It seems that my idea of flame retardant Nehru lab coat has gotten absolutely no traction at work. It’s a pity.
Nehru lab coat with breathing apparatus.
Nehru Lab Wear
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Category Archives: CounterCurrent
A few sentences relating to Power
Power is as power does, or the fact of power is the act of power.
Just a reminder. In the fable of the emperor’s new clothes, what is important to understand is not that an emperor can be highly delusional. The real lesson directs your attention to the ease with which those around him facilitate his delusion. This is an insidious condition that creeps in silently like a fog that soon envelops everyone. It takes a child-like innocence of perspective to see through it. Regrettably, child-like innocence is rarely encouraged in organizations.
Power is in the ability to allocate resources. A successful business person must excel at accumulating and centralizing the power of resource allocation.
Business power stems from centralized control by a few. Representative democratic power is granted by voters. What is behind the fascination with setting up a businessman in a legislative or executive power position? Business is inherently non-democratic.
What a Meth Lab is Not
It is time that someone questions the use of the phrase “meth lab”. Just as a cook would object to the phrase “meth kitchen”, those of us who spend our careers in the laboratory should push back on the use of the word “lab” in this manner. The use of this word confers the notion that a workspace is fitted for chemical handling activity and is operated by someone who knows what they are doing. Dubbing a meth operation as laboratory surrenders too much credit to the operator. These people are moonshiners skulking around on the periphery of society.
A meth lab is not a lab. It is the workshop of a criminal enterprise where unscrupulous people manufacture a dangerous substance. Its sole purpose is to profit from the uncontrollable neurological train wreck of methamphetamine addiction. This is not laboratory work. It’s just crime.
Fulminating Belief and the Drake Equation
It seems to me that the character(s) who produced the YouTube video that has caused so much religious fulmination in the sandy parts of the world ought to be parachuted into Cairo to answer for their actions. Surely they can give the best explanation of what their movie represents.
Another thing has occured to me. Perhaps we should make a minor adjustment to the Drake Equation which describes the number of civilizations in our galaxy with which communication might be possible. The equation can be found at this link. The L factor defines the length of time a civilization releases detectable [radio] signals into space. Given the self destructive behaviours of beings capable of generating radio signals on at least one planet, maybe it is time to define L*.
L* = L(1 – P*/P) where P = average number of intelligent inhabitants of a planet and P* = average number of intelligent inhabitants willing to die/kill for their magical or political beliefs.
Perhaps the reader has a better modification. Here is the Drake equation copied straight from Wikipedia:
where:
- N = the number of civilizations in our galaxy with which communication might be possible;
and
- R* = the average rate of star formation per year in our galaxy
- fp = the fraction of those stars that have planets
- ne = the average number of planets that can potentially support life per star that has planets
- fℓ = the fraction of the above that actually go on to develop life at some point
- fi = the fraction of the above that actually go on to develop intelligent life
- fc = the fraction of civilizations that develop a technology that releases detectable signs of their existence into space
- L = the length of time for which such civilizations release detectable signals into space
General remarks
I wish to make a few remarks on current news items of interest.
Country singer Randy Travis was found in a ditch in north Texas allegedly drunk, naked, and belligerent following an apparent one car accident. Crimony! It’s that awful Nashville music that he sings. If I sang that twangy, mornful, depressing stuff all the time, I guess I’d be sloppy drunk in a ditch too. He should dry out and switch to show tunes or something a bit more cheerful.
It seems that while the televisions and internets of the world are busily dulling enchanting us into the delusion that our ever accelerating consumption of resources and expansion into wild spaces are having no effect on the “natural world”, the global ecosystems are actually in trouble. I emphasize natural world only because so many of us are preoccupied with the on-line world. In fact, many are worried about a “state change” in the global ecosystems.
In Approaching a state-shift in Earth’s biosphere, a paper just published in Nature, the authors, whose expertise spans a multitude of disciplines, suggest our planet’s ecosystems are careening towards an imminent, irreversible collapse.
