Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Mark Lorch penned the May 2013 column.

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Are bloggers the new peer reviewers?

Back in January a chemistry blog with a difference popped into being. Blog Syn is more than the usual opinion, analysis and amusing Twitter memes (try Magdeline Lum‘s account of #dangerous5 for a good version of that). Instead, this new blog has the laudable aim of using crowdsourcing to reproduce chemists’ published results.

The third reaction tackled by Blog Syn, with posts in February and March, is from a 2002 J. Am. Chem. Soc. paper from K. C. Nicolaou’s group. There ensues an interesting series of failures, genuinely helpful dialogue with some of the authors (including Phil Baran and Tamsyn Montagnon) and finally the missing factor is found: water!

Writing at Grand CENtral, Fredrik von Kieseritzky nicely summed up why there is a place for Blog Syn, as he laments the decline in the quality of methods sections of papers and calls for journals to promote experimental procedures from supporting information back into the main text. Moreover, in the wake of Blog Syn’s early success some interesting arguments arose about (pseudo)anonymity in blogging. The point being that Baran’s comments can be easily attributed to him but most of the contributors to Blog Syn remain pseudonymous. Points for and against anonymity were discussed by von Kieseritzky and also Rich Apodaca at Depth-First.

Baran’s encounter with Blog Syn may have made him reconsider his feelings towards bloggers; his lab now hosts The Open Flask. Nevertheless his opening post does start with a quote from one of his colleagues about blogs: “Never before have so many people with so little to say said so much to so few…”.

Written by Mark Lorch, who blogs at https://www.chemistry-blog.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 May 2013 article]

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, DrRubidium penned the April 2013 column.

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Changing the tune on chemistry’s bad rap

Chemophobia has led manufacturers and proprietors to advertise ‘chemical-free’ goods and services; it pops up in literature by activist groups like Safer Chemicals, Healthy Families — and has even infected popular media outlets. The rise in the fear of chemicals and chemistry has many chemists, as well as scientists in all fields, asking what can be done to eradicate chemophobia.

One way to counter chemophobia is for scientists and science writers to tackle it head-on. Michelle Francl, a professor of chemistry who blogs at The Culture of Chemistry, responded to a February New York Times Magazine article ‘The Boy With a Thorn in His Joints’ about parents treating their child’s arthritis with ‘natural’ alternatives instead of the recommended methotrexate. Writing in Slate, Francl pointed out that the parents’ ‘natural’ alternatives were also chemicals — ones that have their own safety concerns. Stressing that everything is a chemical and all chemicals have risks are tips that Francl gives for fighting a ‘chemophobia pandemic’.

ChemBark offers another way to fight chemophobia — by chemists doing outreach. “I think it is important that every chemist spends some time engaging the general public for the purposes of education and promoting the benefits of our field” wrote ChemBark in his post ‘Combatting Chemophobia‘. Writing as if he’s talking to an outreach naysayer, ChemBark answers typical questions like “What’s in it for me?” and charges like “I can’t put that on my CV!”

Why fight chemophobia? For one thing, chemistry is “…the amazing and beautiful science of stuff…” as Hank Green puts it in his video on the nucleus for Crash Course — a YouTube channel where you can learn about topics from literature to ecology to chemistry.

Written by DrRubidium, who blogs at https://scientopia.org/blogs/thirtyseven/ and https://www.thejayfk.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 2013 article]

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, JessTheChemist penned the March 2013 column.

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Is a PhD bad for your health?

Graduate students will be all too familiar with the trials and tribulations that PhD research brings, but is it bad for your health? Chemjobber and Vinylogous at ‘Not the Lab’ hosted a blog dialogue on ‘Is graduate school in chemistry bad for your mental health?’ to raise important issues that rarely get discussed. Chemjobber shares his personal experiences including “the feeling that [his] entire life was an utter failure”. Vinylogous recounts that his “weekends had been given up, as had hobbies” and “7-day workweeks were expected; dinner was eaten hurriedly at one’s desk; stealing was frequent and hoarding of reagents and glassware was necessary”. Not only are the five posts excellent, but the comments that the posts have produced are insightful and eye-opening.

