Blogroll: Better online science

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Matthew Partridge penned the September 2015 column.

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Pictures taken in a lab and pictures of far-away worlds underpin great examples of scientific communication.

As scientists, we all strive to be better at communicating our work. Paige Jarreau at From the Lab Bench explains this very succinctly in her post about a talk she attended on scientific story telling. The Picture it… Chemistry blog goes into more detail with a step-by-step guide on how to write a science blog post. This fits with Laboratory News‘ newly launched Shout It Out service which aims to encourage scientists to start shouting about their science — even if they don’t have their own blog.

But science communication is not always about sharing your own work — sometimes it’s about discussing and better communicating other popular science. Nowhere was this more important than the recent flyby of Pluto, as eloquently explained by Phil Plait at Bad Astronomy. And to help fill in some of the details for non-astrophysicists, C. C. Petersen at TheSpacewriter’s Ramblings prepared a great primer on planetary geology to help explain Pluto’s apparent geological activity.

Finally, there are some excellent examples of communicating science via YouTube. Maren Hunsberger‘s superb video series at Lunchbox Science has recently tackled ‘How fire works’. The very popular Vsauce3 takes time to try and explain the real physical implications of being Ant-Man. And Tom Scott teams up with Robert Llewellyn to try and answer ‘Are batteries heavier when they’re full?’. Even if we might already know the answers, these videos show how we can make science more engaging.

Written by Matthew Partridge, who blogs at https://errantscience.com/ and tweets as @MCeeP.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the September 2015 article]

Blogroll: Chemistry education

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Michael Seery penned the August 2015 column.

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Embedding scholarship into the teaching of chemistry.

With teaching quality high on the agenda, chemistry education research is beginning to emerge as a discipline within some chemistry departments. Tina Overton writes on the RSC’s Education in Chemistry blog of the need to support staff who wish to carry out pedagogic research in chemistry departments, including supporting the development of expertise and creating a community of practice. In the case of the latter, chemists in the Twitterverse might like to follow and contribute to #chemed.

Lots of expertise is available on the Staff and Educational Development Association blog, currently running a series called #53ideas by Graham Gibbs. These are short posts on various thoughts and ideas that “teachers should know about” underpinned by substantial literature. Some of Gibbs’s own work was with the chemistry department at Oxford. In a recent post, he advocated a more pragmatic framework for programme design in lieu of distinct educational objectives.

Greg Ashman keeps a well-written blog on cognitive science (and educational research generally). His post on ‘cognitive load theory’ challenges some widely held assumptions about what ‘guided instruction’ is, raising the bar for all of us interested in improving student learning. Ashman’s blog is one of the many compiled by the aggregating website The Echo Chamber which is well worth a perusal to find decent blogs about education.

Back to chemistry: while the Compound Interest posters are deservedly well known, lots of use could be made of the This Week in Chemistry series. I’d love to see student-generated examples shared with #TWIChem.

Written by Michael Seery, who blogs at https://www.michaelseery.com/ and tweets as @seerymk.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the August 2015 article]

Blogroll: Patently inventive

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Luke Gamon penned the July 2015 column.

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Toxicology, the odds of discovering a drug and creativity in design.

Spurred on by a tweet from C&EN’s Lisa Jarvis, an active discussion has developed on Twitter and in the blogosphere about the odds of a chemist discovering a drug over an entire career. Some number crunching by Derek Lowe, writing at In The Pipeline, produced a figure around 1%. Ash Jogalekar at The Curious Wavefunction argues that the question is more complicated and wonders whether “the patent system has become biased toward chemists”. In the protracted, multidisciplinary development of a drug, who is truly responsible for its invention?

Over at The Dose Makes the Poison, ForensicToxGuy writes of the more illicit innovations in synthetic cannabinoids and what can be considered to be the ‘wild west’ of drug design. The creativity of these outlaw medicinal chemists in developing chemical diversity never ceases to amaze and is creating a “public health nightmare” of substances with unknown pharmacological and toxicological effects. Meanwhile, writing at amphoteros, Andrei Yudin talks of chemical aesthetics and the merit of elongated molecules in drug design, however ugly they may be.

While the chemical sciences continue to innovate, Vittorio Saggiomo delves into the history of Parafilm — another ugly, yet incredibly handy invention — on his blog Labsolutely. Many would shudder to think of a laboratory without that greasy, stretchy film. Finally, the ever-present Kristof Hegedüs at Pictures from an Organic Chemistry Laboratory tells a cautionary tale of a nitration gone wrong and the importance of a good lab coat. Even the most commonplace of innovations may well be the most vital.

