opinion

Taking a dinosaur’s name in vain.

This is my first post here so imagine my excitement when I came across this attention grabbing title from the JACS press room “Could “advanced” dinosaurs rule other planets?”. Something cool to write about on my first day! Excellent.

So of I trotted to look at the paper that was the bases of the press release. It has the more mundane title “Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth”.

What’s this got to do with dinosaurs I thought? Best delve a little deeper into the paper.

The paper describes how the homochirality of sugars and amino acids in life on Earth may have originated from a small excess of L-amino acids and D-sugars in meteorites.  These then seeded early life, leading to their near total dominance in life as we know it.

Sorry, still no idea what this has to do with dinosaurs. The paper is pretty interesting in it self, but I still don’t get the press release. I’d best read a little further .

Ahh, it turns out that astronomers think that neutron stars may act like cyclotrons and produce circularly polarized light. And if this light has enough energy it could account for the deracemization of amino acids on asteroids.

Still no dinosaurs.

OK, maybe the link with dinos will be clearer in the conclusions.

“An implication from this work is that elsewhere in the universe there could be life forms based on D amino acids and L sugars depending on the chirality of circular polarized light in that sector of the universe …”

Wow, that’s pretty cool (no Dinosaurs though), but it goes on..

“ Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth”.

WHAT! THAT’S IT! Can somebody please explain to me how we get from homochirality of life to that!

Is it just me or does this smack of blatantly sticking an irrelevant reference to dinosaurs in the conclusion in an attempt to get some press coverage?

Maybe we could all try it. Here goes, the new conclusion from my last paper.

“In contrast, conventional NMR spectroscopy would require several months to collect the same quantity and quality of data. This massive boast in NMR signals could one day mean that we will be able to collect NMR spectra of scarce dinosaur proteins”

By April 11, 2012 11 comments chemical biology, opinion, science news

Skillful writing of an awful research paper

Apparently, laboratory instructors and undergraduate mentors aren’t the only ones with the bane of reading insanely terrible research papers – the editor of the ACS journal Analytical Chemistry, Royce Murray, clearly has had his fill as well, according to his editorial in the current ASAPs.

His humor is very similar to that found in The Onion, and reminded me of How to Write a Scientific Paper on Improbable Research.

Brilliant. The only thing that has made me laugh out loud this hard lately was catching a part of the show ‘Ancient Aliens’ on the History Channel last night in which someone said that “one possible explanation of why the Mayans vanished was because they were aliens.”

In all seriousness, though, it is an understatement to say it’s quite obvious that scientific writing isn’t emphasized as well as it should be, it should be addressed at the undergraduate level as early as possible.

By January 27, 2011 0 comments chemical education, opinion

The Wiley Interscience Blues

Hello, everyone!  Since this is my first post on Chemistry Blog, I should introduce myself.  My name is Nick, and I’m a Ph.D. student in organic chemistry at McGill University, in Montreal.  Mitch contacted me via the chemistry subreddit, and I’ll be writing a few articles with what I hope is a unique perspective.  In advance, I would ask that you excuse my Canadian spellings; the letter “u” will pop up a lot more often than you’re used to.

As anyone who regularly reads scientific journals may have noticed, Wiley redesigned some of their website earlier this year.  Mid-way through the summer, they slicked up their Interscience pages to look more “Web 2.0”, and in the process, broke integration with one of my favourite things, which is Zotero.  Zotero was previously mentioned on the site quite some time ago, as one of several reference management programs available to modern researchers.  Given that it’s free, absurdly easy to use, efficient, fast, allows proxies, and acts as a bridge between OpenOffice and Firefox (with downloadable reference formats), I unabashedly support the abandonement of every other reference management system in favour of it.  Zotero makes collecting references and writing papers a breeze, and a whole lot more enjoyable than any other option I’ve tried.

What Wiley did to break Zotero’s flow was very simple.  Instead of having direct links to actual PDF files as part of their abstract pages (as nearly every other online publishing website does), they now direct you to a PDF file within an “iframe”, meaning that Zotero is not able to “see” the PDF as an actual PDF.  This allows them to place a highly annoying “Wiley Interscience” bar at the top, including your institutional logo, and links to citing articles, abstract, and supplementary info, as seen blow.