Earth’s accelerating loss of biodiversity, its climate’s increasingly extreme fluctuations, its ecosystems’ growing connectedness and its radically changing total energy budget are precursors to reaching a planetary state threshold or tipping point. [ The Automatic Earth, August 6, 2012. ]
I know, I know. Sounds like Chicken Little. But we should pay more attention to our small planet. The atmosphere is thinner than most people think, the fisheries are stressed, desertification is happening in Africa, and human population pressures are mounting in many locations. We can’t keep the extractive industries going forever. We need to find an economic model or culture that allows us to do with less mass. Reduced consumption per capita. Look, it’ll happen anyway as key resources dwindle.
We should be aggressively recycling lithium, gallium, tellurium, indium, and the rare earth elements in particular. These are key elements in our much beloved electronic devices. There are other materials to watch, including hydrocarbons in general. A society with infrastructure causing one to hop in the SUV and drive 5 miles from their isolated subdivision to buy cigarettes and beer is a society that is on a rendezvous with destiny.
Thoughts on crystals, symmetry, and perfection
Bismuth crystals on my desk
Nothing too unusual here. Just some bismuth crystals sitting on my desk. A metallurgist friend died recently and his family passed along some of his samples to me. Virg was a great guy. He knew how to conduct himself with decorum like a civilized human being. I don’t confer this praise on everyone.
Bismuth City
I think many people find some kind of solace in the orderliness of crystals. Nature has seemingly betrayed the prevalent trend of disorderliness to produce a latticework of pristine stuff in appealing shapes. Crystals appeal to our innate desire for symmetry and rectilinearity. We subconsciously associate symmetry with goodness and calm. Properly stacked goods in your basement suggest orderliness. Shoes lined up in the closet or socks neatly arranged in the drawer provide a reassurance that something in life is at least predictable.
Crystallinity infers a repetitive array of subunits asssembled under the austere constraints of efficient stacking. It represents subunits held in confinement and subject to limits on motion.
Crystallinity is in a sense sterile and lacking in diversity. Living things are not crystalline for the most part. Crystallinity is static and devoid of the many necessary degrees of freedom needed for life. Living things often have superficial symmetries, though on closer inspection something inevitably cracks the symmetry. Humans have a bilateral symmetry across a line taken from the head to between the feet, as do butterflies and hippos. Internally, though, the symmetry is less than obvious. Our genetic polymers of DNA have a gross secondary helical symmetry as do some peptides, but even that yields to partial symmetry when the monomeric units are accounted for. Sure, there are instances of crystallinity in living things. But living things require a fluid internal environment to allow molecules to collide and react.
If you take crystallinity as an allegory of perfection in the sense of a way of being- that is, orderliness and freedom from defects- then you might conclude that a perfect being would be constrained by symmetry or the attributes of perfection. It would seem that the attribution of perfection in a being might pose the possibility of limitation.
Instead of getting wrapped around the axel philosophically, perhaps we should gladly rejoice in the lack of perfection in ourselves and the ultimate absurdity of perfection in the fanciful dieties whom we imagine control the vibration of every molecule in the fleas that ride on the tailfeathers of every sparrow.
Thoughts on Academia
The blog post by Terran Lane of the University of New Mexico provides a good example of the frustrations in academics today. Much of this is well plowed soil. I link to it because I think he is spot on about more than a few things.
The availability of external funding for the last 30 years has equipped American colleges and universities with a great deal of equipment and facilities. The availability of funding for grad students and post-docs has energized a vast educational complex that has come to depend on external grant money to maintain built up infrastructure. Naturally when an institution expands in good times, it finds itself top heavy in overhead when the good times end.
Ambitious people step forward when presented with the opportunity to grow programs and institutions when times are cash rich. But when the cash influx begins to taper off, these same people find themselves in the position of having to decomission or dismantle parts of the very organization they helped to build. It is hard for people in any circumstance to feel like they are moving forward when they have to make do with less.
