CAS Polysyllabic[multi(digital)poly(character)]nomenclature

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I write to lament the state of chemical nomenclature today.  There are several forces in the nomenclature world- Chemical Abstracts, Beilstein, and IUPAC.  Near as I can tell, with the globalization of CASRN’s, CAS nomenclature is the predominant nomenclature in the world.  At least the world open to English language.  I have no idea of how the nomenclature works in texts written in Mongolian, Tagalog, or Ubangie. Are there translations or transliterations- I don’t know or care much, truthfully.

I can say that the introduction of new chemical entities into commerce presents the issue of what to call a thing.  A name that has 80 characters, including greek letters like mu or kappa, strings of digits delimited by layers of commas, brackets, dashes, and parentheses, poses certain practical problems with business data systems and catalogs.  It also poses problems for the many non-chemical people who have to deal with it on a daily basis.  It becomes hard for people to understand what the hell they are referring to. In fact, it actually intimidates non-chemists to the point of locking up. They become convinced that the slightest error will lead them down the merry path of ruin.

One of my duties is to define nomenclature for products at my day job. We dutifully collect the 9CI names for the TSCA nightmare, and then we decide what we’re going to call it on a commercial basis.  I’m finding myself using the IUPAC nomenclature module of ChemDraw more and more.  The nomenclature coming out of it seems more human friendly.

I once contacted CAS in Colombus and spoke to a helpful and sincere person who explained that CAS doesn’t offer a handbook that would explain how CAS does its nomenclature.  I haven’t researched this too deeply, but I have not yet found a CAS publication that defines the taxonomy that CAS uses.  Of course, CAS will happily charge you for an official name assignment. I guess for a $26 charge I could look it up in SciFinder.

Whining about nomenclature is like complaining about the weather. CAS has to do something with all of the species cited in the literature.  I just regret the high cost associated with using CAS services. 

All of this feeds into my nagging feeling that ACS and it’s lovechild, Chemical Abstracts Service, has gotten a bit unwieldy and maybe even too big for its britches.  With the publishing and the registry database business, it has grown to be the major force in the sales and distribution of chemical knowledge. It is an economic engine.  Maybe even monopolistic.  Oops, there is that word.

Back in the USSR

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Alexander Litvinenko’s death, now deemed a murder by Scotland Yard, brings the topic of “what’s up with Russia?” right up onto the table. It’s like finding an earwig in your half eaten salad.  I gather from the tone of news articles that many are startled not just by the criminal use of a radionuclide, but by the layers of intrigue that are beginning to peel away.

Concurrent with Litvinenko’s demise, former Russian Prime Minister Yegor Gaidar suffered an event in Dublin that may have been a poisoning. His recounting of the episode in a Financial Times article is interesting. 

In some ways the transfiguration of the USSR into contemporary Russia was less of a transition from some larval stage into a butterfly than it was the color change of a chameleon. To be sure, there were substantial changes in the geopolitical tectonics. But their rigid sphere of influence is definitely smaller than in the Soviet days. 

I visited Russia not so long ago.  I had studied Russian language as an undergraduate, so I wasn’t completely helpless. Nevertheless, I had to rely on Russian speakers to help with the details of travel. Russians are like everyone else- cynical towards their own politicians, but deeply patriotic.  Truly, to know Russia is to love Russia. I love the people and the rich culture. But, in my view, to know Russia is to fear it a bit as well.

As a post-doc I sat with Soviet colleagues and watched CNN coverage of the collapse of the USSR.   We watched coverage of the rise of Yeltsin in Moscow and the failure of Scud Missiles in Gulf War I.  My friends came to the US as Soviets and returned as Russians.  It was an odd time.

So, this matter with Litvinenko is surprising but not surprising.  That this place could produce a Putin and a Gorbachev within a few years of each other is not unexpected.  What does surprise me is the low priority that the west apparently places on constructive engagement with Russia.  The west has wasted a golden opportunity following the collapse of the USSR.  

The Smell of Xylene in the Morning

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I’m on of those freaks who worked for a few years before entering college. I made poor choices in utero with regard to the family I was born into and consequently have had to do everything the hard way. A few weeks before I started my freshman year in college I completed my pilots license (single engine, land).  The goal was to get a flying slot in USAF and then move into a flying career with the airlines.  My nearsightedness killed that dream deader than a rat.  Who wants to be in USAF if you can’t fly jets?  Crimony. So I went into chemistry by accident. Some would say that it has been a major accident.