Written by Luke Gamon, who blogs at https://lukegamon.wordpress.com/ and tweets as @lgamon.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the July 2015 article]

Materials Girl: End of the beginning

[Posted on behalf of Materials Girl]

Just a few months ago, I was floundering to bring my projects to a reasonable stopping point and unify them into a coherent story (aka: my dissertation). The postdoc in our research group assured me that any self-perceived lack of direction and internal bursts of sheer panic were normal, while our sole PhD alumnus offered advice and described his similar tribulations on the road to graduation. YKW (my advisor) was perpetually ‘busy’ and stuck to his ‘hands off’ strategy, leaving me to forge my own path (and procure my own funding). More than once, I felt completely and utterly lost.

However, only one option existed. Nothing was going to keep me from earning my doctorate, so I pushed past the bouts of fear, anxiety, doubt, anger, and hopelessness. Even when the path was unclear, I set deadlines, sat down, and forced myself to crank out manuscripts. Although half of my projects ended up excluded from the dissertation, I made something out of what previously felt like nothing. I wrote frantically, I set my defense for April 1st (no joke), I made slides like a madwoman, and I finished.

And so, everything now ends, and begins – it is the end of my journey as a graduate student, and the beginning of a real career. Baby steps are still in order, to avoid freaking out about real life and my future. (Do people really know what they want to be when they grow up? At age 27, I’m still wondering). The next step is a postdoc position, which has been waiting for me since last fall and helped motivate the rapid progression toward finishing my PhD. I’ve moved out of sunny SoCal and joined the chemistry department of a small, STEM-focused school that works closely with one of the national labs. Time to return to my roots! Materials are still the basis for my research, but it’s refreshing to be back in an environment where, say, people know what NMR is or think that o-chem is actually fun – not a dreaded undergraduate requisite.

The future is no clearer to me, but it is brighter (and significantly snowier!). Call me Dr. MG. The journey wasn’t impossible after all.

Elements of Stockholm

The illustration in the holmium In Your Element article deserves a little explanation of its contents, hence this blog post, an extended figure caption for the article.

holmium-IYE-drawing-medium

{credit}Illustration by Emma Karlsson{/credit}

Per Teodor Cleve (1840-1905) suggested Stockholm as the namesake for his newly discovered element in 1879 because the Stockholm area “contains minerals rich in yttria” (ref. 1) — minerals containing yttria are a source of many rare earth elements, including holmium. Stockholm was also Cleve’s hometown, and as we noted in the IYE essay, already quite rich in chemistry history. Some other reasons that Cleve might have cited are the subjects of the illustration, with an emphasis on Stockholm-related element discoveries.

The raven — Korpen pharmacy

The raven refers to Korpen (the raven) pharmacy, located in the old town of Stockholm. This pharmacy was founded in 1674 by Jurgen Brandt, a German immigrant to Sweden. Coincidentally, Jurgen Brandt was the father of Georg Brandt (1694-1768), the first Swede to discover a chemical element (cobalt). The apothecary was at first called Örnen (the eagle) apothecary, but after being unsuccessful in its first location south of central Stockholm, the pharmacy was moved within a few years to the old town (Gamla stan); there it also received its present name, Korpen.

In 1768, Carl Wilhelm Scheele (1742-1786) moved to Stockholm and worked at Korpen for a time. Dissatisfied with his career progress in Stockholm, he moved to Uppsala, where he came in contact some of the more important chemists of the time… and where he discovered oxygen. Today, another pharmacy in Stockholm is named for Scheele.

“STOCKHoLM” façade — Ugglan pharmacy

Pharmacies continued to be prime places for Swedish chemists to work in the 19th century; at Stockholm’s Ugglan (the owl) pharmacy a young Carl Gustaf Mosander (1797-1858) was apprenticed. Mosander later went on to work at the Swedish Museum of Natural History in Stockholm. While at the museum he discovered of the elements lanthanum, terbium, and erbium. In the drawing, the façade with false columns and the word STOCKHoLM — with holmium’s symbol highlighted — are modelled after present-day front of Ugglan pharmacy (the actual sign reads “APOTEKET UGGLAN.”).

Portrait in window — Berzelius

The portrait in the shop window is Jöns Jacob Berzelius (1779-1848), perhaps the most famous Swedish chemist of all time, whose work was vital in the discoveries of cerium, selenium, silicon, zirconium, and thorium. (Berzelius is not always credited was discovering zirconium: he was the first to obtain zirconium metal, but its existence had been suggested decades earlier by Martin Klaproth.) Berzelius and his students combined to contribute to the discoveries of 10 elements (ref. 2).