Derek Lowe also joined in the mental health discussion at ‘In the Pipeline’ and at ‘Periodic Boundary Conditions’, Miss MSE adds her personal viewpoint. She highlights the need for a life outside her PhD and concludes that “the most important thing I can do for my mental health is this: talk to people who aren’t in grad school”. Finally, MB at ‘Colourblind Chemistry’ reveals the consequences of picking the wrong principal investigator and how he dealt with that. He summarizes the mental health posts nicely with the comment that “grad school is incredibly difficult, but it doesn’t need to be demoralizing”.

If the posts described above don’t put you off life as a graduate student, then head over to ‘The Drew Lab’ where Joshua Drew gives out some first-rate tips on how to apply to graduate school, from GRE scores to the personal statement, noting that “there are no set formulae as to what makes a good candidate”.

Written by JessTheChemist, who blogs at https://theorganicsolution.wordpress.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 2013 article]

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, DrFreddy penned the February 2013 column.

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Kevlar-suit-wearing synthetic chemists and the art of nomenclature.

Some interesting nitrogen-based chemistry featured in the chemical blogosphere in 2012. Several bloggers commented on a peculiar (and perhaps somewhat terrifying) compound containing 10 nitrogens in a row, reported in Inorganic Chemistry. David Perrey at Chemical Space wrote, “The graphical abstract tells the story eloquently: the structure with a back-drop of broken lab equipment,” and muses “inadvertent explosions is a lovely expression”.

A picture of a Klapötke group member working with these materials was posted on the blog Reactions from Last Night — “notice the full Kevlar suit he’s wearing” notes the caption! There are strict rules about who can do what in the group; undergraduates don’t handle explosives, masters students only work with known compounds, and PhD students are the ones who “make and characterize anything novel”.

At the other extreme, in a post on ‘Handheld chemistry’ over at The Culture of Chemistry, Michelle Francl-Donnay advises the reader to “wash those hands” if you are going to repeat an experiment described in a 1937 chemistry-kit manual for “making ammonia in your hand,” by mixing calcium oxide and ammonium chloride with your fingers. Francl-Donnay further admits to “using Hess’ law for fun,” but follows with a serious calculation on the heat of formation for the reaction: “–635 kJ […] for about a tablespoon of material,” to be precise.

And finally, at The Heterocyclist blog, dipolar-cycloaddition veteran Will Pearson ponders over an apparent mix-up between nitrogen imines and ylides in the title of a paper in Angewandte Chemie International Edition and throws out a “What am I missing here?” Judging by the lack of objectors so far — nothing.

Written by Fredrik von Kieseritzky, who blogs as DrFreddy at https://syntheticremarks.com/

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

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Adam Azman stepped up to the plate for the January 2013 column.

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Chemists and proteins tell all, exposing their inner workings.

Tweeting chemists around the world will always remember the seventh of November as the inaugural ‘RealTimeChem’ day. The event was hosted by Jason Woolford, who blogs at Doctor Galactic and the Lab Coat Cowboy, and saw chemists of all kinds tweeting about their daily lives in chemistry. All interpretations of ‘doing chemistry’ were represented, including teaching, writing, going to meetings and of course pictures of reactions, extractions and chromatography. For a sampling of some of the contributions, check out Woolford’s compilation of his 24 favourite tweets.

Woolford explained that the seventh of November was chosen to honour Marie Curie’s birthday but he stressed that every day can be #RealTimeChem day (the official hashtag for RealTimeChem). He subsequently wrote of the importance “in this modern age of social media in particular that chemistry continues to engage with the masses and chemists are able to pass on their knowledge, enthusiasm and general love of their subject onto others in an entertaining way”.

Meanwhile, Derek Lowe at In the Pipeline highlights a very literal interpretation of RealTimeChem. He discusses the use of ultra-short (100 ps) X-ray pulses to watch the tertiary structure of a protein change in response to a stimulus. Lowe describes the technique — picosecond time-resolved Laue crystallography — and its potential applications as “the sort of thing we chemists need to really understand what’s going on at the molecular level, and to start making our own enzymes to do things that Nature never dreamed of.”

Written by Adam Azman, who blogs at https://www.chemistry-blog.com

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

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Karl D. Collins took care of the December column for us. Sorry that we’re a little late (again) posting it on here…

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From pesky biochemists winning the Nobel Prize in Chemistry, to the social construction of scientific ideas. Is it all just a matter of perspective?