Flying is an amazingly fun thing to do. In fact it is odd that more people don’t try it.  It is an adrenaline rush to taxi an aircraft onto a runway, point the nose down the centerline, and push the throttle to the firewall and fly off the ground. To have such raw, barely-contained power mashing you against the seat is a real thrill.  Once you lift off the realization dawns on you that the only way you’re going to survive this is by the skillful application of your wits.  Getting the aircraft configured for landing and rolling onto final approach and coasting down the glide slope to a touchdown on the numbers is true poetry.  It is an intellectual and emotional stimulation with which few things compare.

The fuel that piston driven aircraft use has a higher octane rating than that used by automobile engines.  The longer the stroke of the piston, the more power the engine can deliver to the propeller. But the longer the stroke, the greater the compression and the greater the need for higher octane. Consequently aromatic additives are put in Avgas to decrease the tendency for predetonation. One of those additives is is xylene.

One of the rituals of flying is the preflight walkaround of the aircraft.  You inspect the flight control surfaces, the leading edges of the prop for cracks or chips, the wing for tell-tale wrinkles, bugs in the pitot tube, and you drain a bit of the fuel from a low point in the fuel line.  You drain a fuel sample because you are looking for water droplets. Water in the fuel could lead to a loss of power during the flight, which is regarded as bad. 

During the fuel inspection, you get a whiff of the aromatic tang of avgas. It is the smell of adventure. The faint smell of avgas is in the cockpit as you strap the airplane to your backside and begin the engine start checklist. It is there during the taxi roll to the run-up pad where you try to convince yourself that the engine is operating nominally. Only after this when the task of takeoff is imminent do you ignore this smell and concentrate on the act of takeoff.

The other day I ran a reaction in the lab using xylenes. Without even realizing it I got a whiff of xylenes and my mind drifted off into the realm of flight.  For a moment I could smell the scent and hear the sound of an airplane clawing full throttle for altitude. I could rememeber trimming the airplane for cruise and dialing in the VORTAC frequencies for navigation.  I remember the dreamy sensation while cruising at 10,500 feet, listening to the Morse code of the VORTAC on the radio intruding into my consciousness over the comforting drone of the engine.  I recalled the words of my instructor- “Attitude, altitude, crosscheck…” and “keep your head on a swivel”. 

Then I realized that the solution in my sep funnel had emulsified so I set it down for a while and became lost in the memory of flight.

Fabulous PGMs

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I don’t know what other people out there think but I have this nagging grievance with Platinum Group Metals- PGMs. They’re too expensive.  I receive a weekly newsletter from BASF Catalysts listing prices of the various precious metals.  Some of them have taken an astounding uptick in price in the last year.

As of last friday, ruthenium was at $375 per troy oz.  Rhodium continues to be in the stratosphere at $4925.  Platinum is down a bit at $1159. Pt prices are greatly affected by demand in Asia for Pt jewelry, according to the newsletter. Osmium and iridium have been at $400 per troy oz for quite a long time. Gold was at $650.50 and even silver was a lustrous $14.07 per troy oz. Palladium is at $328.

Don’t get me wrong. PGM catalysts are fantastic in almost every way.  I’m not so cold hearted that tears don’t well up at the sight of an X-ray of some resplendent Rhodium complex proudly thrusting its phosphines about. My god it is beautiful.  How could I be against PGMs?  My post-doc was doing rhodium chemistry.

It’s just that they’ve gotten so darned EXPENSIVE. Price out some rhodium (II) acetate sometime, but try to be sitting down.  The price volatility is not the fault of companies like BASF or Matthey. There is just a deficiency in supply. These metals are traded in the world market place.  BASF and Matthey are venerable and upstanding companies.  I have no beef with them.

But, here is what we need.  We industrial folk need to try harder to implement transformations catalyzed by the other metals- Ti, Zr, Fe, Co, Ni, Cu, or zeolites, etc.  Part of the problem is familiarity. All of the important textbooks on organometallic chemistry, advanced synthesis, etc., cover the mechanisms of catalytic transformations, but they highlight the PGM mechanisms. That’s not a bad thing, but we all get out of grad school with “palladium on the brain”. 

