Bright, young and photogenic

Having a quiet beer in Cambridge with friends yesterday evening our peaceful drinking session was disrupted by the arrival of a boisterous group of snap-happy first-year students. Eager to impress these bright young things, my friend Paul offered to take a couple of photos of the whole group, but came unstuck when attempting to grab the second snap.

Fortunately, one of the freshers pointed out that the camera needed “winding on” and all was well.

But, it got us thinking…winding on..? Wasn’t this Cambridge, international centre of academic excellence at the heart of the so-called Silicon Fen high-tech industry?

Maybe, given the number in their crowd wearing tweed jackets and the like it wouldn’t have been any more surprising if they’d been using a Box Brownie.

Green Fluorescent Protein

The eerie green glow of a jellyfish protein is perhaps nothing sinister, but the anti-science lobby will be having a field day when they hear about the latest amazing research underway at Rockefeller University.

There, Albert Libchaber’s team has created a vesicle that can express genes as if it were a living cell, and in particular the gene for the jellyfish’s green fluorescent protein (GFP). The artificial cell comprises lipids from egg white, various bits of E. coli, and a viral enzyme for good measure.

All of which, to many non-scientists, will sound like a Sci-Fi recipe for disaster. The reason for using GFP is that it provides such an obvious indicator of success, just imagine the headlines if they had used the gene for botulin or some other deadly bacterium. Indeed, who’s to say they haven’t? Watch out for another Michael Crichton blockbuster coming to a bookstore near you soon…

UPDATE: The discovery and development of GFP has won three US scientists the https://www.sciencebase.com/science-blog/nobel-prize-for-chemistry-2008.html.

Scholarly Silliness

The American Chemical Society is suing Google to defend its trademark SciFinder Scholar from confusion with Google Scholar. There’s a lot of worthy discussion about the problem on the CHMINF list. ACS is obviously worried about that word "Scholar" being used by Google and that Google’s millions of users might assume there is a connection. But the pundits should get real, I’m pretty sure that outside of chemistry, 99.999% of the world’s population will never have heard of the American Chemical Society let alone, SciFinder Scholar and only a fraction of those billions have even heard of Google, and of those that have, even fewer will have heard of or be even vaguely interested in Google Scholar.

Anyway, isn’t the word “scholar” a generic term relating to education in some way? Surely, it’s analogous to the word quot;cola" which comes in many flavours made by many different companies? If Google had called their academic search engine Google Scifinder, I suppose that would have been very different. The lawyers must be rubbing their hands with glee. (Incidentally, there are 29 hits when one searches PubMed with the author field "Scholar"), I wonder if I could change my name to Dr Searchengine Scholar?

Accidents will happen – laboratory health & safety

TL:DR – Short feature article by David Bradley Science Writer on laboratory health & safety that originally appeared on BioMedNet.


A friend of mine who works in a biotech lab in Europe suffered a bout of what he thought was hayfever this year…snuffling and runny nose, itchy and sore eyes, the usual thing…except this was in February!

He took a few days sick leave – it was that bad – and the symptoms subsided. Until he went back to work, where he took up his experiment – enzymatic chemical synthesis – where he had left off. The devastating result was far worse than the snuffles he had suffered before his sick leave – his neck and face went bright scarlet, he started shaking and collapsed gasping for air. Anaphylactic shock was the diagnosis. He had to leave his job although the lab in question has implemented very strict protein-powder handling control systems, it’s the kind of accident that is almost impossible to predict and potentially more common than ever.

There are more unusual accidents. In December 1999, Emory University in Atlanta paid out $66,400 in fines and changed its procedures following the death two years earlier of primate researcher Elizabeth Griffin who contracted herpes B after being hit in the eye with fecal material, urine, or saliva while putting a rhesus monkey in a cage at the Yerkes Regional Primate Center.

A small-scale lab accident may involve someone mixing something and getting an unexpected exothermic or explosive reaction. The results often reach the community by word of mouth and through a note in the literature. For instance, Toshi Nagata of the Institute for Molecular Science, Okazaki, Japan, recently reported an accident while following a literature procedure published ten years ago.