Considering the time of year, it would be rude not to mention this year’s Nobel Laureates in Chemistry, Robert J. Lefkowitz and Brian K. Kobilka. Being awarded the prize “for studies of G-protein-coupled receptors” resulted in a tedious furore owing to the awarding of the prize to biochemists. The usual heavyweights of the blogosphere have done their part deriding these banalities, though I particularly enjoyed John’s article at ‘It’s The Rheo Thing’, highlighting the ‘impurity’ of two of the world’s leading ‘chemistry’ journals.

The role of society in science, although not a new concept (I would say one as old as science itself), is one that is increasingly developing in importance. For example, society’s perception of genetically modified food has had widespread consequences for its development, production and distribution worldwide. Two pieces relating to this boiling pot of anguish have recently caught my attention, one by science-policy academic Jack Stilgoe of Responsible Innovation who in response to an article on the Rothamsted protests highlights the dangers of unstructured and polarized debate on such ethical dynamite; and a second by Michael Eisen of ‘it is NOT junk’ challenging the basis of “Proposition 37, which would require the labeling of genetically modified foods” in the USA.

Finally, academic Alice Bell, of ‘through the looking glass’, writes an intriguing piece on the social construction of science, challenging the perception (presumably of ‘scientists’) that describing science as a social construct is negative. Bell writes “Saying science is a social construction does not amount to saying science is make believe” and continues to discuss the ‘social construction’ of St Paul’s, CERN and scientific ideas.

Written by Karl D. Collins, who blogs at A retrosynthetic life

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

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, Ashutosh Jogalekar took care of the November column for us. Sorry that we’re late posting it on here…

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Pity the poor teaching assistant, and a history of chemical notation.

Being a teaching assistant (TA) is as much a learning experience as a teaching experience, a fact most apparent in the student evaluations that TAs are handed at the end of the semester. These evaluations put the spotlight on those who have been accustomed to putting it on others. On his blog, Chembark has a whole two-courses worth of student evaluations that convey his lesson that “teaching is excellent at identifying even the smallest gaps in your knowledge, as students are quite proficient at exposing inconsistencies in the material presented to them.”

Meanwhile, Master Organic Chemistry implores undergraduates to know thy TA and realize that the TA is essentially a poor graduate student whose main allegiance is to his or her research.

And speaking of the basic chemical principles that TAs try to drill into their students’ heads, do you know where those much feared and respected curly arrows came from? Henry Rzepa traces their origins to a 1924 paper by the famous Robert Robinson. Rzepa analyses Robinson’s curly arrows and finds a few deficiencies in them that diligent undergraduates should be able to point out to their TAs.

Finally, Rzepa provides us with another window into chemical history by looking for the first noted instances of the ubiquitous wedges and dashed lines that indicate stereochemistry. After examining the work of two masters of the art — Derek Barton and R. B. Woodward — a commenter points us to a fascinating collection of articles on chemical history by William Jensen that locates the first wedges and dashes in a 1932 paper by R. Kuhn.

Written by Ashutosh Jogalekar, who blogs at https://wavefunction.fieldofscience.com

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

Editor’s note: As we continue to invite bloggers out there in the wild to compose our monthly Blogroll column, fourth up is BRSM.

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Why is discovering new drugs not as easy as designing passenger aircraft?

Do you remember how slow your computer was back in 1995 — that is, if you even had one? Remarkably, that was the year that the Boeing 777 entered the history books as the first aircraft designed solely using computers. Ash at The Curious Wavefunction has been pondering the reasons why, despite all the technical advances made recently and the huge impact they’ve had on other fields, computers have yet to make the design of even small-molecule drugs significantly easier. He muses, “we can routinely design airplanes, bridges and skyscrapers on a computer but are still light years behind when it comes to designing even ‘simple’ drugs”. If that seems a little disheartening, let’s not forget that it was only a little more than a century ago that the celebrated physicist Lord Kelvin declared heavier-than-air flying machines entirely impossible.

Meanwhile, lively debate between veteran medicinal chemist and blogger Derek Lowe and the authors of a recent paper in the British Medical Journal has dominated recent posts over at In The Pipeline. The topic: the ‘innovation crisis’ plaguing the pharmaceutical industry. Interestingly, it turns out that one of the authors in question is Professor Donald Light, a man who previously drew flak from Lowe over his co-authorship of a controversial 2011 paper that estimated the average R&D cost of a new drug at the rather low value of just over $40 million.

