Chemistry Blog

Sep 17

How many ways can you say something without plagiarizing?


In a recent post by Derek Lowe on a Chinese journal’s finding that 31% of its submitted papers contained plagiarized material, an editor for a scientific journal noted in the comments that he randomly selected a Tetrahedron Letters paper from a developing country and Googled the first sentence. That sentence (“Multicomponent reactions (MCRs) are important for generating high levels of diversity…”) shows up in very similar form in three different papers, all from institutions in Iran and China. In two of the papers, the second sentence of the paper is exactly the same, all 22 words.

Also, compare the two first sentences, the first by Shaterian et al.[1] and the second by Adib et al.[2]  The highlighted words are the same.

Multi-component reactions (MCRs) are important for the achievement of high levels of brevity and diversity. They allow more than two simple and flexible building blocks to be combined in practical, time-saving one-pot operations, giving rise to complex structures by simultaneous formation of two or more bonds, according to the domino principle.”

Multicomponent reactions (MCRs) are important for generating high levels of diversity, as they allow more than two building blocks to be combined in practical, time-saving one-pot operations, giving rise to complex structures by simultaneous formation of two or more bonds.

While cutting and pasting other people’s introductory sentences is certainly embarrassing and almost certainly plagiarism, there is some difficulty in summarizing a set of facts in a different way each time. It certainly can be done — below are three different labs’ introductory sentences for chemistry towards the total synthesis of the azaspiracids, which are marine natural products. Again, the same words are highlighted in red.
Nicolaou et al.[3]: “The azaspiracids are a group of notorious marine neurotoxins whose accumulation in mussels causes serious human poisoning known as azaspiracid poisoning syndrome (AZP) upon their consumption.”
Geisler, Nguyen and Forsyth[4]: “The azaspiracids are remarkable natural products that combine a unique, complex structure with an acute and perhaps chronic human health hazard.”
Evans et al.[5]: “(-)-Azaspiracid-1 is a structurally complex marine neurotoxin that is implicated in seafood poisoning.”
You can see that Nicolaou, Forsyth and Evans all have specific ideas they’re trying to get across: what the compound is, where it comes from and what it does to people. But they’ve all managed to have relatively few words actually overlap.

Is this sort of cutting-and-pasting ‘real’ plagiarism? — it’s just the quotation of a particularly useful string of words, one might assert, not the stealing of ideas. I don’t think this is a very good way of thinking about things, but I can’t quite reason why. In addition, I doubt that any of the authors of the MCR papers were native speakers of English. Clearly, that plays some role in their choice to cut and paste; again, not an excuse, but another contributing factor. I’m trying to see if I can come up with extenuating circumstances, but I just can’t.

My adviser in graduate school held out “the same five words in a row” as a general rule of thumb for how to spot and/or avoid plagiarism — what about the same five ideas in a row? What do you think, reader? How do you avoid cutting and pasting? And what should we do (if we should) to stop this sort of thing? Do we need TurnYourJournalSubmissionIn.Com?

References:
1. Shaterian, H.R.; Yarahmadi, H.; Ghashang, M. Arkivoc. 2007, 16, 298-313.
2. Adib, M.; Mahdavi, M.; Bagherzadeh, S.; Zhu, L.-G.; Rahimi-Nasrabadi, M. Tet. Lett. 2010, 51, 27-29.
3. Nicolaou, K.C.; Frederick, M.O.; Petrovic, G.; Cole, K.P.; Loizidou, E.Z. Angew. Chem. Int. Ed. 2006, 45, 2609-2615.
4. Geisler, L.K.; Nguyen, S.; Forsyth, C.J. Org. Lett., 2004, 6, 4159-4162.
5. Evans, D.A.; Kvaerno, L.; Mulder, J.A.; Raymer, B.; Dunn, T.B.; Beauchemin, A.; Olhava, E.J.; Juli, M.; Kagechika, K. AngewChem. Int. Ed. 2007, 46, 4693-4697.

Sep 14

Why is High Fructose Corn Syrup so bad for you?


Is high fructose good for you or bad for you?

How many of you said bad?  Leads to obesity, right?  Gotta stay away from HFCS, right? That’s what ‘everyone’ says, right?

Consider: The sugar we call ‘table sugar’ is sucrose: a disaccharide: a molecule of glucose and a molecule of fructose (two monosaccharides) covalently bonded to each other.  Sucrose is broken into fructose and glucose by enzymes within living organisms (like humans).  Humans don’t use sucrose for energy, first we break it into glucose and fructose and metabolize the monosaccharides for energy.  So we ingest sucrose, digest it to glucose and fructose, then use the monosaccharides for energy.