Dynamite — Alfred Nobel

The fuse and dynamite bundle refers, of course, to the late 19th century industrial chemist, Alfred Nobel (1833-1896). Nobel patented dynamite in 1867, and had factories near Stockholm. Nobel’s namesake element, nobelium, was the most recent element discovery to be claimed by Stockholm scientists (ref. 3); though the name stuck, the discovery credit did not (ref. 4).

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Brett F. Thornton is in the Department of Geological Sciences, and Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden.

Emma S. Karlsson is in the Department of Analytical Chemistry and Environmental Science, and the Bolin Centre for Climate Research, Stockholm University, 106 91 Stockholm, Sweden.

Shawn C. Burdette is in the Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, 01609-2280, USA.

References

1. Cleve, P. T. Sur deux nouveaux éléments dans l’erbine. Comptes Rendus Hebdomadaires Des Seances De L Academie Des Sciences 89, 478–480 (1879).
2. Trofast, J. Berzelius’ Discovery of Selenium. Chemistry International 33, 16–19 (2011).
3. Fields, P. R. et al. Production of the new element 102. Physical Review 107, 1460–1462, doi:10.1103/PhysRev.107.1460 (1957).
4. Thornton, B. F. & Burdette, S. C. Nobelium non-believers. Nature Chemistry 6, 652–652, doi:10.1038/nchem.1979 (2014).

Blogroll: Those who left

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Brandon Findlay returns to pen the June 2015 column.

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What happens to students who leave graduate school without defending?

Continuing a conversation from years past, Vinylogous and Chemjobber have revisited the strain that graduate school can place on mental health. Now further into graduate school, Vinylogous has had some dark days — with a multi-month project in ashes and friends outside of academia doing better with less effort, he even prepared a farewell speech. Rather than deliver it, he stepped back and examined the future benefits of a PhD, and the opportunity costs. Working with his supervisor, he then made changes to foster sustained health and productivity.

Some readers may have found themselves in a similar situation, and know the solution is not always the same. Chemjobber requested feedback and posted the responses under the label ‘I quit grad school in chemistry‘. For some it took years for their love of science to return, but many have found fulfilling outlets for their skills, whether as adjuncts in smaller centres or from lucrative careers in industry that started earlier than expected. One, LB, even returned to graduate school, finding more success in economics than chemistry.

The factors behind each respondent’s departure vary in details, but often stem from either a mismatch in interest or skill-set, or a toxic work environment. Each entered graduate school as an adult, responsible for their own decisions, but the effects of PIs not experienced in — or poorly suited to — management are obvious. With new reports from those who left continuing to be posted, Tehshik Yoon has called for experiences from successful graduates. If you have a story to tell, let the world know.

Written by Brandon Findlay, who blogs at https://chemtips.wordpress.com and tweets as @chemtips.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the June 2015 article]

UCLA brings home the BACON

Editor’s note – this is a guest post from Professor Neil Garg at UCLA.

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Notorious for being the ‘weed-out’ course that crushes the hearts and souls of our students, organic chemistry has a bad reputation. To help counter this unfortunate perception, we have recently developed a series of online tutorials that connect organic chemistry to topics in human health and pop culture. We call it B.A.C.O.N. at UCLA (Biology and Chemistry Online Notes and Tutorials) and our students love it.

We would like to make these tutorials accessible to educators and students anywhere in the world at no cost, so we are raising funds for software development with the help of the UCLA Spark crowdfunding campaign starting on May 4.

If any chemists or science enthusiasts would like to help us out in the meantime, you can support us through our Thunderclap page by clicking “Support with Facebook/Twitter/Tumblr”. There is no cost and your support helps to spread awareness.

We would be very grateful if you would be willing to add your support to BACON and its science-education goals!

Blogroll: Comment etiquette

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, François-Xavier Coudert penned the May 2015 column.

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Post-publication peer review is a reality, so what should the rules be?

Scientific discussions about published papers, which used to take place in lab meetings or over coffee at conferences, now also happen on blogs (especially in their comment sections), discussion boards and Twitter. Websites such as PubPeer and BioMed Central host or aggregate these discussions, but the standards and etiquette of modern post-publication peer review remain to be codified.

