InChI Tales

Th’ Gaussling has been dabbling in the strange land of cheminformatics lately. I’m trying to develop some productivity tools in on various platforms to make chemical information more accessible to fellow staff members.

One particularly useful tool is the InChI, or International Chemical Identifier. The InChI is a character string that is derived from a chemical structure. This string can be hashed (irreversibly) into a shorter string of alphabetic characters called the InChIKey. Using ChemSketch, one can draw a structure and generate an InChI string and an InChIKey string. What you’ve done here is to jump the gap from chemical structure to a searchable character string. These InChIKeys can be planted into documents such as Excel spreadsheets, Word files, and Access databases. A search for the InChI character string can find all of the documents in a folder containing the string or to a record in a database containing it.

Granted, this can be done in other ways. A chemical name can be searched as can a CASRN. Names are subject to syntactical variation and could complicate the search. If you have generated a new structure that is not listed in CAS and the nomenclature is complex, then an InChIKey identifier can serve as an unambiguous term for subsequent searches.

If you hate using the Java based drawing module in SciFinder, an InChI string or SMILES string can be used instead. Just open the structure drawing module and look in the upper left hand corner of the window. There will be a screwy looking button to select for pasting in an InChI or SMILES string. This will cause the Java module to draw the structure for you. It’s pretty handy.


Gilded Blight

After a weekend in the Alma, CO, mining district, I have come around a bit on the merits of gold mining. Oh sure, I have always known that it was a dirty business, what with the mercury, the cyanide, the acidic tailings piles, and the blighted landscapes. But for God sakes man, it’s GOLD!

Last weekend was different. It wasn’t a dispassionate examination of mining history. I could see miles of blighted landscape heaped with spent alluvium along the road from Fairplay to Alma. To the north, over Hoosier Pass, are the McMansions of Breckenridge where new and old wealth mingle.  To the south of Fairplay is a sizeable expanse of gravel and cobble heaps from past placer mining.

Placer mining north of Fairplay 6-14-14

The photo shows just a short stretch of the creek bed undergoing placer mining on the north end of Fairplay. Granted, the mining company is using gravity separation by way of the sluice to recover the gold. The stones are all rounded and well weathered, so one might expect the tailings to release little in the way of toxic leachate. But what a colossal mess they have made of the landscape. Perhaps they have put up a bond assuring that restoration of the landscape will happen when the mining ceases. I don’t know. That does not seem to be the way of past mining in the district.

My point is this. Isn’t there some madness in gold mining? At best a handful of people get wealthy from putting more gold on the market. I would argue that gold does not have the utility of iron, aluminum, or copper for instance. It does not go into items that advance civilization and economics like tractors, bridges, ships or wires. Gold does not go on to enable the growth of industry in the manner a base metal. Some of it adorns our fingers but most falls into the hands of anonymous individuals and governments who hoard vast caches of the metal. Granted, a bit of the annual production goes into electronics and a few other applications.

The madness in gold mining is that people are willing to go to any length or bankrupt themselves to obtain a metal that in the end benefits approximately no one. Most of the metal will quietly sit in a vault somewhere producing nothing. It won’t support a building or a roadway over a river. It won’t produce goods or services, nor will it bring a silent heart back to life. It can only support abstractions like the notion of value. We’re willing to put up with scarred landscapes, mercury pollution and acidic runoff produced by other people for an abstraction. That is pretty funny.

 


It’s Show Time!

I sit in solitude in the lower dressing room, below the stage, at the Rialto Theatre in Loveland, CO, waiting for my cue to go on. The rest of the cast are upstairs in the new green room dressing and applying makeup. My preference is to get some self time before I go on. I have a bit part in our production of Father of the Bride.

The stage is set and the popcorn machines in the lobby are popping away, blowing a magical waft of diacetyl and hot corn into the dimmed auditorium. The curtain is closed and the blue low-wattage lights backstage are shining on the floor and black curtains in the wings. The stage crew are making last minute adjustments to the set dressings. Background music is playing and a few patrons are shuffling to their seats.

In a minute I’ll apply some makeup so my pasty white face topped with whitish hair will display a bit of facial expression in the bright stage lights. A bit of mascara to darken the eyebrows and some eyeliner to make the whites of the eyes pop out a bit:  All to accentuate the emotional spin I will apply to the lines. This will emphasize vocal nuances contrived to convey the emotional intent of the playwright.