One molecule of sucrose becomes 1 molecule of glucose and 1 molecule of fructose.  That means that sucrose is digested to a 50/50 mixture of fructose and glucose.

Consider: High fructose corn syrup is a straight mixture of unbonded glucose and fructose.  There are two common types of HFCS: HFCS 55 and HFCS 42.  HFCS 55 is ~55% fructose and ~42% glucose.  HFCS 42 is ~42% fructose and ~53% glucose.

So what’s the difference?

Sucrose becomes a 50/50 mixture of fructose and glucose.  HFCS 55 is a 55/42 mixture of fructose and glucose.  Chemically, there’s no difference between fructose from sucrose and fructose from HFCS.  Our bodies can’t tell the difference between fructose from sucrose or fructose from HFCS.  We’ve been fretting so much about a 5% difference between the fructose content in the two sweeteners.

If our body can’t tell the difference, and the percent content of fructose is essentially the same, why is HFCS so much worse for us than ‘natural,’ or ‘organic’ sugar?

It’s not.

HFCS is no worse for us, and causes no more obesity than table sugar.  Once ingested, table sugar and HFCS are metabolized by our bodies in exactly the same way.

So what’s the problem?  Well, the problem is sugars (both sucrose and HFCS) are in EVERYTHING.  Too much sugar (again, either from sucrose or from HFCS) IS bad for us, and will lead to higher caloric intake, and eventually weight gain.  So the problem is too much sugar – not too much HFCS, and the solution is to eat less sugars overall – not to ban HFCS from everything.

But that’s not what ‘everyone’ is saying.  And the court of public opinion can be quite harsh.  So harsh, in fact, that the HFCS manufacturers are attempting to rebrand.  No longer will we find HFCS on the ingredient list.  Now, we will see ‘Corn Sugar.’  This means the same thing.  It’s the same 55/43 mixture of fructose to glucose, but they’re rebranding to move away from the negative associations.

What do you think?  Good idea or bad idea?  Should we just ban HFCS/Corn Sugar?  Should we regulate the amount of sweetener that’s allowed to be in a Suggested Serving Size?  Do you agree with the decision by the HFCS manufacturers?



Sep 10

Chemical Contests


I’ve been asked to drop a reminder about C&EN Photo Contest. The contest offers hard cash for pics of your science. On an aside, if you also happen to be photogenic I would suggest you put some science action shots of yourself in their Flickr collection; a perennial complaint from C&EN is that they need more pictures of people doing science. C&EN Flickr group

Science-artsy flickr group abound as RSC also has their own too, Art on a Chip. They sadly only have 4 members compared to C&EN 52 members.


Irony

An other competitive extracurricular activity to partake in is crafting graphical abstract puns. There is a new website TOC ROFL dedicated to highlighting the creative abstracts of chemical authors.

I’ve decided to jump on the funny-abstract bandwagon too. If you come up with a witty pun or see an interesting graphical abstract at ChemFeeds leave a comment on the paper and your comment will immediately be featured in the upper right hand corner of Chemistry Blog under “LATEST FUNNY CHEMISTRY”. Have fun and be creative.

Mitch
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Sep 06

Lab Horror Stories


After Jyllian Kemsley’s story on the non-supervised cavalier graduate student and his missing fingers, members of the chemistry reddit shared their own harrowing experiences around the lab. I would suggest we all try to learn something from these stories, the most important lesson being always wear your safety glasses!

bri1232001:

I work in a chemistry lab and last week an intern was involved in an accident. The intern sealed a glass vial with water and dry ice inside. The vial exploded and glass shrapnel gave him multiple lacerations on his face and arms. He was taken to the emergency room where he received stitches. His safety glasses had some extensive chips removed from them. He was very lucky to have had them on.

myarlak:

I saw someone get 2 large drops of sulfuric acid on their arm, and the acid ran down their arm about 4 in. they now sport scars that look like something with large fangs bit their arm and ripped… I personally have been sprayed in the face with phenyl Grignard, not horrible but burns when it gets on you, burns when you wash it off. I saw a gas tight syringe full of diethyl zinc lose it’s gas tightness, caused a small fire and that was it. I saw the results of someone leaving lithium open in a glove box… melted through one layer of steel and bowed the 2nd layer as it burned in nitrogen… that’s about it, mostly a bunch of close calls.

