Category Archives: Science

October 10 Nobel Prize Announcement

Note added 10/10/07– Gerhard Ertl won the prize for his work relating to surface science.  Looks like there is no future for me in the prediction game. That’s why I’m not Th’ Oracle.

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Any guesses as to who is going to win the Nobel Prize for Chemistry? I’m guessing Whitesides will be one of them. But, opinions are like noses- everyone has one. What do you think?

I mean, after all, he’s won everything else. Well, except for a slot on American Idol.

Publishing in Open Access Journals

In the course of searching chemical topics I keep running into the on-line publication Molecules, A Journal of Synthetic Organic Chemistry and Natural Product Chemistry.  This journal is part of MDPI, Molecular Diversity Preservation International, with an office in Basel, Switzerland.  MDPI is also dedicated to the “deposit and exchange of molecular and biomolecular samples”.

The idea behind this journal is to provide open access. The journal asserts that, with this approach, articles get substantially higher citation numbers. Open access is an alternative to paid subscriptions. In this model, the author pays the publication fee up front for peer reviewed editorial oversight and rapid publication.

This was covered by C&EN in the July 3 of 06 issue. It was stated in the article that Elsevier was planning to offer the same service for authors who wanted free access for a cool US$6,000 per article.  The Public Library of Science has a similar program, but with a more reasonable price structure.

What I find especially exciting about this publication mode is the MolBank service. Have you ever ended up with new compounds or data that was perhaps deserving of disclosure but not part of a body of work that would develop into paper?  Here is a blurb from the website-

Molbank (ISSN 1422-8599, CODEN: MOLBAI) publishes one-compound-per-paper short notes and communications on synthetic compounds and natural products. Solicited timely review articles will also be published. Molbank was published during 1997-2001 as MolBank section of Molecules (ISSN 1420-3049, CODEN: MOLEFW). Since 2002 it is published as a separate and independent journal. Molbank is a free online Open Access Journal. To be added to the subscriber’s mailing list, write your e-mail address into the “Publication Alert” box on the right side, and press the “Subscribe” button. Molbank is indexed and abstracted very rapidly by Chemical Abstracts.

Interestingly, this could be a possible venue for defensive disclosures in intellectual property. Hmmm … 

The question is, will paying-to-publish be cheaper than paying-to-subscribe? And, how will library administration have to change to accommodate this? 

But perhaps the bigger issue may be related to a certain snobismus that exists in regard to publishing. At some point, the rock stars of research (Whitesides, Trost, etc.) need to wave their hands over this mode of publishing and utter something like “verily, it is good” so the rest of the herd will thunder in that direction.

The writer of this blog has vented on this issue several times.  Putting public financed research results into free public access is the fair thing to do and should contribute to innovation and get new technologies into use at lower cost.  Turning over copyright of research papers to private third party groups only adds to the expense and complication to the use of this national treasure.

No doubt this will be vigorously opposed by the publishing establishment. The US$6000 fee charged by Elsevier is absurd and in reality is the beginning of the end of their publically financed milking of the R&D cash cow.

Dawkins: Speaking the Ineffable

Warning!! The following text contains links and declarative statements that may cause chafing or philosophical infarct.

The Richard Dawkins BBC programs “The Root of All Evil, Part 1 and Part 2“, are quite worth the time to view. It will no doubt be uncomfortable for some. Dawkins is very much a promoter of reason and doesn’t restrain his blunt questions at all. 

What is interesting to witness is Dawkins’ genuine surprise when a few characters respond with an absolute and even threatening rebuff to his reasoning.  I think he truly expected to move these people to see his point of view by the force of reason.  In many ways, this program portrays a world very hostile to the analysis of belief.

The whole notion of belief as an inviolable, sacrosanct capsule of “vital essence” seems to be hardwired into our brains.  For many, the prospect of another person drilling into your personal theory of the universe (God or physics) is both profane and invasive.  Like most people, I am not keen on being “examined” like some analytical sample either. But in the end, a “theory of everything” that can’t survive scrutiny is not worth having.

Perhaps where Dawkins goes astray is at grasping the difference between being analytically correct and just being comfortable with an idea.  Few people have the overlap of both curiosity and the opportunity to cover some new ground in the scholarly examination of the Big Questions.  In fact, it seems that the methodical pursuit of novelty is not a universal trait in culture.  A great many people are perfectly happy to live and believe as the ancestors did. 

Dawkins is not shy about drilling into the bedrock of belief. I think between Dawkins, Harris, and Dennett, there is a growing realization that religion should be studied analytically as a natural phenomenon rather than exclusively as a subject of devotion. 