One of the key ideas in acting is listening. An actor must listen to the lines being said not only for the cues they may contain, but for pacing and to convey a realistic sense of the interplay. For many of us in life, conversation consists of waiting for others to be silent so we can talk. The best actors sound natural in part because they are also listening.

Opening night of our 2 week run went well. We need to fill the seats with backsides to fund the next production. Snow is predicted for tomorrow, Mother’s day. Hard to tell what effect that will have on attendance.

7:30! It’s show time!

 


Americans and Distrust of Science

The news feeds are piping articles across the internets about Americans and their views on matters of science. Of particular interest is the finding that 51 % of respondents expressed a lack of confidence in matters of the big bang and cosmic origins and age. Predictably, scientific models of human origins and evolutionary science also elicited a considerable lack of confidence.

As the linked article in The Atlantic suggests, there is nothing new in America about ignorance of science and its panoply of theories, models, images and data. I’ve come to believe that wide spread ignorance of science may be contracting a bit. Some folks might be a little less refractory to science if gently brought into the discussion.  It is especially evident when you engage someone in conversation about the concepts with which they might anonymously criticize in a survey. Often if you can get a person past a key mechanistic concept, their dogmatic view of things may soften.

Scientists tend to look at new things analytically and with skepticism. Others may have a devotional world view. The devotional approach is the programming language of faith in and preservation of doctrines. For the scientist, the goal is to strip doctrines to their bare mathematical essence- a single equation that describes the relationships between variables and fundamental constants. If something is observed, measurements can be taken.

Molecular medicine and microbiology unavoidably force one to come face to face with the plasticity of DNA and the short term variability of genetic change. Resistance to drugs or the spread of BT or glyphosate resistant traits into insect and weed populations are a great entry point for talking about molecular evolution. It also allows one to get away from the troublesome paradigm of Darwin, whose work carries religious baggage for many. Irrespective of what Darwin wrote, modern molecular biologists would have eventually postulated and substantiated evolution from the molecule up, as opposed to the Finch down. The Darwin model of evolution has become tired and a little worn. We really should be giving more credit to molecular biology for advances in the understanding of genetic change.

I think those who have devoted their lives to understanding science tend to forget the tremendous expenditure of time and effort that goes into a deep  and quantitative understanding of nature.  My experience in teaching and in public outreach in science has been that a great many people are willing to be entertained by presentations on extrema, that is, the biggest, the most powerful, the most dangerous, the most poisonous, etc. Folks like to hear about extreme phenomena and scientists are only too happy to talk about the dangers of black holes or volcanoes or ferocious animals.  One can spend an evening talking about such things to a general audience and go home with the impression that the public eats this stuff up.

However, if you closely converse with your audience, you may find in many that their interest is genuine but superficial. They are entertained by the gosh-wow aspects of astronomy, but are unwilling to commit the time and effort to enough study to be competent in a topic. They often only want to see the moon through a large telescope and then go home. This is just human nature and science folk cannot be offended by the slender attention span of the public. Learning science requires a good deal of work and focus. That a large slice of the population is suspicious of the big bang theory suggests that said population has not made the time and energy commitment to learning the science.


Adenocarcinoma Chronicles. After the Radiation.

Last week I finished 38 x-ray treatments on the Varian Linear Accelerator with IMRT for my prostate cancer. This device uses a variable leaf collimator for continuous dose adjustment as the beam rotates around the patient. Each treatment is preceded by a CT scan with a built in CT scanner mechanism on the accelerator. This is performed for purposes of alignment of the target area to the beam which rotates about a fixed axis, coincident with the center of the target.

Along with the 76 Gy of x-ray therapy is hormone ablation with Lupron. The standard treatment for advanced prostate cancer, Gleason 8 in my case, is hormone ablation and radiation therapy to the prostate.

Initially, the trick to impeding the growth of the cancer is to suppress testosterone which is needed for reproduction of the cancer cells. The pituitary controls the signaling for testosterone secretion from the testes.  The adrenal glands secrete a small amount of testosterone as well.  Lupron suppresses the signaling by the pituitary gland. This is effective for a period of time, perhaps as long as 24 to 36 months.

