously we have enemies. We’ve earned it. The US is not a target simply because “we love freedom”, a slogan so infantile that it is a wonder that Bush II was able to utter it with a straight face. We are a target because of decades of foreign policy overreach.

The US federal government and allied corporations are so brain addled over Middle Eastern politics and security that congress is deadlocked over what amounts to a new form of the guns v. butter problem.  Congressional members, I’ll say Republicans in particular, live in another world distorted by wealthy patrons.  In their view, civilization is something that markets do rather than the other way around. This is a natural viewpoint if you control a lot of wealth- or hope to.

Simplistically, we input defense dollars into the military machine and privately owned petroleum comes out the other side. So, the stockholders of Exxon, Chevron, etc., are protected from risk on foreign territories by the US armed forces. US taxpayers pay for this but petroleum companies seem to carry little of the burden.

What we have gotten in return for our foreign petroleum adventures is pushback in the form of guerrilla warfare, commonly called terrorism. The term “terrorist” has been transmogrified into some form of supernatural evil. Really, a terrorist is a criminal. Killing people and destroying property is a crime and it is immoral. It is not evil incarnate. We are not in a supernatural battle between good and evil or God and Satan.

If Snowdon’s action was to shine a little light on how the government commits espionage on its citizens, then I say good for him. In doing so he broke the law. He violated contractual agreements on disclosure and should pay a price for that. But in regard to accusations of treason based on what facts are available, I cannot agree with that charge.

Suggestions for future customers

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Being a grey haired chemist in the manufacturing field, allow me to make a few suggestions regarding the design of custom chemicals. If you as a customer would like to have a custom product that has minimal cost, maximum quality, and minimum variability, please consider the following attributes of an ideal custom synthetic chemical product.

Boundary conditions must be set on my comments:  custom or proprietary product; produced under batch or semi-batch conditions; non-pharma-food-neutriceutical related.

To the greatest extent possible the raw materials for your product are preferably-

  1. existing items of commerce unencumbered by composition of matter or process claims.
  2. available in a grade suitable for direct use.
  3. unencumbered by import restrictions, law enforcement watch lists, and relevant EPA restriction lists.
  4. TSCA and REACH listed already.
  5. those free of problematic isomers.
  6. those not requiring tight fractional distillation to purify.
  7. free of explosaphors like azide or nitro esters.

Your costs are best contained if your product-

  1. does not require enantiomeric purity or is not subject to facile isomerism affecting the specification.
  2. does not require more than one protection/deprotection scheme.
  3. does not require tight fractional distillation for final purity.
  4. does not require bulk high pressure chemistry (shops that can do this are limited).
  5. is air stable.
  6. is soluble enough in process solvents to maximize space yields (if it is, say, <10 wt %, batch costs will start to get high).
  7. does not require solvent changes in a process unit operation.
  8. is amenable to parallel synthetic strategy.
  9. does not require serious chilling of the reaction mixture (say, < -20 C).
  10. has been screened for real purity requirements rather than those based on the desire for tidiness.
  11. can be isolated by a simple Buchner filtration rather than, say, a centrifuge or other more elaborate solids isolation scheme.
  12. can be isolated by simple distillation.

It is important not to underestimate the cost of excess purity. A process may afford 96 % absolute purity on first isolation with say, 1 % solvent and 3.5 % side products or starting materials. The cost of taking this to >99.5 % is often very high in plant time and in product losses from added operations. Maybe you can get by with 98.5 % purity with some constraints on certain contaminants for your application.

Products and their intermediates may be designed in the early development stage to have properties that aid in low cost manufacturing without too much alteration of utility. For example, consider not using an n-octyl ester group in favor of 2-ethylhexyl ester. There are many structural motifs that derive from large scale items of commerce. Products that are strictly polyaromatic with or without hetreroatoms, are zwitterions or salts, or have a large heteroatom-to-carbon ratio, often have organic solubility problems. Will a bit of aliphatic shrubbery in a side group enhance processability? Maybe. If it allows your vendor to have better process economics, that helps everyone.

Does the process require nitromethane as a solvent? Does it require an exotic PGM catalyst that is patented? Do you have to use a patented transformation in the scheme that requires pencil-necks from the University IP office to audit annually? If so, try to find a better way.

The Squamous Chronicles. Going down the rabbit hole.

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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.

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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.

Curious ice formation. Copyright 2013 Th' Gaussling.

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.

Ice Stalks 2

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.