Chemical Business in Russia- One Experience

Hearing of the passing of Boris Yeltsin, I can’t help but remember my trip to his northern empire in 2000.  We boarded a Lufthansa flight in Frankfurt, seemingly filled to the scuppers with jabbering Russian tourists anxious to return from their trip abroad. We left rainy Germany for the port city of St. Petersburg, near the mouth of the Neva River. Most of the terrain was obscured beneath heavy clouds so there was nothing to see until our descent at 10:30 pm. The sun sets late at 60 degrees north in the spring.  As we were coming down from cruise altitude, the lush green landscape became visible through breaks in the clouds.  We were going to land in Russia.

While the purpose of the trip was business, I was determined to soak in as much of the experience as possible. I had a total of one paltry year of Russian language in college so I could at least sound out the words and recall a tiny bit of vocabulary. 

In the late 1990’s doing business in Russia- that is, buying Russian goods- could be complicated. This was late in Yeltsin’s term and a kind of cynical take on the free market was beginning to set in.  Earlier, the eastern bloc had imploded and the communist hold on Russia was in deconstruction. Under Yeltsin a select few had managed to amass wealth- the so-called Oligarchs.  But as a few like Khodorkovsky were to eventually learn, wealth does not automatically confer political power in Russia.

Doing business in Russia was a highly manual activity. In 2000, the start of the Putin years, Russia lacked much of the business infrastructure that we in the west take for granted. When I say “business infrastructure”, I refer to the whole picture- commercial credit; internationally compatible contract and tort law; credible mechanisms for the flow of currency; GAAP; a multimodal transportation network; a comprehensible market exchange for commodities; and a market place with suppliers and specialists for the many instruments of finance and insurance. 

In the Yeltsin years, many formerly state-owned factories came under control of people who conducted business in facilities through quiet arrangements behind the curtain.  Factories would operate at low intensity or would even be shut down until orders came in.  Workers were furlowed and operated taxi’s or did other odd jobs until an order arrived.  Maybe this still happens today.  I don’t know.

We needed product that was made by a very few specialists in the world and one of those vendors was in central Russia.  Russian manufacturers are as skilled as we are of course, but there are differences in business culture that may be hard to anticipate.  Western standards concerning documentation was a particular problem.  I recall that our vendor was quite carefree about lot traceability and packaging.   They also had the maddening habit of reusing old lot numbers.

Then there was the problem of shipping.  Russia did not then, and still may not, have anything remotely similar to Aldrich.  Now, you probably think of Aldrich as the “chemical supply house” and you’d be right. But I’m thinking of Aldrich as the “master of logistics”.  Logistics in Russia was a problem.  Ground transportation was unreliable. Our solution was to hire a local to bird-dog the whole process.  It was worth every penny.

One of the differences I found was in the attitude of the few manufacturers I was in contact with.  They were usually aware of western prices for their goods and were never afraid to demand Aldrich-type pricing.   In the west, the customer is king.  That is just taken for granted.  Uppity suppliers are soon former suppliers. 

What I ran into in Russia was something that I hadn’t seen anywhere else, including China or Taiwan.  Our Russian supplier wanted to dictate terms and was unwilling to budge- I think they call it “Vlast”.  We absolutely needed better prices for the raw material.  I’m sure that there were urgent arrangements behind the curtains that were part of the need to stand fast. But in the end, it was their absolute inflexibility that caused them to lose the business. 

While in Russia I did try to source other raw materials and “vendors” who could supply spot buys of particular compounds.  At the time, many chemical factories were partially shuttered, so custom chemical processing capacity was very much hit and miss.  Processing equipment sat in dark and idled buildings waiting for a purchase order and prepayment. 

We met with principals in an empty flat to talk about the manufacture of custom compounds. But the same problem always arose. They wanted cash up front, preferably deposited in a European bank.  I was very clear that this was not the transaction model that we were accustomed to and in fact, this requirement was a showstopper. My Russian contacts were mystified that an American would come all this way only to refuse to pony up the cash to get the ball rolling. And that is where my attempts at trying to do business with Russia ended. 

The operators of the factories I was in contact with had the pots and pans, skilled staff, and expertise in the technology- these guys were first rate technocrats. At first glance, what they lacked was the benefit of investment capital to plow into their operations to find and service customers.  But, digging deeper, it wan’t just the hard cash they lacked. There was a system-wide lack of free market history and culture that, elsewhere, would have provided the institutions and mechanisms to exploit opportunity. 

I admire Russia and I believe that they will eventually get their system working well.  But they do need to get away from the fascination with the strongman model of governance. From my travels I have concluded that countries with cultures that date far back are simultaneously blessed and cursed by it.  They are blessed by the warm embrace of cultural richness. But they are also cursed by it because it can be a sort of ball and chain that complicates the adoption of change.