Yes, of course, there are some things that will probably always be done with PGMs. But what about the beautiful coupling chemistry using Grignards by Furstner, Kambe, or Knochel? 

Take a walk on the wild side. Try something different.

Polonium Facts

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One of the interesting parts of having a blog is that you get to see the search terms that people use to find your site.  We’ve been getting lots of hits lately from persons trying to squeeze polonium information out of the web.  I went through some venerable reference books on my shelf and collated some general fun factoids on that fashionable metal – polonium.

Polonium Table

Polonium is actually a natural element found in thorium and uranium deposits.  In the Radiation Health Handbook I count 33 isotope entries for polonium, 7 of which are metastable, or isomeric, states. The known isotopes are Po-193 through Po-218. Po-209 has the longest half-life at 103 years.   Bismuth 209 is the heaviest stable nuclide. Nuclei heavier than bismuth often emit alpha particles, and do so exothermically or spontaneously.  Polonium, one atomic number above Bi, has no stable isotope. 

Loss of an alpha particle results in a drop of atomic weight of 4 and atomic number of 2.  You can think of an alpha particle, or helium nucleus, as a good leaving group.

Polonium is very scarce.  Its discovery, well known for being famous, was by Marie Curie and was accomplished by isolation from tons of ore. It was named after her home country of Poland. Today the the production of Po is effectively limited to Po-210  and is bred in nuclear reactiors via the transmutation of Bi-209 by neutron absorption to afford Bi-210.  Neutron rich nuclides can drop their neutron count through the emission of beta particles (electrons) with a subsequent uptick of atomic number by one. So the Bi-210 nucleus transforms to Po-210 by beta emission.  The polonium is isolated by fractional distillation from the remaining bismuth.

One gram of pure Po-210 is said to evolve 141 watts of heat. Consequently, one use of Po-210 has been for thermal electric power generation. It’s near exclusive emission of alpha’s minimizes shielding problems.  Another important use of alpha emitters is for the generation of neutrons. This interesting process uses alpha particles to interact with beryllium nuclei to afford the extrusion of neutrons.  In this way it is possible to have a compact neutron source.  Place the source in a tank of water or paraffin, arrange for an opening, and presto! You have a cheap neutron beam source- sometimes called a neutron Howitzer.  Plutonium-beryllium (PuBe) is more common than polonium because of the long half-life of available non-fissile plutonium sources. The neutron Howitzer is commonly used in neutron activation studies.

The chemistry of polonium is exotic by virtue of it rarity and the pragmatics relating to its high specific activity.  It’s high specific activity causes it to radiolyze the solvent that the reaction or other manipulation is occuring in.  This is especially problematic for organic solvents. The high activity will pose serious safety risks for the chemist in handling. Advances in organopolonium chemistry have been complicated by the pyrolysis of the organic fragments via radiolysis.  This also complicates the preparation of crystals for x-ray crystallography. A properly equipped facility night have a remote manipulation setup for handling high activity materials.  This is especially critical when the permissable body burdens are in the picogram range.

Gas Music from Jupiter

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For the last few months I’ve been taken with what is becoming an unwieldy fascination.  It’s called radio astronomy. Turns out to be something that amateurs can actually take up.  There are a few websites devoted to the subject.  It’s not like antique cars or photography for which there are hordes of devotees and whole industries supplying equipment.  Oh no.  This field requires some freakish overlaps of interest- e.g., RF electronics and astronomy.

Lost in Space

For some years now I have been a volunteer at a local observatory. It is a very nice facility and it is operated by some gifted folk. We have a custom setup featuring an 18 inch Cassegrain in an automated dome.  Because of other obligations my participation waxes and wanes like the phases of Venus.  We volunteers give star talks to visitors who arrive in great squirming masses for a glimpse of the cosmos.  We give star talks because we often have to wait for the sky to darken or for the clouds to pass. When the sky opens up, we take a dozen visitors up into the dome and skate around the celestial sphere for the eye candy.

Being a chemist and not an astronomer, I have to avoid delving too deeply into the science during a star talk because, again, I’m not an astronomer.  But this business of being a chemist (an atom scientist) in an observatory has forced me to think about what it is that we’re really trying to do in introducing the public to astronomy. 