This would be okay, except that with Zotero absolutely none of those links are necessary.  When you do the one-click save on an abstract it automatically generates a snapshot of the abstract page, including links to all that information.  Normally, it also saves a copy of the PDF, but Wiley has now made this significantly more complicated.  You must now either save the iframe page as a snapshot (including the annoying header and useless links), or download the PDF separately, import into Zotero, then delete the original download to avoid having duplicate copies on your hard drive.  So basically, instead of a one-click save, you now have an option of a four-step non-PDF download (via the “add item” button, seen above at the bottom left), or a five-step (take snapshot, navigate to “pdf”, download, import, delete) rigmarole.

Compare this to ACS Publications, or ScienceDirect, where you click once on the address bar icon, and get all the above done in about 5 seconds (see below), or even ThiemeConnect, where you simply have to add the PDF as a separate item, and Wiley’s “site improvements” actually begin to look like a big step backwards.

I’ve e-mailed Wiley about this twice, and it seems that their support staff have no idea what Zotero is, or why this is important, and don’t seem to care.    Ultimately this isn’t a huge issue, but I would really love to see a return to the old functionality; as it stands right now I cringe every time I see a paper I want hosted by Wiley Interscience.

Nick

By November 26, 2010 14 comments opinion

Something Deeply Wrong With Chemistry

An example of what is currently wrong with chemistry culture, even though it is dated.

Future chemistry faculty will have to be twice as smart, work with twice the efficiency, and reach the correct positions of influence if they want this type of unhealthy cultural attitudes to finally be put to rest. This is my goal at least.

Update 1: Guido Koch now.

Update 2: The underlying macroeconomic cause for why professors can get away with this behavior.

Update 3: This story has really struck a cord, thank you for sharing this link and supplying our first 20,000 visitor day!

Update 4: A transcribed letter from Robert Tjian

From now on, I or someone designated by me will take attendance at group meetings starting at 9:10 am. If you are not there, I will not sign your salary sheets. Also, if you haven’t noticed the number of people working on weekends and nights in the lab is the worst I’ve seen in my 17 years. The frequency of vacation, time taken off and other non-lab activities is bordering on the ridiculous. In case you forgot, the standard amount of time you are supposed to take is 2 weeks a year total, including Christmas. If there isn’t a substantial improvement in the next few months, I’ll have to think of some draconian measures to “motivate” you. I also want to say that the average lab citizenship and community spirit of keeping the lab in functioning order is at an all-time low. Few people seem to care about fixing broken equipment and making sure things in the lab run smoothly. If the lab were extremely productive and everyone was totally focused on their work, I might understand the slovenliness but productivity is abysmal and if we continue along this path we will surely reach mediocrity in no time.

Finally, those of you who are “lame ducks” because you have a job and are thinking of your own nibs, so long as you are here you are still full-fledged members of this lab, which means participating in all aspects of the lab (i.e. group meetings, Asilomar, postdoc seminars, etc.)

I realize that this memo won’t solve all the problems. so I am going to schedule a meeting with each one of you starting this Saturday and Sunday and continuing on weekends until I’ve had a chance to speak with everyone and to give you a formal evaluation. Sign up for an appointment time on the sheet outside my door.

This is the first time I’ve had to actually write a memo of this type and I hope
it’s the last time.

Robert Tjian

Update 5: Erick Carreira responds in an interview with Christopher Shea from The Boston Globe, vaguely claims the letter may have been a joke (link: Chemist who ordered night and weekend work replies to critics). Selected quote below:

I wonder whether you would think it fair to be judged on the basis of a letter 14 years old, especially when the comments and rash judgments are made without knowledge of the context or the circumstances surrounding the individuals involved. Indeed how does anyone out who is so quick to pass judgement and who is coming to conclusions know that it is not part of a 14-year old joke (or satire as you state) that backfired? …

Update 6: Comparatively tame letters from Paul Gassman and Albert Meyers, but they have some good information in them about standard expectations.

If you have similar letters you would like to share send them in. Any identifying information can be removed upon request.

Mitch

By June 22, 2010 264 comments opinion