May Linkfest

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A friend sent me the link to Wolfram|Alpha  just a while ago. So far it seems to be a bit lean in textbook-style content in the chemistry area. For instance, when you enter “aromatic solvents” into the dialog box, it returns with

Wolfram|Alpha isn’t sure what to do with your input.

But if you type in “toluene”, suddenly it is the CRC and is flush with data. The stated goals of the Wolfram|Alpha developers are-

Wolfram|Alpha’s long-term goal is to make all systematic knowledge immediately computable and accessible to everyone. We aim to collect and curate all objective data; implement every known model, method, and algorithm; and make it possible to compute whatever can be computed about anything. Our goal is to build on the achievements of science and other systematizations of knowledge to provide a single source that can be relied on by everyone for definitive answers to factual queries.

I do not yet know enough about this resource, but it seems to be a data engine rather than a prose engine.

Landscheidt Cycles Research is a site devoted to the Planetary Influence Theory. This theory pertains to the possible gravitational influence of the planets on solar cycles. it is worth a look.

Watts Up With That? is a blog concerned with global climate issues. The blogger and many of the commentors seem to have their facts straight about global climate change. The site is very data intensive.

If you are a scientist or manage scientists, it is worth considering the file drawer effect.

An online NMR predictor can be found at nmrdb. In my experience the splitting and chemical shifts seem to be in the “not too awful” range.

Biohackers

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A recent article in the WSJ solemnly described several amateur biologists who were doing simple molecular biology experiments in their homes. Naturally, this has not escaped the attention of certain authorities and certain deeply conservative establishment news corporations.

What is distressing is the reflexive conclusion that their activity is automatically dangerous and likely to be symptomatic of malevolent intent.  It is common for those in power to look over their ramparts and view the world as a spectrum of threats. And so it is in this case that distrust has arisen and reporters are using the words “weapons of mass destruction” or “ebola virus”. 

Could it not be that some people outside of the heavily in-bred fields of science have a genuine and scholarly interest in molecular biology but no interest in grad school?

The entrance to scientific activity is highly formalized with layers of degree requirements, preferred pedigree, institutional infrastructure, regulatory complications, and a mafia-like oligarchy that disperses the resources and opportunity that is so necessary for buoyancy in science.

How does a creative amateur scientist get to take a jouney of discovery in a field that is institutionally inaccessible to them? And how does an interested individual who is clever enough to conduct experiments deal with a government whose reflex is to see WMD and terrorists behind every lilac bush? There are serious civil liberties problems here that pit the brain stem against the frontal cortex.

It is in the nature of some people to be distrustful and find threats behind every shrub. It has been my observation that people who default into a distrustful posture are very often not trustworthy themselves. The distrustful often invoke slippery slope arguments as rhetorical devices to block their opponents move into new conceptual turf. What the distrustful and paranoid fail to see is that we live every minute of every day on multiple slippery slopes, yet we somehow survive and thrive.

The Venue

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This morning we moved our set into the theatre that we will be performing in for the next two weekends. This is my first acting performance in a decent theatre. It has clean dressing rooms below the stage and reasonably up-to-date lighting and sound capability. The theatre seats 400 and has been well refurbished over the last few years.

We have a tech crew running the lights and sound, a props & costume crew for scene changes, a makeup person, a set builder, and a few other gofers who handle the 10,000 details. All we have to do is remember our lines and avoid falling into the orchestra pit. The lead character has been sick for the last 10 days, so the producers have been nervous. He is a quantum computing physicist who happens to dig acting. The physicist gets the girl. The chemist gets to shout at people and whittle.

Last friday’s local paper featured a full page closeup of me, Th’ Gaussling, hamming it up on stage. Mother of pearl! Today’s thrill of standing on the set and looking into the auditorium was soon replaced by waves of nausea at the realization that this thing is really going to happen. Holy smokes. What have I done?

Cresson Gold Mine, Part 3.