Note: This was written a few months prior to posting.

Copyright 2007

Thorium and Methanol

As we track down the back side of the petroleum curve, we will see a transition from the alkane/alcohol fueled Otto engine to a greater reliance on electric conveyance. Here is some wishful thinking-  Ethanol as a direct petroleum replacement will collapse under the weight of scrutiny as better cost data becomes available. Eventually, ethanol will be prized foremost as an oxygenate additive replacement for MTBE. 

Methanol and Fischer-Tropsch hydrocarbons from coal and biomass will provide high energy density fuels for the carbon-neutral future as petroleum scarcity drives other technologies into play. The Fischer-Tropsch liquified fuels technology from 20th century pariah states (Nazi Germany and South Africa) will assume a greater role in the post-petroleum age.

Fermentation of starch-derived glucose to ethanol and CO2 is too wasteful in the end to be attactive.  Fermentation of cellulosic material to acetate is more mass efficient. Esterification and reduction of ethyl acetate affords ethanol. One company, ZeaChem, (former coworkers, actually) is already working to bring this technology on stream. It remains to be seen how it will go over. I wish them well.

Electric power for the future will come from many sources. Distant, centralized power plants will channel energy across the grid to home-charged automobiles. Electrons travel fast and quietly over the lonely wire. They do not require fleets of ponderous 18-wheelers to move them around in limited quantities.

I see a future heavily reliant on electrons supplied from nuclear plants. Uranium-235 infrastructure will continue to supply fuel to nuclear plants for a long time. But the low abundance of U-235 (o.7 %) and the ever present proliferation potential of Pu-239 from this fuel cycle raises questions as to the wisdom of building U-235 nuke plants in the third or fourth tier states.

A more obscure nuclear fuel that is more abundant than uranium will see a phase-in as demand on the present nuclear fuel infrastructure exceeds supply.  That fuel is Th-232. Thorium-232 is  generally more abundant that uranium and has the additional benefit that it’s major isotope, Th-232 , is the nuclide of interest. Th-232 is not a fissile nuclide, but is a “fertile” isotope instead. Th-232 absorbs a neutron in a reactor seeded with U-235 or Pu-239 to provide an initial neutron flux to become Th-233, which beta decays to Pa-233 which further beta decays to U-233.  It is U-233 which is the fissile nuclide.  U-233 then participates in the fission chain reaction that generates the heat.

You can’t make a nuclear weapon out of Th-232, though in principle you could make one from U-233. The downside of a U-233 bomb is the high specific activity of this isotope.  U-233 is intensely radioactive and poses extra problems in handling.

The economics of thorium energy is advantageous in many ways to that provided by uranium/plutonium infrastructure. Thorium is abundant in monazite formations- reportedly up to 16 % thorium oxide.  The present problem with the thorium cycle is handling the intensely radioactive U-233 that remains in the spent fuel elements. Separate processing infrastructure will have to be put in place to supply reactors that burn thorium before this fuel can go forward.

An HTGR  Brayton cycle reactor with a helium turbine could provide up to 50 % thermodynamic efficiency.  Combine this reactor design with the potential cost savings of the more abundant Th-232, and you have a technology that is well set to provide power to keep the lights, cable TV, and the internet going into the post-petroleum age.

Check out the blog dedicated to Energy from Thorium. I’m writing about thorium because I think it is an important fuel and it needs to find its way to mainstream thinking.  

Feral Chemists. Gaussling’s 4th Epistle to the Bohemians.

Like the house cat that returns to the wild state when it leaves the house, chemists can go feral when they get out into the world.  The process begins the morning after graduation from college.  No exams to study for, no lab writeups to hand in. Being enrolled in coursework has a kind of edifying effect; a kind of regimentation that keeps one true to the discipline.

Human behaviour resembles a gas in some ways- we expand to occupy the space available to us. If bench space is available, we’ll find something to put on it. If condensers are in abundance, we’ll find a way to hook them up to something. If other distractions are available, our consciousness will expand into that space.

Some chemists quit learning after graduation.  They lose their gusto for the subject.  They acquired their bag of tricks in grad school and are quite content to stick with those tools for the duration of their careers. They become an intellectual couch potato- a 9 to 5 technocrat. Some companies are unaware of the value of professional interaction and refresher coursework.  Other companies just do not care.

A wise chemist once told me that the worst thing you could do in your career was to be a chemist in a company where chemistry was not the main activity. He was an IBM chemist and he spoke from bitter experience.