One response to restricted university resources is to increase competition for teaching positions and tenure. Candidates with the best potential for winning grants are highly prized in any candidate search. The result of this is that professors today are burdened by administrative expectations in the hunt for resources in order to maintain close to what they already have.
Friends at PUI institutions are also feeling the heat, possibly due in part to the rise in undergraduate research programs that took off in the 1980’s. Undergraduate research in chemistry, at least, has grown into an expectation rather than a plus. This brought the buzz saw of the grant machine into the grassy quads of many quiet institutions.
Certainly no untenured prof is going to throttle down their scholarly activity for the greater good of science funding. Faculty will continue to struggle with this as long as grants are a major metric in rank and tenure.
Which brings me to my final point. Scientific knowledge as national treasure. I am sifting through Chemical Abstracts Service data bases searching for something nearly every day. This resource of ours, scholarly and pragmatic knowledge, is one of the crown jewels of human civilization. It is the collective contribution of people and institutions going into the distant past and across the curved surface of our world. We should cherish it for what it is- an archive of achievement, a repository of knowledge for application to future challenges, and a representation of the best of what we are capable of.
The notion that academia is the apex of the life intellectual has never been entirely true. You do not have to be in industry for very long before it becomes quite clear that there are a great many smart and creative people outside of academia. People who become professors are people who are in love with the very idea of the university and of higher education. We must find a way to allow research active faculty to throttle down the grant cycle just a bit so they may throw their energies into serving their institutions in the traditional manner. By service to their students, to scholarship, and to the advance of civilization.
That said, it seems embarrassingly obvious to say that our academic institutions are a critical part of our civilization past, present, and future. But today our institutions are in peril of substantial decay if left to antagonistic legislators and fulminating demagogues bent on terminating programs in the name of social reconstruction.
We know how to operate our university/research complex. Absent some of the mania in the horse race for grants, perhaps we can offer a bit more student contact with professors. A BA/BS degree must be understood to mean that a graduate has absorbed knowledge, sharpened reasoning ability, accrued some judgement, and has developed a professional demeanor that can only come from the personal interaction between people. We should expect from our institutions that a professor is a professor, not a shift supervisor.
Gluten harvest underway
The annual gluten harvest is underway in northern Colorado. Winter wheat planted last autumn has pushed through the soil, grown to produce a head of grains on every stalk, and finally, transitioned from a sea of lush green grass to the now dessicated amber waves of grain. Giant harvesting machines are cutting the short-statured hybrid crop and somehow rattling it into chaff and grain.
Now that we are avoiding gluten in our household, I view the wheat harvest a little differently. It is somebody else’s harvest. It’s odd way to look at it I suppose.
Microscopic Printing on Aldrich Chemical Labels
OK. I’m going to have to be the bad guy and take Aldrich (SAFC) to task on their labeling. I recently received a 100 mL bottle of 10.0 M BuLi in hexanes. As I looked around for the concentration, I found it written in tiny print away from the name and part number which were written in larger print. I have placed a ruler next to the label in the photo below to show the size of the print. It is the same size as the date on a penny.
Labels do not “just happen”. Someone has to design a label. This involves arranging content on a limited space while meeting internal and external requirments for safety statements and other content. Labels do not fall from the sky in great sticky sheafs. Someone prints them. And that someone assigns font sizes and space for the information. So, someone has caused the font size to be tiny irrespective of the print content. I have numerous bottles with microscopic printing and vast expanses of white space. This smells of automation.
I’ll wager that there is an automated label generator that takes product label data and prints it onto the label irrespective of the actual need for microscopic font size. I can envisage a giant warehouse with automated shelf pickers whizzing about pulling bottles off the milti-tiered stacks and placing them into plastic tubs which course their way to shipping. Elsewhere in this voluminous interior is a widget that prints the labels and sticks them onto the bottle after they are filled. Somewhere a human is pushing a broom.
C’mon Aldrich! Make your labels more legible. Good gravy. What would Bader say? I’m sure your accounting office has no trouble reading the print on the checks that arrive to pay for these products. Consider that you’ve been put on notice.