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The Cresson Mine in Cripple Creek contains a good deal of fluorite. I was able to casually collect a few samples just lying in the road bed. In the photo below, the rock on the top has the most pronounced blue/purple color indicating CaF2 (fluorite). These specimens are not collectors pieces and are entirely unremarkable other than as indications of fluorite.

Cripple Creek Fluorite Indications (Cresson Mine). Copyright 2009 Gaussling.

Cripple Creek Fluorite Indications (Cresson Mine). Copyright 2009 Gaussling.

The mine business model requires heap leaching as a means of extracting the gold value out of the ore. Given that the ore is peculiar in that it contains gold in the form of gold telluride which cannot be leached out by cyanide, approximately 40 % of the gold remains in the host rock. The cost per toz of gold produced must be kept as low as possible and the way you do that is economy of scale.

The heap sits atop multiple layers of clay barriers and the 14,500 gal per minute of extract that flows out of the heap 24/7 is passed through coconut husk charcoal to trap the gold cyanide and the raffinate is recharged to the desired 100 ppm titer of aq NaCN and pumped back onto the pile. pH adjustment is a constant chore. The crushed rock is mixed with calcuim oxide prior to being dumped on the heap to maintain a high pH.

Building the Heap. Cripple Creek Cresson Mine. Copyright 2009 Gaussling.

Building the Heap. Cripple Creek Cresson Mine. Copyright 2009 Gaussling.

Cresson Gold Mine, Part 2.

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We collected samples of the lamprophyre in the bottom of the pit. The formation appeared whitish green in on the weathered surface owing to oxidation. However, if a fresh surface was exposed, the rock was composed of sugary dark xtals with the occasional biotite phenocryst.

Outlined Lamprophyre at bottom of Cresson open pit mine

Outlined Lamprophyre at bottom of Cresson open pit mine. Copyright 2009 Gaussling.

Cresson Mine Lamprophyre Close-up

Cresson Mine Lamprophyre Close-up. Copyright 2009 Gaussling.

Mafic or ultramafic rocks are low in silicates and enriched in Fe and Mg oxides. The lamprophyre above is mafic in composition with a sugary xtal matrix with biotite and other phenocrysts.

Breccia from Cripple Creek Diatreme

Breccia from Cripple Creek Diatreme. Copyright 2009 Gaussling.

The breccia above is characteristic of the Cripple Creek diatreme. Relatively rounded clasts populate the mass of the aggregate, indicating that the clasts were rounded by some process prior to deposition.

The gold is generally too dispersed to see, however, you can see pyrite with a hand lense in many of the samples. Pyrite often accompanies gold.

Cresson Gold Mine, Part 1.

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Early saturday morning 50 intrepid geotouristas packed into vans and drove to the CC&V mine in the Cripple Creek district of Colorado. Most of the group were professional geologists- professors, teachers, and geological survey folks. There were only a few interlopers like myself who were interested but untrained in geology. Not surprisingly, a background in chemistry is nearly useless when the discussion turns to stratigraphy and rock morphology.

The Cripple Creek gold district consists of an extinct volcanic structure called a diatreme. A diatreme is characterized by the presence of a volcanic pipe structure filled with brecciated rock. It is thought that the combination of shallow hot rock and ground water lead to violent explosions that resulted in fractured rock. Cripple Creek breccia has rounded clasts, indicating the rock fragments were exposed to rough, erosive treatment leading to attrition and rounding of the clasts prior to consolidation of the breccia.

In the past, gold mining at Cripple Creek was a underground activity. The district contains an extensive network of remnant subsurface works of drifts and shafts. Today, CC&V’s mining activity is limited to high throughput open pit excavation supplying pulverized rock to a cyanide heap leach field. A constant flow of ca 100 ppm aqueous sodium cyanide solution is leached from the top down through as much as 800 vertical ft of gold bearing rubble.