It is very easy to present astronomy as the science of telescopes and constellations.  After all, we navigate the skies by referencing the constellations and we look at the interesting objects through an impressively large, yet nimble, optical device.  People leave after an evening of viewing being greatly impressed with the telescope and the observatory.  You can’t help it.  It’s cool stuff.

But the telescopes and all the assorted apparatus are really not the focus of the activity. Astronomy is really about the stuff that is across the vast distance in deep space. How much stuff is out there? What is the stuff doing? And, what kind of stuff is it? They’re George Carlin questions. These are really the central questions of astronomy but we largely pass by the details of the stuff in favor of the show business aspect- the whizbang stuff that you need to keep everyones attention for 45 minutes.  But, the goal is to capture the fancy of K-12 students, so juicing up the show with some mind blowing stuff is OK.  It is fascinating to note that it is the adults that have the hardest time keeping on track.

Whizbang astronomy is necessary to keep the public coming in because most visitors do not have a physics background. To really appreciate the subtleties it helps to have some book learnin’.  Public outreach is not about true learning.  True learning requires struggle and most people are not inclined to struggle with a physics concept for very long. Public outreach is about info-tainment.  

This isn’t a condemnation or criticism. It just stems from the nature of population interest distributions and the bell curve.  I’d fall asleep at a car show or a botany conference.

So, the goal is to evaluate a modest radio telescope capability.  There are several parts of the spectrum that offer signals to detect that are within the realm of possibility for a hacker like myself.  One band is from 20 to 24 MHz. The other is the H(I) line at 1420 MHz, or 21 cm. The sun and Jupiter are active in the 20 MHz range. There is a program sponsored by NASA devoted to solar and Jovian radio observation called Radio Jove.  For a few hundred dollars it is possible to assemble a radio telescope- a receiver and a dipole antennna- to listen to 20 MHz signals eminating from Jupiter and Io.  Picking up 21 cm radiation will likely require a 3 meter dish in order to get enough decibels of signal gain going into the detector. Anyway, this antenna technology is part of my learning curve.

Introducing folks to radio astronomy will serve as a kind of counterpoint and will require that people venture away from the narrow optical band. It requires that we think about the observation of signals that have no visual counterpart and what clues it may afford regarding the condition of matter.

Litvinenko

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The story of Alexander Litvinenko, the Russian who recently died of apparent acute radiation poisoning in London, is fast becoming the most bizarre and compelling story in recent memory.  Litvinenko was an ex-patriot former KGB Colonel who was especially critical of the Putin regime. 

A website called Frontline contains a video of a meeting wherein Litvinenko flatly accuses Putin of being behind the murder of Anna Politkovskaya.  Politkovskaya was a journalist writing for Novaya Gazeta and was bitterly critical of Putin and his policies surrounding Chechnya. She was found murdered on October 7, 2006, in the elevator of her apartment complex in central Moscow.

Interestingly, according to a reference in Wikipedia, none other than Mikhail Gorbachev spoke out morning the loss of Politkovskaya-

Gorbachev told the Russian news agency Interfax about this assassination: “It is a savage crime against a professional and serious journalist and a courageous woman”, “It is a blow to the entire democratic, independent press. It is a grave crime against the country, against all of us.”

The whole thing is turning into one of those ponderous Russian sagas written deep in the snowy birch forests of eastern Russia. 

Already the radiological evidence is accumulating tying together the players in this startling tale of assassination.  Several BA jets have yielded clues as to the presence of radioactive materials on passengers. 

I’m guessing that the Brits will do a first class job sorting this one out.  Hopefully, the details will be made public.

Academic IP

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Some years back I was an assistant professor of chemistry. I had a series of sabbatical replacement gigs and as a result had the opportunity to teach in a variety of chemistry departments across the USA. Eventually I got a tenure track slot at a department that had the critical enabler for an organikker- an FTNMR. It was interesting to compare the departments up close.  Honestly, I was treated warmly at every post I held. 

So, zooming back to the present, I can’t help but ponder the opportunities for academics and industry to collaborate.  From a distance, there would appear to be a great many benefits from academic/industrial alliances.  Synergies, even.  But now that I’ve been on both sides, my enthusiasm is limited.