simplemathtome:

two postdocs were working in the glovebox next to me. They spilled some MeLi and were mopping it up with kimwipes. They knew it would be dangerous when they pulled it out of the antechamber, so they prepared an EtOH bath (which, to be fair would safely neutralize a small amount of MeLi, iPrOH would have been better). One postdoc opens the antechamber and, as quickly as possible, took the kimwipes out and dunked them in the EtOH bath, only problem was, the kimwipes burst into flames as soon as the kimwipes were exposed to air, setting the bath on fire. In the panic, one of the postdocs went to get MORE ETOH and poured it on the fire. The bath overflowed, she started yelling for liquid nitrogen, I got out of my box and started running towards the liquid nitrogen. The next thing I know, i hear screaming, the postdoc walks out of the lab (right under a safety shower, without pulling the water release) with her entire pantleg on fire. I cant find LN2 so I take off her labcoat and snuff out the fire on her leg. The other postdoc managed to put out the EtOH fire, but he didnt remember how he did it. They both went to the hospital, one of them stayed for 2 weeks. That was my first summer in a lab, right before sophomore year.

sprouts42:

Teaching a group of 13 year olds a few months ago showing them the decomposition of limestone and running the gas through limewater to show carbon dioxide. You have to get the limestone really hot in a boiling tube using the bunsen. After the practical was over I told the students to turn off the bunsen forgetting to tell them to remove the delivery tube from the limewater. Almost simultaneously the sound of limewater rushing up the delivery tube into the boiling tube and causing it to explode 15 times over. Screaming girls all over the place and glass showering everywhere. Another safety glasses save the day moment.

shyguysays:

When I was in organic lab, my TA closed my heating reaction flask a little too tightly. It blew up. I pulled three pieces of glass out of my forehead right above my right eyebrow. The stopper hit my partner in the head. We lived long enough for the department to let us graduate.
Yay for goggles!

theddman:

My lab neighbor (synthetic organic, read: the jocks of chemists) was running a huge silica column that burst all over him because his girlfriend was distracting him. He had to use the emergency shower!

Same lab neighbor blew up another column or something with concentrated TFA in it, he has a few cigarette-looking burns on his arms from it.

I personally was making some 10 M NaOH in a conical 50 mL tube (“Falcon” tube) early in my career. I added the pellets and the water, closed the screw cap tight and shook vigorously to dissolve it. Well, of course dissolving NaOH in water is highly exothermic. Yep, the entire thing blew the eff up and got NaOH all over me, my bench, and even the ceiling. Luckily I didn’t get burned anywhere important because I was wearing safety glasses.

I overfilled an ultra filtration device with very VERY expensive compound, lost half into the centrifuge rotor. Effing pipetted that shit out and HPLC purified it (shhh, don’t tell the boss!).

I could go on and on…labs are filled with dangerous things and overly curious hands.

thelt:

Last year in our lab we had a 4L waste jug of Piranha (3:1 conc. H2SO4:conc H2O2) solution explode, actually more like geyser, all over the lab. Thankfully no one happened to be in the lab otherwise they would have been fucked. Pretty much everything within about a 10 ft radius of where the jug was destroyed. The paint peeled off the walls and ceiling, lights had to be replaced everything. Hazmat team had to be called in to clean up the mess. For about the next week or so I couldn’t stand to be in the lab for more than about 20 minutes or so before my throat would start to burn.

Note: When storing waste piranha don’t cap the bottle.

smilingfreak:

Well, I’m a comp. chem, so there was that one time I spilled coffee on my lap. It was like, really, really hot.
Yeah.

Screw you all! I’m a real chemist! Honest!

erallured:

I worked in the stockroom in undergrad and was unsupervised a lot, especially in the summer. I was messing around and made some NI3. I knew it was really unstable when dry, so I took just a spatula tip of it out of the beaker and spread it on some filter paper. It couldn’t have been more than a milligram or two. I was working in a fume hood in an empty lab away from anyone else. I kept pressing on the thin streak of powder trying to set it off but it wasn’t going. I decided maybe I didn’t have enough/it was too spread out, so I was going to add some more. I used the spatula to move the paper slightly, and apparently it had dried and this small movement was enough to set it off.

¡BOOM!

I was instantly deafened and after a couple seconds had a loud ringing in my ears. A few seconds after that, a research student opened the doors and walked it. She said something to me, but I couldn’t hear so I just said “hi” and smiled, hoping she was just greeting me. She walked away with no indication she knew anything was up and gradually my hearing came back. I have no idea how she didn’t hear anything, she must have only been a few feet from the lab door when it happened. I was so shaken up, I dumped the rest (I had a good 5-6g of precipitate) into a waste jar and got out of there. All in all, not the worst, but for a few minutes, I thought I’d lost my hearing permanently.