Fine print on Aldrich reagent bottle. Molarity is printed in 1.0 mm font size.
Adrift in Cheminformatics Space. CHETAH 9.0 Fails with Some ChemSketch SMILES Strings.
The ASTM software Chemical Thermodynamic and Energy Release version 9.0, CHETAH 9.0, has many useful features for calculating thermodynamic values of substances. My interest is in the (gas phase) calculation of ΔHf, limiting oxygen concentration, lower flammability level, Cp, entropy, ΔG, maximum heat of decomposition, net plosive density, ΔHc, and minimum ignition energy. The package claims to have the largest known database of Bensen group values at 965 entries.
I would have supplied links but the WordPress Editor is on the fritz. One more bloody software “issue”. – ‘th Gaussling
I recently upgraded from CHETAH 8.0 to 9.0 because 8.0 is incompatible with Windows 7. These upgrades are a kilobuck a pop so they can be a budgetary surprise. After I upgraded I noted that 9.0 is not compatible with Windows 7 either!! Luckily I have a couple of lab computers that are still XP systems and therefore compatible with 9.0. The folks at the University of South Alabama write and support CHETAH.
I understand from private communication that CHETAH 10.0 is in the works in anticipation of the release of Windows 8. Oh joy. I hope that some effort will be put into the user interface and general robustness. My question is this- what about those of us who will be using Windows 7 for the next few years? Will rev 10.0 be compatible? Will it have click and drag features or more of a DOS accent like the current rev?
One of the features that is nice about CHETAH is that it accepts SMILES strings as data input. It parses the string into known Benson groups and flags unknown groups. Previously I had been entering smiles strings from ChemDraw 7.0, an ancient but still useful version. Lately I have been evaluating ChemSketch freeware. And lucky for me, I found another hole to stumble into.
SMILES is not inflexible in its syntax, apparently. ChemDraw will convert a structure to a SMILES string that is different in its sequence from the identical structure drawn by ChemSketch. I have found that CHETAH 9.0 will consistently accept SMILEs string entries from ChemDraw, but with only some ChemSketch SMILES strings.
Consider the following SMILES strings of the same structure- 5-Bromo-7-tert-butoxy-3-methyl-3H-isobenzofuran-1-one. The nomenclature is from Chemdraw. I do not use this compound- I dreamed it up as an example.
ChemDraw 7.0– O=C2OC(C)C1=CC(Br)=CC(OC(C)(C)C)=C12
ChemSketch 12– CC(C)(C)Oc1cc(Br)cc2c1C(=O)OC2C
The ChemDraw SMILES string is accepted by CHETAH 9.0 and parsed into Benson groups, but when you attempt to process the data it gives a “Run-time error 9” warning and then closes the program. From what I can tell, CHETAH 9.0 will only accept 9 Benson groups because when you clip off functional groups, it will accept the string for the next step. However, it still shuts down and indicates another error saying “subscript out of range”. I don’t know why this happens and the handbook does bnot seem to list errors. The programmer put the error routines in the program, but I guess was too busy to tell anyone what they mean.
The ChemSketch SMILES string above is not accepted at all.
I cannot justify switching to ChemSketch for several reasons and this is one of them. The ChemSketch editor is generally balky compared to the smooth operation of ChemDraw. However, I must say that ChemSketch is very feature rich and has gotten much better. If I wasn’t already committed to ChemDraw (and Chem3D) I’d strongly consider it.
CHETAH seems to have limitations on the number of Benson groups it will accept for a molecule. It seems to require a particular edition of SMILES syntax. And, the user interface is is balky and antiquated. I’ll try to uninstall CHETAH and reinstall it. That said, it still seems … brittle.
From what I can piece together by googling SMILES, the system has been evolving. Apparently, chemical graphics software out there has captured particular editions of SMILES at the time when their revision is released. It would be nice if some international standard were in place to devise an enduring syntactical structure. Seems like something CAS could help with.
Lamentations on Chemistry 