At the most basic level, the imperatives of industrial and academic scientists are quite different. I am limiting my comments to experimentalists.  The unmistakable sign of progress for an industrial scientist is getting a profitable product to market. For an academic scientist, it is uncovering some insight and getting a publication.  Industrial scientists develop proprietary technologies and carefully guard company secrets.  Academic scientists develop technologies with the intent of folding the work into the big picture. 

In general, when industry wants something special from an academic, they want it kept quiet.  The academic must agree to the strictures of secrecy in order to play the game.  In fact, it is somewhat complicated for industry to engage an academic for some problem solving.  There is the problem of the ownership of inventions that may arise.  What if you engage the professor and his/her group to work on a problem and they invent something? 

For the professor, this is a kind of freelancing that the university may or may not be pleased about.  Who owns the invention? Most universities will require a professor to turn over the ownership of an invention to the university.  Who gets paid for work done in the university lab? Can the student use the work towards a dissertation? How do you handle having the professors work done in the same lab as the proprietary industrial work- do they have separate secret and open group meetings? Secret and public lab notebooks?  Is the professor being absolutely scrupulous about disclosure, documentation, and inventorship?  All of this can float to the surface during litigation and sink a patent or clinch a charge of infringement. 

If the company owns the IP, what’s in it for the university and the students involved?  If the University owns the IP, why should an outside company commit resources to fund it’s development? Licensing a university’s IP could work well, or it could tie your ankle to a boat anchor when competitors jump in the water, as they have a maddening habit of doing. 

One way to handle this matter is for universities to back business startups with their own IP.  This technology incubator approach been going on for quite a while now with some schools racking up spectacular results.  In the early Reagan days the Dole-Bayh Act enabled universities to patent work funded by grants from federal agencies. There are a few strings, but generally it isn’t onerous.

So, what is wrong with this? Seems like a vigorous way to get technologies and industries on stream.  Well, in a sense, it is.  But, think about it from a public policy perspective.  Is this what our universities should be doing? That is, using public grant monies for patenting compositions and processes and receiving a 20 year monopoly on its use? That is, barring the taxpayers who paid for it from practicing it?

Our university system is a key structural element of our vitality as an advanced technological culture.  Until recently it was accepted  by our society that resources are set aside for centers of learning and research and from this the culture as a whole reaps the advances through open access.  Most students pass through the system and move on to contribute productive activity in our industrial culture.  But the system will snare unusually productive persons who will make step changes that advance the system into new paradigms.  Their work in particular has been available for everyone to apply to the advancement of our culture.

Until recently, that is.  If you’re paying attention to this, and you do if you’re in industry, you’ll see more and more that the fabulous reactions found in journal articles may be claimed in one or more patents.  And these patents may not surface for several years.  I have yet to see an journal article where the authors are up front about this matter. 

It is quite possible for a company to adopt a literature transformation into a process only to find out well after the due diligence research that the process they have been practicing is suddenly claimed in a freshly issued patent. 

So here is the situation in a nutshell.  We pay taxes that fund a variety of grants that enable research at university institutions both public and private. We pay Chemical Abstracts Service to have access to the literature.  We pay ACS for memberships and journal subscriptions or downloads.  The work gets patented and we are either barred outright or are required to enter into a licensing agreement.  We pay fees up front to enter the agreement and pay royalities on sales.  Quite possibly, the technology has an exclusive licensee who then has a monopolistic hold on the technology and the public pays a premium for products manufactured under the monopoly. 

Oh, there is more. Since the university requires the faculty member to assign inventions to the institution, the institution pays for the patent prosecution and for the annuities for the lifetime of the patent.  For a US patent prosecution, figure nominally $15k to $50 k. But for foreign patents, there could be dozens of countries with many foreign law firms doing office actions that are orchestrated from the US patent attorney.  This means big bucks flow away from the institution years before any of that elusive royalty stream comes in.  The annuities on foreign patents come up every year, unlike US patents, so an institution is burdened with annual payments to keep the foreign patents valid.  And Gawd help you if there is litigation- US or off shore. That is when you open a big vein and the real bleeding starts.

The run up to litigation can be fantastically expensive.  At this point, you have many attorneys involved- a lead attorney, junior attorneys, mock trial specialists, jury consultants, videographers & transcript stenographers to record depositions, contractors who do graphics for presentation to the jury, and maybe even specialist litigators. Even IP specialists in companies have trouble grasping the possibilities.