The chemical preparation involved synthesising a brominated bipyridine (Can. J. Chem. [69, 1117 (1991)] but instead of using standard quantities Nagata’s team had scaled it down to a tenth. While they were purifying the product, the 100 ml reaction flask exploded violently injuring one of the team in the arm. Nagata suspects that the problem lay in the formation of a peroxide by-product that would have been less concentrated on a larger scale. Nagata, wrote to Chemical & Engineering News saying, “I do not intend to blame the authors for not describing the danger, but all chemists should be aware that this procedure could be dangerous.”

Guidelines and regulations are all well and good but what about insidious threats like this? Such incidents beggar the question of how might they be predicted. Should there be stricter guidelines for the way procedures are described in the literature? If so, what might they be and how would they be applied?

In 1995, a seemingly small-scale spill of hydrofluoric acid killed a technician in Australia. He died from multi-organ failure two weeks after the incident. Several factors contributed to his unfortunate death, according to the official report – he was alone, wearing only rubber gloves and sleeve protectors but nothing covering his lap, He was working in a crowded fume hood. The lab had no emergency shower, nor any calcium gluconate gel antidote available. The lessons may be obvious. But, accidents happen to even the most experienced of scientists.

The slow death that befell Dartmouth chemist Karen Wetterhahn when she was exposed to a few drops of the highly toxic dimethylmercury in August 1996 took several months to kill her. Although Wetterhahn was wearing latex gloves this compound rapidly penetrated them and was absorbed through her skin. Ironically, she was at the time using dimethylmercury to examine the effects of toxic metals, such as chromium, on human cells. While, in October this year, Michal Wilgocki of the University of Wroclaw in Poland, a chemistry professor of thirty years experience, died after an explosion in his laboratory. Firefighters have suggested the accident may have happened while Wilgocki was drying unstable perchlorates.

So, who ensures that rules and regulations are adhered to in order to prevent accidents? Who makes sure the fume-cupboards and filters are up to a high enough standard and the reagent bottles are stored safely?

According to Jim Kaufman of The Laboratory Safety Institute (LSI) https://www.labsafety.org, “There are three levels of responsibility. First is Management. Safety is their responsibility. Preventing accidents and injuries is their responsibility. If you manage others, you are responsible for their health and safety. You have to enforce the rules,” he explains. “Second is the Chemical Hygiene Officer and the lab’s safety committee. They are advisors and recommenders. Third is everyone. Everyone needs to be responsible for health and safety. Follow the rules, report accidents, injuries, and unsafe conditions.”

Organizations such as LSI – formerly the Laboratory Safety Workshop a not-for-profit center providing a focus for safety in science education, work, and our everyday lives. The LSI makes several assumptions about the level of knowledge of those “in the know”, they say “You know the hazards, you know the worst things that could happen, you know what to do and how to do it if they should happen, you know and use the prudent practices, protective facilities, and protective equipment needed to minimize the risks.” But, when the pressure is on, there can always be a proverbial roller-skate left on a stair to wreck the best of intentions.

With the ubiquity of the Internet, every lab now can have instant online access to its health and safety rules and guidelines. The Biological Safety Policy of Washington State University at Pullman is a typical example of the materials freely available. One aspect of safety that is often ignored is that while personal protective equipment (PPE), such as eye protection, lab coats and fume hoods are usually essential, there is an alternative and that is to better design an experiment so that the hazards are controlled without resorting to PPE. If safer materials or processes are available or the whole experiment can be enclosed then that reduces risks.

There are numerous career opportunities in the field of safety. And quite a few glamorously named positions available, many of which are fairly synonymous job description minutiae aside. There are process/equipment safety engineers and technicians, laboratory safety officers, environmental protection agents, industrial (and chemical) hygienists, environmental, safety and health specialists, occupational health specialists and many others.

Most of these positions require at least a Bachelor’s degree in a technical subject, usually chemistry, biology, engineering, or physics, and it is, of course, possible to graduate in Industrial Hygiene or the related Occupational Safety too. One important aspect of many of these positions is that they usually require that the jobholder can physically wear appropriate personal protective equipment (PPE) and be capable of functioning while wearing respiratory protection. Which precludes some applicants on medical grounds.

An experienced industrial hygienist might work within an institute’s Occupational and Environmental Safety Office, for instance, and be responsible for coordinating support for the various laboratories, and ensuring employees, students, visitors, (patients, if they are working in a hospital), and the surrounding environment are protected.