Abandoned Drift and Blue Bird Dike

Abandoned Drift and Blue Bird Dike

Columnar formations can be seen in certain locations of the mine (See photo: some features are enhanced with lines to show the margins). As the pit expands, drifts and shafts are exposed as seen in the photo above. The Blue Bird dike is an igneous intrusion into the surrounding formation. It is no coincidence that the drift in the photo is near the dike. It is common to see disturbed zones along the intrusion where gold can be found in higher abundance. The goal of the drift miner was to follow the enriched rock for more efficient reclamation of value.
Exposed Drifts During Pit Operations

Exposed Drifts During Pit Operations

A feature seen in the pit is a Lamprophyre, or igneous dike comprised of ultramafic, silica-poor, magnesium-rich rock. Biotite phenocrysts can be seen in samples. This is regarded as an unusual feature.

Lamprophyre formation in Cresson Mine

Lamprophyre formation in Cresson Mine

 The big haul trucks carry 300 tons of rock from the mine to the crusher. The crusher is actually a series of crushers that reduce the ore to pieces roughly 3/4 inch in diameter.

Haul Truck Carrying Rock from Blasting Site to Crusher

Haul truck carrying rock from blasting site to crusher The crushed rock is blended with lime and then driven to the leach pile for extraction. Another load for the leach heap.

 

A Massive Au/AuTe Deposit

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Th’ Gaussling attended a geology seminar thursday evening at the Colorado School of Mines. It was given by the chief geologist at the Cripple Creek & Victor gold mine (now AngloGold Ashanti) and was concerned with 3-D modeling of the volcanic formation that forms the center of the deposit.

What is unusual about the CC&V mine is the extent to which tellurium is present. There are a dozen or more tellurium minerals and many of them are present in the ore body. The CC&V load was discovered relatively late- about 1891. Due to the extensive fraction of AuTe and AuAgTe minerals, the presence of the ore body was not detected by placer prospecting. 

Prospectors panning for gold in local streams had no way of knowing that extensive gold was present because AuTe(Ag) minerals do not have a gold-like appearance.  Legend has it that it was discovered by a drunken cowboy who noticed some native gold in an outcropping in the area and took a sample down for assay. As I have mentioned before, the Cripple Creek district has produced about half of all the g0ld to come out of Colorado.

What is key to the formation is the fact that it has zones of extensively altered volcanic rock disturbed both mechanically in the form of fractures and faulting, and chemically in the form of its potassic-alkali nature. The formation has strongly brecciated zones and is desribed as “vuggy”, meaning that there are extensive voids. Native gold and gold telluride mineralization can be found on the surfaces of the vugs. The mineralization was deposited by hydrothermal streams extracting Au and Te from unknown source rock.

Presently the operation is surface mining which feeds to a cyanide leach field for gold extraction. The surface pit mine is working downward, digging through the extensive network of mineshafts. In the early days at Cripple Creek the mining was limited to underground activity. Miners would follow the extensive subsurface network of gold-rich veins in whatever direction they might go. The result is a very complex and extensive matrix of tunnels and shafts that extend downward to as low as 3000 ft. In the early days, the economics of subsurface vein mining were attractive enough to sustain the operation. Today, the economy of scale dominates and pit mining with heap leaching of the lower grade ore is what sustains the operation.

The gold is recovered by a cyanide leach field that is 800 ft thick in places. This method produces ca 300,000 toz/yr. The process does not recover Au from AuTe. It is left untouched in the leach heap and constitutes ca 1/3 of the total gold present.

Curiously, during the many eruption cycles in the distant past (~32 ma), debris from the surface has washed back deep into the formation. Bits of woody debris have been recovered within cementitious rock hundreds of feet below the surface. The CC&V geologist showed a core sample with a wood fragment imbedded within it. For a time reference, the current episode of Rocky Mountains (the Laramide Orogeny) began ~65 ma.

Chemist Gaussling will blend in with a group of geologists tomorrow morning and take an extensive geology tour of the mine site. Hopefully, there will be pictures to share. We’ll be going up to ~10,000 ft, so it will be chilly.