One of the joys of owning a patent is paying defend it. In fact, seasoned patent experts will say that a patent is only as good as the last attempt to bring it down.

In the end, why does a unversity need to defend its IP?  Who is it defending it from?  The public? 

But that is the wrong question.  Universities get involved in patenting because they think that a revenue stream can be tapped from an invention.  There are cases where some inventions have paid huge royalties. But if you ask the patent office, they’ll tell you that they estimate that only 2 or 3 thousand of the million and a half or so patents in force actually make a profit for the owner. 

The matter of academic IP seems to be poor public policy and more people need to raise hell about it. If an academic wants to be a business person, then he/she should be a business person.  Raise the money and take the risks like the rest of us do.

Ninnies

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If you don’t read The Atlantic magazine, you should.  The writing is good and the content seems to be reasonably researched.  James Fallows is especially amusing to read.  A while back he wrote an essay called a “Nation of Ninnies“.  Perhaps my fondness derives from the fact that this essay expresses my own sentiments on risk and how we respond to threats.  Fallows observes that whereas at one time our national character might have been exemplified by the Gary Cooper persona, we now resemble Mr. Bean or Pee Wee Herman. 

When uncertain, when in doubt, run in circles, scream and shout

There has been another outbreak of good news.  Dr. Senator Bill Frist, M.D., is returning to the healing arts and away from a run in the 2008 presidential campaign.  Somehow the prospect of being up to his elbows in smelly bowel resections or skewering goiters was preferable to running for president.  It’s just my opinion, a shameless personal bias really, but I’d like to see someone from north of the Mason Dixon line live in the White House for a term or two. We could all use a breather.

Finally, the US has banned the sale of iPods to North Korea.  Darned tootin’.  That’ll fix their wagons.  Makin’ nuculer weapons … we’ll show ’em.  According to the AP, this was designed to personally aggravate that tufted Stalinist weasel, Kim Jung Il. OK, I’m for that.

One Quantum Unit of Radiological Terror

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I keep thinking about this Alexander Litvinenko character who, as the media reports, was mortally radiolyzed.  Irrespective of the intent of the bad guys, the effect of it may go far beyond the mans unfortunate death.  It is a kind of vignetted picture of what terror with radioactive materials might look like. 

In a quiet location, a lab perhaps, or a public storage shed, the bad guys had to formulate some kind of potion, some kind of concentrate that could be added to Litvinenko’s food or drink without alerting him to the change.  And I think it is reasonable to assume that the perpetrators are not “suicide poisoners”, so they would have to do the deed without contaminating themselves. So either the poison was prepared in the field by the perpetrators, or it was prepared in advance by others elsewhere.  It might even be that the person(s) who administrated the poison were unaware that it was a radiological hazard.

Because Po-210 only emits alpha’s, in principle a hermetically sealed container with a small quantity could be moved past radiation detectors at ports of entry without triggering alarms made to detect gamma radiation. This assumes that the polonium is highly pure. Trace contaminants that are gamma emitters could be detectable.  And because Po-210  as the pure nuclide is a strict alpha emitter, it’s shielding requirements would be minimal.  This nuclide seems well suited for villany.   

On the plus side to this scary scenario is the short half-life of Po-210.  Admittedy, this offers scant comfort for those who might ingest or inhale the material.  But, by comparison with gamma radiation where heavy shielding and/or a goodly distance from the source is needed, the short half-life of Po-210 and the poor penetrating ability of alpha particles makes remediation a little easier, at least in principle.  Inhalation and ingestion are the main exposure problems with alpha emitters.

It will be interesting to see if the Chicken Littles in congress will rush back to the hen house extrapolating furiously (flapping and clucking noises) about this “new threat” to homeland security.  Lordy.   Let’s hope they don’t screw up things too badly for legitimate users of radioactive materials.

It is hard to say just how widespread radiological crimes could become.  Because of the short 138 day half-life of Po-210, an accumulated stockpile would rapidly dilute with Pb-206. This event may result in a tightening of the supply of such materials.  My guess is that terrorists will look to other rad materials for their maleavolent designs. The Litvinenko murder has the appearance of an assasination by an organization that actually has a mailing address.