Jason Worden has just completed his first year as a Laboratory Safety Technician at the University of Idaho, and has enjoyed the experience so far. “I work at a University in the Environmental Health & Safety Office,” he says, “My job includes surveying/inspecting labs on campus and testing and maintaining safety equipment. Another part of my job includes Radiation Safety duties as well as responding to Hazardous Material Emergencies and general office duties.”

There are important differences between the various job descriptions though, for instance, a safety engineer deals with protection of people and property from injury and damage investigating incidents. Whereas an industrial hygienist may be looking at protecting people from more insidious threats, injuries and illnesses that come about because of exposure to chemical agents or materials that may not be such an obvious hazard as a boiling vat of solvent outside a fume hood.

Jay Jamali is Environmental Health & Safety Director at Enviro Safetech Incorporated, a San Jose based company https://www.envirosafetech.com. So, what routes are there into safety? “I have a client that went from researcher to safety specialist in a biotech company,’ says Jamali. “In other cases the safety staff have no background in biotech.” He adds that the position of “safety officer” is usually dependent on size of an organization or institute. “Smaller organizations assign safety to multiple site personnel,” he explains, “some doing chemical hygiene plan, same radiation safety, some bloodborne pathogen safety, some laser safety, some doing the personal protective equipment and some the lab safety.” On the other hand, outside contractors, such as Enviro Safetech, can take on the entire safety support operation on an as needed basis.

Bill Paletski of the Pennsylvania Technical Assistance Program (PENNTAP) https://ww.penntap.psu.edu points out that “flexibility and diversification is your key to beginning a career and improving it in the field of safety.” He suggests that without, belittling education, “Degree after Degree will not help…getting your feet wet is a good start.”

Many countries have regional safety departments that also inspect laboratories while every university should have a safety officer or section. Companies too, of course, are usually bound by law to ensure the safety of their staff and visitors to their labs. Pay with a government agency, such as OSHA or EPA, is generally not as high as with a permanent position within an organization but they do offer good experience and training, according to Jamali. On the whole though pay is usually commensurate with experience, degrees and initials.

“The work is very addictive,” Jamali enthuses, “and very few leave the field after they get in because it gets under your skin.” He adds, that, “The key to success is to be a generalist, specialize in one of the three [main] fields and be an expert in at least two topics in your specialty.”

There are many specific problems that have not previously been such a concern in lab safety. Bio and chemical terrorism. Post-September 11, safety issues have been brought into sharp relief. Although most institutions are carrying on essentially as normal, security will ultimately impact on working practices in laboratories around the world. According to a spokesperson for Cornell University, “We’re still discussing all of this at various levels and there aren’t any clear answers. The one place that’s definitely involved is the College of Veterinary Medicine, where research on anthrax has been ongoing for years.”

Merle Schuh is a chemist at a small college – Davidson in North Carolina. He reckons in terms of the safety of faculty and students, “We have not instituted any new security measures or management procedures as a result of the increased threat of terrorism. We have always been conscious of safety considerations and lab and building security, and our present activities and procedures are deemed adequate,” he told HMSBeagle. “Since we are a small college, most students and faculty recognize each other, and any strangers to the chemistry building and other science buildings during daylight hours would generally be noticed.”

Working down a mine or on the high-seas, one might anticipate a real sense of danger when applying for the job, it might even be one of the thrills of the chase, but most researchers, perhaps with the exception of those delving into active volcanoes or deep beneath the waves do not actively seek out the hazards.

Instructors at colleges and universities have a duty to emphasize and teach safety to their students. Proper education leads to awareness of safety issues and self motivation for their personal safety and the protection of others. “By the time science students graduate,” says Schuh, “ideally their conscientiousness about safety issues should be as well developed as their skills in doing laboratory work.” These days, not even the smallest or most ill-equipped lab has an excuse for failing to do its best to keep its researchers safe. But, still, in real life there is no safety net.

This article first appeared in my Careers column on BioMedNet

Doubling up biological names – Tautonyms

I wrote this tiny snippet back in the day and a long time ago discovered that they’re called tautonyms, they basically represent the “type” of a given genus. I wrote about it recently with respect to the many birds that I’ve photographed with tautonymic binomials. Also, some more recent items on tautonyms here and here.