Eventually the cancer becomes resistant to this approach and enters the so-called refractory or castration resistant stage. In response to the lower testosterone titer in circulation the cancer cells produce more testosterone receptors, called AR for Androgen Receptor. The number of AR’s multiply by 3x to 5x, increasing the sensitivity of the cells to what little testosterone (or dihydrotestosterone) there may be in circulation.

Blocking the androgen receptors is an approach to treating castration resistant cancer, but it does have limitations. This will be explored in a later post.

An observation from a patient’s perspective. Insurance will generally not pay for off-label or experimental therapy. So unless the patient is self-insured, the treatment profile will follow the board approved protocols for a given diagnosis. This isn’t a bad thing, but often a medication or other treatment will show effectiveness in other applications.  While the doc has some discretion here, the insurance company may not approve payment. And, they may decline to pay months down the timeline when their internal review staff have had a look at it. They make their profits by declining services, not offering to pay for it.

Initially I had hoped for the possibility of participation in a treatment study if this disease went south, as it is likely to do. What I was told is that because I have had 2 cancers, throat and prostate, I am almost certainly disqualified from participation. This was disappointing but I understand the reason for it. Even so, I am barred from a Hail Mary pass down the road.

So, what now? Well, it is watchful waiting. While PSA numbers are given less importance in checkups for ordinary patients owing to the history of overtreatment, for a post-treatment Gleason 8 patient like myself, the PSA number is a direct indicator of disease progression. Once the disease becomes castration resistant, I  suppose that some kind of AR therapy is next. The docs have been evasive when asked. Apparently there are several paths available. But I suspect they would rather the patient focus on the present and not the damaged bridge miles ahead of the train. We’re all headed for that bridge, it’s just that some are further up the tracks.

 

 


Liptonian Symbolism

Originally posted on Lamentations on Chemistry:

Never one to allow reason to interfere with sentimentality, my blackened heart is softened somewhat by the recent shipment of Lipton Tea bags delivered to Th’ Gaussling from an online admirer via the US Postal Service. 

The tea in this gift shall be symbolically applied to the local waterway, but not before being used to formulate some refreshing iced beverage via aqueous extraction.  A vessel filled with aqueous goodness (OPE-Our Pure Essence) will be charged with the anthocyanin and alkaloid laden forest litter for extended exposure to solar radiation. Brownian motion will be relied upon to disperse the colloidal value away from the biomass.

Once so processed, the fortifying beverage will be passed through a pair of kidneys as a symbol of my dark contempt for the IRS. This nephro-raffinate will be discharged into the municipal fluid collection system for a kind of Nicene rectification that will provide further philosophical processing of the…

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US Russian Policy is Pathetic

I just have to say that in regard to the deteriorating situation with the Soviet Union Russian Federation, it does not appear that either the EU or the US have their best thinkers working on it. I think US leaders have misunderstood Putin from the beginning and I see very little to convince me that Obama’s people, the Congress, or any other high level functionaries known to me have a clue how to get their arms around Russian behavior or a workable diplomacy.

Certainly recent (post-Ford) US incursions into foreign lands with troops or drones have taken us off the moral high ground in this regard. How can the US lecture Russia on the invasion of Crimea when we invaded Iraq based on lies, subterfuge, and outright errors?

Bush 43 and Clinton had historical opportunities to gain better alliance with Russia. But we supported Yeltsin in the Clinton years and ignored Putin’s offers of assistance after 9/11. The Russian people were mystified when the US supported Yeltsin, widely regarded as a drunken buffoon. Gorbachev’s memoirs paint a lackluster and untrustworthy picture of Yeltsin.  And the US has done nothing but confirm Putin’s paranoia about US intentions by adding membership to NATO, ABM’s in Poland, petroleum wars in the middle east, and the general appearance of weakness by in-house political fratricide.

We have no use for milquetoast administrations like Obama’s, nor do we need rabid swingin’ dicks like John McCain or his hawkish brethren. We do need Russian and Slavic scholars who speak the language and understand the history of Russia at least back to Peter the Great. They can be immigrants from former Soviet territories of the ilk of Zbigniew Brzezinski, Madeleine Albright, or even a world savvy guy like Henry Kissinger. Who are the current brain trust for eastern European politics and is the CIA giving them good intelligence? Did the CIA predict the takeover of Crimea?


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