One of the most valuable assets of a scientist is curiosity and keeping it well honed is crucial.  Industry can bleed you of all of your professional enthusiasm if you let it.  Or, it can tempt you to go to the dark side- the business end.  Industry can exhaust you with endless administrative requirements and supervisory duties.  Insane deadlines and fickle management can bind you to seemingly impossible projects like a modern Sisyphus.  You’ll wear leg irons bearing the letters SAP, and speak in tongues- TSCA, MSDS, ROI, and CYA.

Through the years, unopened journals stack up on the floor. You can’t remember what an ACS meeting was like.  The paper in your college textbooks begins to yellow, and you become aware of your prostate. 

But the feral chemist has to resist. You have to rage against the stupifying isolation and indifference. It is important to periodically experience that rush of adrenaline that you get when some new concept opens before your eyes.  Open a journal and don’t set it down until you learn something new!

TED

Check out this video of Daniel Dennett talking about dangerous memes. Dennett is a philosopher specializing in the study of conciousness.  In another TED conference, he offers insights on this difficult topic. Our consciousness is not a universal chip set capable of processing all inputs with equal fidelity. In fact, our consciousness has rather serious limitations.

The TED conference videos are extremely rich in insights.  It is worth browsing the site for good talks.

The mechanism of consciousness is fascinating- it is one of the most important of all unresolved problems.  The existence of consciousness means that the universe is self-aware to some extent and is able to do experiments on itself. It also means that the universe is capable of acts that are set into motion by the compulsions of creatures, rather than the direct search for ground state. 

These acts are executed through the agency of physics, but sentient beings have altered the notion of spontaneity.  Life forms are able to counter the natural direction of entropy (locally) by channeling large amounts of energy to achieve improbable ensembles of atoms. With large energy inputs, creatures can move about, reproduce, or send robots to Saturn.

Ok, this is obvious, but it remains a rather curious attribute of the universe. 

Uranium Business Returning to Critical Mass

There is a saying that opportunity doesn’t beat the door down, it only knocks quietly. So it seems to be with uranium.  The American uranium extraction business took a big hit when the Three Mile Island accident happened in the late 1970’s. Nuclear power growth was tabled and only recently has it shown signs of recovery. 

With few exceptions, the rebound of the North American nuclear fuel business is largely invisible, apparent only if you go digging for signs.  One exception is happening in north central Colorado, near the town of Nunn.  A Canadian company, Powertech Uranium Corp., has acquired mineral rights to a sizeable parcel of land northeast of Ft Collins along the eastern side of I-25. It is called the Centennial Project and circumscribes an ore body estimated to hold 5.1 to 9.6 million pounds of U3O8, according to a technical report posted in the public domain at the Powertech website. The extent of U3O8 recovery would depend on the percent cutoff level of acceptable ore. The ore body is a discontinuous series of subsurface deposits with the top of the uranium mineralization at ca 82 feet below the surface. 

According to the report by Gorski and Voss, the average grade of the ore is 0.094 % and the average thickness of the vein is 8.8 ft (Table 1, latest estimate). Powertech has mentioned the possibility of in-situ extraction with bicarbonate leach as the means of removal of the mineral value rather than underground mining.

Naturally, the locals have not warmed up to the news that there might be a uranium mining operation in the area. A local group, Coloradoans Agains Resource Destruction (CARD), has put up a website (NunnGlow) and are vigorously lobbying against the development. In particular, the matter of leaching has brought a large negative sentiment to the forefront and Rep. Marilyn Musgrave (R-CO) has intervened with the NRC to allow a more lengthy public comment period in the permitting process. Locals are rightfully concerned about their aquifer and are entitled to some straight talk about the matter.

While I am generally in favor of uranium mining, I have to agree with NunnGlow in regard to contamination of the aquifer by this in-situ leaching process. Powertech needs to offer some compelling evidence that the aquifer won’t be harmed by their leaching operations.

Etymology of the Elements

Th’ Gaussling was interested to learn of an obscure author detailing an alternative and systematic nomenclature of the elements of the periodic table. The book is “Chemistianity“, by J. Carrington Sellars, F.C.S., printed in 1873.  The link provided is part of a larger chemical etymology website authored by historian Peter van der Krogt called Elementymology & Elements Multidict

Chemistry is such a large field and so rich in detail and history that we may forget how much struggle occured to give us even the most basic of concepts.  The science of chemistry largely rests on the behaviour of valence electrons confined to oddly shaped patches of 3-space called orbitals.  The nuclei set up the charge fields, but the chemistry is in how the electrons behave. It is the electrons that we manipulate in the laboratory to afford the wonderful spectum of chemical substances.

What is astonishing is the number of technologies and the extent of groundwork that had to overlap in order for our now cherished quantum/electronic theory of chemistry to arise. A long line of chemists like Berzelius had to produce and characterize new elements so Mendeleev could chart the patterns and predict new elements. Other workers would fill in the gaps.