Rattus rattus (black rat) is coming to a town near you, while Gallus gallus (wild chicken) has got scientists all in a flap (you’ll find out why later this week). Then there’s Bubo bubo (the eagle owl)…Buteo buteo (common buzzard), and many others. Some tautonyms are trebled – Gorilla gorilla gorilla, being the Western Lowland Gorilla.

UPDATE Christie Wilcox just mention Boops boops on twitter, it’s a seabream colloquially called a bogue.

Genetically Modified Cocaine

Developed nations continue to argue the toss about the safety of genetically modified crops and foods, but meanwhile in remotest Colombia, coca farmers are reported to have produced a GM coca plant.

There is much bluster from the authorities that the plants are nothing but a product of improved fertilisers or a better compost. But, that smacks of denial to me. The plants are almost three metres tall, are resistant to most common weedkillers and apparently produce four times (according to the Financial Times; eight times, says The Independent) as much cocaine as normal plants. If that’s just the result of a trip to the local garden centre for a sack of soil improver, then someone can send me a couple of bags for my tomato plants next spring!

Burning Water

Photo from www.joe-ks.com

Just this minute, I received an email from someone claiming they had discovered how to burn water.

No matter what experimental conditions they set up this is physically impossible – fundamentally standard combustion involves the oxidation of some material into the oxidized form of that material and water. The reaction 2H2 + O2 –> 2H2O puts it at its simplest. Energy is released in this reaction. The reverse process is possible, it can be done by adding a small amount of ionic material to the water to make it a salt solution and passing through it an electric current. That splits the water molecules, releasing hydrogen gas and oxygen in a process known as electrolysis. But, this is not combustion, energy must be fed into the system (electrical in this case) to split the water molecules, the ionic salt particles simply act as carriers of the current.

The notion that somehow you could overcome the bonding between hydrogen and oxygen atoms in H2O might be overcome in a combustible manner rears its ugly head on a frequent basis. But, as you can see it’s just not tenable. If you were stupid enough to connect a car battery’s terminals to a bowl of salt water, you could ignite the resulting hydrogen bubbling from the mixture, but that could be no more describes as “burning water” as baking a cake by mixing and freezing the ingredients in a cake tin.

The idea that burning water might be possible is yet another example of the kind of thinking that repeatedly suggests perpetual motion might be possible, it’s desperate grasping, it’s almost a cry for help: “We have messed up the world, but I can fix it, if you listen to me!!!” That kind of thing!

And, while we’re at it, there’s a College in the UK that offers absolutely no science courses, but does offer dowsing, and advanced dowsing! It’s the Women’s Institute Denman College, apparently.

This post, was originally published in the old Sciencebase blog – SciObs – on December 8, 2004, but I’ve resurrected it and edited it up in the light of events that took place in 2007. You can read about the posts that emerged here:

How not to grab the blogosphere – this one is very closely related to this old post.

Free cure-alls – not just cure-alls for disease but for all the problems that ail the world. Yeah, right!

Telesales Revelations

A British telesales company recently sent off its workers’ computer keyboards for analysis to a nutrition expert to find out exactly what its staff were doing at their desks in terms of eating habits. Unsurprisingly, the analysis of the detritus stuck in and among their keys revealed that most staff were snacking heavily on sandwiches, cakes, pasties and the like while working at their desk. Splashes of tea and coffee were also commonly observed. Fragments of crisps, grains of sugar and nail clippings (toe and finger!) too emerged from within many of the keyboards after a good shake.

But, never mind the snacking and personal grooming. A male pubic hair found stuck under one worker’s "ESC" key has not yet led to a dismissal. The company, however, is planning to move to an open plan office rather than its current cubicle-based layout to reduce the alleged, ahem, "time-wasting" that was presumably underway in at least one workstation prior to the analysis.

Chemical Image Problem

It’s not been a hot week for the image of the chemical industry. This week marked the 20th anniversary of the Bhopal tragedy. There were more revelations about problems with pharmaceuticals. Researchers reported that benzene is worse than we thought even at low levels. And, the industry is denying WHO claims that chemicals harm kids.

Couple that with further discussion about the future, or rather lack of, chemistry teaching at British universities and the supposed benefits of downsizing the number of chemistry departments and one begins to wonder whether there will be any chemical industry to speak of in five years time.

Chemophobia has been high on the agenda perhaps since even before Rachel Carson’s Silent Spring. What is to be done about redressing the balance? Industrial visitors to Sciencebase may wish to get in touch with their ideas…