DessicatedDogsDick:

A guy in my lab was cutting titanium sponge off an electrode (molten salt process) when it caught fire. There was probably around 2 kilos of the shit that went up in a very large, hot fire. He emptied two CO2 extinguishers onto it, which only made it worse. In desperation, he picks up the metal tray it’s sitting on (still burning) and bolts outside. The tray melted through just as he reached the door. The lab bench and stuff around were basically ruined from the heat.

zlukasze:

I was adding “dry” ether to stannic chloride, prepping to make tetrachlorobis(DMSO)tin(IV).S omeone had mislabeled the ether, and it apparently had a very high water content because the lab promptly filled with hydrogen chloride gas and shrapnel. The space abutted some department offices and they had to be evacuated.

Farrar:

There was a pretty bad one where someone had to go to hospital; they were pressing the bung onto a conical flask, when the glass smashed. Because of how they were holding it, a rather large piece sliced up their arm, slashing open their wrist and it required quite a few stitches.

There was also an incident where an evaportating dish exploded and it cut open atleast three students, but luckily those were only minor surface injuries.

Oh, and one where someone ate some copper sulphate and had to have their stomach pumped…but that’s more of a ‘don’t be so stupid’ rather than a horror story…

calladus:

In high school chemistry class, way back in ’81 or ’80. Due to budget problems, the chemistry teacher was let go and the job was given to the woman who usually taught English. Class was pretty boring – very few experiments, mostly reading and explanations of what “ought” to happen when this is mixed with that.

But there was one experiment with mercury that she wanted us to do. So she went into the chemical storage area, and came out with a container of mercury. It was a very heavy container – well over 20 pounds. She dropped it.

Mercury ran in little balls all around the classroom. To fix it, the teacher gave us all 5×9 index cards and had us scoop the mercury together to the middle of the classroom where she swept it all up with a broom and dustpan and returned it to the container.

When everything was “cleaned up”, we all continued with class. The container of mercury was put back into the chemical storage area. As far as I know, she never mentioned this to the principle, or anyone else..

barrysagittarius:

I worked two years in an Organic Lab and two years in a Chemical Physics laser lab. The worst two to strike me were: – In my organic lab I was putting glassware in some basebath and the flask dropped from my tongs. As it sunk, the air escaping splashed bath into my face. Some minor scars on my forehead and thank god for my safety glasses :D – In my laser lab, i passed through the beam path; a common practice since the laser is focused – usually – inside the reaction chamber. However this time, one of the beams was focused outside and I brought my hand through it. I still remember the SNAP sound and the burning feeling inside my hand. Much fun.

The worst things happened to others in my lab. I spent a summer making precursors for this very lengthy organometallic compound we were making. One of the reactions was to bromenate a compound and was HIGHLY reactive – I was adding the bromine solution dropwise while the target flask was at -5C and it still fizzled with each drop. Anywho, after the reaction, it had to be quenched and washed with ether. After I did this on a 100mL scale a couple times, the grad student I was working with decided to try and scale it up to 1L (…). I was out the day, but when I came in the hood was brown. And the floor, and the ceiling, and… and we had much less glass ware, including the entire glass vacuum line. Apparently he didn’t completely quench it, and with one shake in the separation flask (can’t remember the name, been a while) it exploded. Horrible chemical burns and stiches later… he was back at it a week later.

The second worst thing was my laser lab. Me and a grad student were building an electron gun from spare parts for an experiment. We had to hack together the power feed into the vacuum chamber, so it was just a flange with a bunch of copper leads. To power the gun, we used these flimsy connectors we had to clip on and off the leads (until we got the final connectors in). Oh and our Power Supply was 10kV floating (in a lucite box :D). Well, again, I was out sick, and my grad student got his thumb too close to one of the leads and WHAMMO! 10kV to the chest; blown across the room into a wall but otherwise okay.

relampaguear:

At first here, I must confess this happened to my lab partner and not myself. I work in an organic lab that does a lot of solid phase peptoid synthesis, and after the desired residue length is reached, we cleave the peptide from the resin using TFA. My lab partner was using a 10 mL syringe to measure the aliquot needed and pulled the stopped out all the way, splashing concentrated TFA all over her face and arms. Thankfully the only lasting casualties were her goggles and a gnarly scar above her eyebrow.
Go goggles go!

abyssuk:

I used to work for a major peptide synthesiser in the UK. The worst part of a peptide SSPS (solid state peptide synthesis) reaction is the cleaving of the peptide at the end from a silica bead basically. Most times this can be done with TFA but for some more difficult peptides you need to cleave with 99% HF gas cooled to a liquid with solid CO2 pellets in polypropylene flasks. All contained in specialist equipment from pressurised cylinder to flask in a fume hood. . I’ll stress now It wasn’t me who did this.. but once the poor soul who was doing the reaction couldn’t open the HF cylinders valve because it was rusty.. so hit it with a hammer!! The valve broke off and the HF gas started venting out to air very quickly. The whole building was evacuated very quickly and the fire brigade was called out, luckily nobody was hurt as the hood vented most of the gas out of the building. Afterwards once the fire brigade deemed it safe the damage to the fume hood and roof of the building looked like that scene in aliens.

pfschmit:

I was making a catylist using LiAlH4 and reacting it with a diglycol, not realizing a byproduct was H2O. I soon found out when the temperature went through the roof and a explosion followed. Fortunately, I had a blast shield in fromt of the flask. Nice fire though

palad:

In high school, our chem instructor warned us very clearly about the flammability of acetone. So naturally, my lab partner and I wanted to see if our teacher was correct. On the last day of a week-long lab, after everything had been cleaned up, we filled a small beaker with acetone and carefully placed it in one of the deep sinks. As I lowered the lit match toward the mouth of the beaker, I failed to notice the puddles of acetone spilled on the tabletop moments before by other students. One giant WHOOOSH later, and we had the attention of every student in the room, including those 30 feet away who claimed they felt a wall of heat blow past them. Fortunately, the acetone was the only thing flammable nearby, and it quickly burned itself out.

When I got home that afternoon and looked in the mirror, I started wondering why some of my hair had changed color. As I touched it and it flaked away into ashes, I realized just how close the flames had come.

merlin2112:

Around 12 years ago, I was given the task of preparing Azomethane. No, not Diazomethane, but Azomethane. This was to be used on the surface of Pyrite via FABMS. Anyway, the procedure called for: dimethyl hydrazine NaOH H2O Mercuric Oxide Following a reference (see Surface Science(279)79(1992)) the procedure is fairly straightforward; the problem lies when You have to evaluate the solid Azomethane to determine if any color is present.

After making ~25gm of Azomethane a normal procedure was called when I had to wipe off the frozen vacuum tube. POP! The tube exploded, giving Me lascerations to my hand, side of my face, and shattered my glasses, which gave Me a lascerated cornea!

Luckily all glass was removed and I was back in the lab after 7 days recovery making Azomethane again!

Mitch
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Sep 04

ACS Feeds: Two Steps Forward and One Step Back


I know everyone hates rss posts, but the latest ACS feeds updates is causing havoc for chemists dependent on their graphical abstracts fix (3000 people have visited the JACS feed in the past 9 months through ChemFeeds). It was bad enough that it dragged me from experiments to patch ChemFeeds and make me write this post.

The good parts of the ACS feeds update: 1) ACS now includes author names in the feeds instead of only the first author and appending “et al.“. Thus, I have updated ChemFeeds to display authors for ACS journals (simply hover over the abstract title) 2) The journal Analytical Chemistry now has graphical abstracts.

The Bad: 1)They don’t provide a link to ACS’s abstract page. The link provided takes the user to dx.doi.org which may not resolve to the publisher’s website for days.

I’m not sure why ACS decided to run all their in-house feeds through a third party like feedburner. My best guess is they wanted to track who and how people were using their feeds, but there are better ways to accomplish that.

Also covered by Sam.

Update (Sept 6th): After submitting this post ACS has again updated their feed structure and removed author names, dois, and all XML elements. Their feed architecture is nonexistent. ACS is basically running backwards at this point. It would be impossible to make it compatible with ChemFeeds or extract any information from it based on how badly the code is written. Apparently this is a feedburner feature that hides the source XML from view.

Mitch
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Aug 01

(Visible) scars of chemistry


Another mark of the chemist?Mitch’s post showing the video of “the mark of the chemist” reminds me of one of the most visible remembrances I have of graduate school: the scar on one of my middle fingers (see left.)

On a lovely Saturday in the lab (my music playing, no one else around), I dropped a Dewar flask from a shelf onto the lab bench. Along with the pop that announced its destruction, I saw that my finger was bleeding. My adviser brushed off my protestations that I was fine with “[CJ], you’re bleeding all over the floor.” He was right and off I went to the campus health center.

It’s been at least 6 years since I’ve had the scar. It’s healed, but left the interesting black mark that you see and a lump that I suspect may be embedded glass. But when I think about chemistry and potential dangers that I could face, all I have to do is look down at my hands.

UPDATE: The Curious Chemistry Grad Student shows off a couple nice burns.

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