Finally, in somewhat contrasting posts, See Arr Oh, who blogs at Just Like Cooking, reflects on the tendency of studious chemists to work weekends, while Jess over at The Organic Solution discusses the chemistry behind a problem frequently faced by students: hangovers.

Written by BRSM, who blogs at https://brsmblog.com/

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

Editor’s note: Now that Neil has left the Nature Chemistry fold to move over to Chemistry World, we have invited bloggers out there in the wild to compose our monthly Blogroll column. Third up is See Arr Oh.

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Practical synthetic chemistry shows an artistic side with synthesized doodles, logos and colouring-book molecules.

It’s been a busy summer in the blogosphere! Between ‘arsenic life’ and the newly discovered Higgs boson, science blogs seem more relevant than ever. In all the fuss, though, they may have overlooked some promising chemical artists in their midst.

First up, let’s turn our attention to the 2012 London Olympic Games. Chemists at the University of Warwick decided to commemorate the event by synthesizing a new molecular version of the famed Olympic rings. ChemConnector’s Antony Williams explains that a chalkboard ‘doodle’ evolved into a synthesis of olympicene; the RSC’s ChemSpider SyntheticPages later published the step-by-step details. IBM-Zurich (of pentacene-imaging fame) posted a series of finely resolved atomic images to Flickr.

Next we’ll talk high fashion. At Chemistry World, Phillip Broadwith noted a neat undergraduate synthesis project: making a hydrocarbon to match a clothing label’s logo. After just three steps, Plymouth University’s Mark Cockerton and Simon Belt had their target…but still no word on whether they’ve tied up a sponsorship deal with the apparel company in question!

Speaking of synthetic art, we’d be remiss not to wish a happy belated birthday to organic chemist K. C. Nicolaou. Blogger BRSM prepared a special tribute to his penchant for flashy colours and ancient mythology in the figures that adorn his papers and the graphical abstracts that accompany them. A small group of Blogroll’s ‘usual suspects’ — including Adam Azman, Chemjobber and Dr Freddy — re-imagined K.C.’s classic molecules with new artistic twists. Perhaps these entries will finally prompt publication of that chemical colouring book.

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 September’s article]

Editor’s note: Now that Neil has left the Nature Chemistry fold to move over to Chemistry World, we have invited bloggers out there in the wild to compose our monthly Blogroll column. Second up is Paul Bracher.

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Bloggers breathe life into wounded chemicals and contemplate the death of organic synthesis.

For about a week, the chemical blogosphere became a toxic environment, but the only thing that bloggers sought to poison was public misperception. In a carnival spearheaded by Matt Hartings of American University, over 20 bloggers authored posts about their favourite toxic chemicals. Hartings hosted the carnival on his site, ScienceGeist, in an effort to emphasize that many chemicals demonized in the media as ‘toxic’ have safe uses of immense practical value. “Chemicals aren’t inherently good or bad,” he writes, “in most cases, the danger is in the dosage.”

Dr Rubidium, an analytical chemist who blogs at the Journal of Are You Fucking Kidding, contrasted several cases of homicide by the paralytic agent succinylcholine with its medical use in life-saving tracheal intubations. Although that post was shockingly free of swear words, an ode to tetracyanoethylene (TCNE) on Carbon-Based Curiosities was as vulgar as it was informative. Long-time blogger Excimer noted that “even the chemical industry is starting to shy away from chemicals” before proudly hailing applications of TCNE in the synthesis of the first organic ferromagnet and as a “highly efficient unicorn killer.”

And speaking of death…debate over whether to sustain research in organic synthesis flared up again when Chemjobber sifted through a 120-page report on graduate education and found a rather provocative question inspired by Harvard chemist George Whitesides: “Should U.S. graduate students be doing organic synthesis if most organic synthesis is being done in China?”. Derek Lowe at In the Pipeline prefaces his analysis with the statement, “If it hasn’t crossed your mind, you haven’t thought hard enough about the issues yet.”.

Written by Paul Bracher, who blogs at https://blog.chembark.com

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