Category Archives: Chemistry

Biohackers

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.

Cresson Gold Mine, Part 3.

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.

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.

A Massive Au/AuTe Deposit

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’

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

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.

“Don’t Even Taste Like Sewage”

I spent 4 1/2 hours saturday touring our town’s water system from both ends. It was quite a detailed tour and, since it involved chemicals, how could I not tag along?

We began with the sewer reclamation plant first. Lots of interesting details here. Turns out that one of the big problems to running a waste treatment plant has to do with keeping large debris out of the pumps- rags, underwear, shoes, plastic parts, etc.  Once you get past the shock of learning what your fellow citizens can and do flush down the toilet, it is plain to see that a bit of money spent on screening out the the big chunks is returned in the form of reduced down time and pump repair costs.

Our little hamlet of 6,000 souls sends 450,000 gallons of waste water to the reclamation plant on an average day. The flow peaks at about 8 am every day in the form of a sudden 5-6 x increase in flowrate. It takes about 90 minutes for an average volume (i.e., a flush) of wastewater to get to the plant. A lot of groggy citizens hop into the shower at around 6:30 am.

After the incoming stream passes through a grit removing station at the entrance, it is lifted to the first treatment operation for aeration and fermentation. This is the physical high point in the process, meaning that the stream is subsequently transferred by gravity for the remaining process steps.

I won’t go into further process details other than to say that the final step prior to discharge into the stream is a sanitizing step where the effluent is exposed to a large jolt of UV radiation. At this point in our tour, the plant manager dipped a sampler into the flow and withdrew one liter of clear, colorless liquid with a few strings of algae floaters. Only too eager demonstrate his faith that the water was sanitary, he dipped a finger into the effluent, put it into his mouth and exclaimed with a grin as wide as his mullet

“It don’t even taste like sewage!” 

As he passed the sample around so others could share in the experience, I wandered over to the control panel and feigned interest in the LCD display. The UV just renders the wee beasties non-viable. Their little microbial carcasses are still there. Pathogen free it may well be, I didn’t have the stomach to taste it. Yes, I know that microbes are everywhere and that our notions of what constitutes “clean” are merely a fantasy. But I just couldn’t do it.

A hot little number

hot-load-on-the-interstate1

I see these shipping casks on the highway at least once a month.  This time I had a Canon with me (Powershot A470, you know, a camera). While sitting at the off-ramp stop light next to this container I began to wonder how much activity shines through the shielding. I began to daydream … if I could see in the gamma spectrum, would this thing be bright or dim?

Then, in the blink of an eye the spell was broken. The light turned green and I parted company with this hot little number.

Franz Ritter von Soxhlet and the Hungarian Siphon

Franz Ritter von Soxhlet is credited with inventing an extraction apparatus in 1879 that now bears his name. Soxhlet was a German agricultural chemist of Belgian “extraction” from Brünn (now Brno in the Czech Republic) working in the area of milk characterization at the Vienna Agricultural Institute.

Soxhlet spent most of his career in the analysis of milk and its constituents. In an attempt to isolate the fatty constituents from milk, he (and students) had been attempting to use an extraction apparatus developed by another Brno chemist, Professor Zulkowski. Soxhlet developed a technique whereby milk was absorbed into a quantity of calcium sulfate powder and then submitted to extraction by ether. The Zulkowski apparatus proved problematic, however. Solids were able to find their way over the extraction tube and into the solvent reservoir. Modifications of the design also suffered from inefficiencies that apparently required extended operation.

A student of Soxhlet, a Hungarian fellow by the name of Mr. Szombathy, contrived a solution to the problem. Szombathy is credited with coming up with the clever siphon feature that so distinguishes what we now call the Soxhlet extractor.

It has been lamented that the efficiencies gained by the siphon discharge design have been partially lost due to the entertainment effect. Generations of chemists have dropped what they are doing to stand and watch the collection thimble fill and subsequently discharge dramatically through the siphon. You have to take your fun where you can find it.

Well done, Szombathy!