LC Dreamin’

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When I get to work this morning I’ll be greeted with a brand spankin’ new Agilent 1200 HPLC sitting on the bench in my lab. It has a diode array detector (no flippin’ MS this time). Pretty sweet.  Gosh, early 1990’s LC capability- already!

It is interesting how the installer assumed I’d be doing reverse phase work. Must be what most of the weenies in pharma are using. Carbon-heteroatom-carbon-heteroatom-carbon-heteroatom-carbon=heteroatom-carbon-heteroatom- … maleate.

Organic Symposium at CU

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The 41st National Organic Symposium starts 7 June, 2009, in Boulder at the CU campus. I’m trying to decide if I want to go bad enough to pay the admission price.  The registration is rather pricey- $400-425, depending on your membership status. The symposium features a lineup of some of organic chemistry’s top rock stars and illuminati.

The whole fandango begins with a homily by Bobby Grubbs on what else? Metathesis. Good lord. I don’t think I can bear to see it again. I wonder if he’ll disclose the patented art during his talk? (These guys never point out that the cool and useful stuff is tied up in claims!)

I popped into a few web sites of the various rock stars who will be presenting. I noticed that Dale Boger is selling his lecture notes on-line for US$120 for a CD.  Fancy that.

Apparently, he is still working on Vinca alkaloids. Buried in the Boger website is a graphic showing the various and complex compounds that his groups have prepared. It is pretty amazing, really. But it is as much an indication of what generous funding and hordes of rabid post-docs and grad students can provide as anything else. Boger is listed as an inventor on 25 US patents (with Scripps as assignee) by my count. Scripps owns a bunch of Boger technology. I wonder if any of it is commercialized? I don’t know the guy, so I don’t want to be too obnoxious here.

If an advisor is patenting the work that a student is doing for her/his dissertation, how do they manage the notebooks (i.e., disclosures) and the meetings with the students committee? If the student is helping to develop IP for someone else, are they decently paid for it? Does the student have multiple notebooks for confidential and “public domain” work? What kinds of liability does a student have in terms of proprietary information after they graduate? Lots of sticky issues for a fresh graduate.

NCC 1701

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“To boldly go …”.  The worlds most famous split infinitive lives on. Better yet, tatted Romulan skinheads bring doomsday to a theater near you.  To the delight of Trekkies everywhere, the latest incarnation of the Star Trek franchise was just released. Clearly, it was designed  for the Yuppy Trekkie crowd of viewers who were assimilated decades ago into the original Star Trek setting.

Rather than introducing a new crew of characters with a new set of quirks and dynamics, this movie sets the stage for the original cast and crew. The time setting of this episode puts it between Star Trek: Enterprise and the original TV series. The movie is well cast with strong character conformance with the original crew.

The stark difference between this production of Star Trek and the original made-for-TV series is the highly engineered style of film making. The cinematography and editing are best described as frenetic and delerious. Decades of television production are recorded via standard sound stage cinematographic sensibilities where the cameras are firmly planted to dollies castering around on a flat surface. Perfect focus and reference frame squareness and stability were as consistent as the print on a dollar bill.

In this production of Star Trek the camera is an extension of the viewers senses rather than just a means of recording scenes. It’s use is meant to amplify and focus the confusion and danger of the scene. Closely framed scenes of objects in wreckless motion, off-focus shots, and obtuse tilt angles bring the action past your retina and into your brainstem. It is quite effective.

And yes, Kirk suffers from chronic lackanookyitis. He does get a bit of technicolor action, but it is only slightly more racey than the classic shot of him pulling on his boots after a romantic encounter. If you see the movie with your mother, sunday school teacher, or kids it is unlikely that anyone will be too embarrassed.

I attended with a quantum physicist friend and we agreed that some of the physics was deeply flawed. Scotty’s cabbage creature friend was odd and the ending was less than satisfying. Nonetheless, I would rate this movie a strong thumbs up and most preferably viewed in a decent theater with a big screen.