One question is that of anonymity. As Dave Fernig discusses at Ferniglab Blog, anonymous comments are typically associated with negativity, rather than constructive engagement. Nevertheless, Fernig argues the case for anonymity, stating that without it the academics with the least power (for example, early-career researchers) would not be able to speak their mind.

However, allowing anonymity or failing to verify identities can lead to dirty tactics. Julian Stirling shares on PhysicsFocus his first-hand experience of identity theft and sock-puppetry (multiple accounts used by a single person) from comments on his recent paper in PLoS ONE. This question of anonymity in post-publication peer review also has legal ramifications. Alison McCook, at Retraction Watch, reports that PubPeer was allowed by a US Circuit Court judge in Wayne County, Michigan to protect the anonymity of its commenters in relation to a lawsuit brought by a scientist aggrieved at the treatment of his papers on the site.

Finally, Philip Moriarty experimented, at the Winnower, with post-proposal peer review, posting online for discussion a freshly submitted grant proposal to the UK’s EPSRC. So far, the concept has attracted more comments than the proposal itself. Maybe this was fated, being the first of its kind?

Written by François-Xavier Coudert, who blogs at https://blog.coudert.name and tweets as @fxcoudert.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the May 2015 article]

Blogroll: Tasty chemistry

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Joseph Meany penned the April 2015 column.

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Chemistry usually conjures up images of sterile or hazardous environments, but there’s a mouth-watering side too.

Almost a quarter of the way through the year, the resolutions that many of us made just a few months ago are probably starting to lose their appeal. Food is almost certainly a focus for many of the promises that we made to ourselves, but we shouldn’t forsake all thoughts of delicious treats.

Esther Inglis-Arkell, writing at i09, describes how chemistry can fool our senses into tasting apple pie even when there is no fruit to be found in the recipe. With some cream of tartar, Ritz crackers and cinnamon, you can create an ‘almost real’ apple pie despite the fact that real apples are just budding in the orchard.

Over at Food Chem Blog, Emily Buehler covers how bread goes stale, including some tips on how to store your bread for maximum shelf-life. Importantly, she also highlights the Twitter hashtag #breadchat for all bread enthusiasts. At the same time, Compound Interest’s Andy Brunning published a handy graphic on the Maillard reaction showing how it affects the flavours, aromas and colours of food during cooking.

Getting out of the kitchen and into the fresh air, Justin Brower at Nature’s Poisons recounts his hijinks with growing horseradish and the chemistry behind why it smells so spicy. He ropes his unwitting father into his experiment and outlines some of the reactions that happen in the plant as it gets turned into a condiment.

Everyone is familiar with cooking and baking on some level and these posts demonstrate that the connection between cooking and chemistry can help to explain basic scientific concepts to a wider audience.

Written by Joseph Meany, who blogs at https://jsphmeany.blogspot.com.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the April 2015 article]

Blogroll: Coding chemistry

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, See Arr Oh returns to pen the March 2015 column.

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Why the rise of the machines is a good thing for chemistry.

No matter your research interests, I’ll bet you depend more on computers — databases, scripts, templates, macros, electronic laboratory notebooks, sketching tools, machine learning — than ever before. Luckily, the chemblogosphere has you covered.

First of all, Mark Wolf, blogging at Magic Acid, wants to help you build a grad-school dream machine — capable of mapping 3D changes in battery electrodes — for less than US$1,000. Need to learn a programming language? Then take a look at Chemistry Apprentice, who has laid out a nice (and free!) path to learn JavaScript and Python using online resources.

Next, Martin Stoermer, of the aptly-named Chemistry and Computers blog, opines on indexing open-access chemistry data. He desires a model similar to that set by physics (with arXiv) or biomedical research (with PubMed). Meanwhile, Egon Willighagen at Chem-bla-ics, makes budding programmers aware of the Royal Society of Chemistry’s efforts to promote open science. They are providing access to their databases in exchange for Wikipedia contributions.

Finally, there was a lively debate at In the Pipeline over some seemingly odd structures from a molecular dynamics paper published in Nature Chemistry. Derek took issue with an extra methylene group and a potentially unstable hemiaminal before the lead author of the study quickly confirmed in the comments that they were simply drawing errors. The discussion continued, however, with academic heavyweights Henry Rzepa and Peter Murray-Rust chiming in, calling for reforms against what they consider to be outmoded publishing customs in the Internet age.

Written by See Arr Oh, who blogs at https://justlikecooking.blogspot.com.

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[As mentioned in this post, we’re posting the monthly blogroll column here on the Sceptical Chymist. This is the March 2015 article]