Friday, October 01, 2010

Thursday, September 30, 2010

Plagiarism rampant in Chinese science journals

There have been several discussions on plagiarism lately on the intertubez (note to self: compile list), so when the following article was sent to my email this afternoon (via Biotechniques) I took note.
Over 31% of submissions to the National Natural Science Foundation of China English-language publications show signs of copying, self-plagiarism, or copyright infringement, according to Helen Zhang, journal director at the Zhejiang University Press in China.
Almost a third?!?
In an article published earlier this year in Learned Publishing, Zhang and her colleagues analyzed manuscripts submitted to the three journals between October 2008 and May 2009. They discovered evidence of plagiarism in 151 out of 622 papers, or about 22.8% of submissions during that seven-month period. In a recent opinion piece published in Nature, Zhang reports that continued data collection analysis shows that the problem is only escalating as the percentage of plagiarized submissions has increased to 31%.
So why all of this plagiarism? The authors of the study claim that it "is a result of the academic world’s emphasis on publishing quantity over quality". I've frequently referred to it as the LPU (least publishable unit) but it seems that some researchers are taking it even further than that.

QR Codes

I've been enamored with the idea of QR codes lately. Over at LabSpaces, I mentioned that I'd like to include them on my next round of business cards.

I've found two applications which have proven useful in my quest to QR code things.

The first is a web app by Kaywa. If you give them a URL, they will generate a QR code image for you which you can then download and do anything you want with.

The second is ScanLife, which produces an app that I have for the BlackBerry. It takes some getting used to, but if you hold your camera back far enough (I'd say at least 6 to 10 inches) it'll actually work fairly well. There are also applications for the desktop where you use a webcam as a barcode reader.

Tomorrow is going to be a big day ...

... I can feel it already.

Wednesday, September 29, 2010

Latest Manuscript

Went into manuscript tracker for the latest first author manuscript I put together. It's the one on the topic that I find totally uninteresting but which yielded some interesting results. Other than a delay getting it into the hands of the associate editor, things have been going smoothly. Maybe too smoothly. One of the reviewers took a total of five days to get their review back. Usually these things sit for a couple of weeks before the reviewer hands them in, and I'm wondering if this is a case of the jury not taking much time to deliberate.

I've got two likely scenarios running through my mind*:
1. Reviewer is someone I don't know, but didn't like the work and tubed it.
2. Reviewer is someone I do know and they gave me a favorable review.

I hope it's #2. What do you think?

*The ones I consider to be the most likely.

Remainder of the day

I'll be AFB (away from blogger) until I finish the revisions for one of the latest manuscripts my collaborators and I submitted. We've gotten one of the two accepted, and we hope to get this one accepted ASAP.

ETA: Only took a couple of hours, not as bad as I thought it would be.

Wednesday Micro Hits

So the hump day has begun. As such, it's time for my second weekly rollout of my Wednesday Micro Hits. Here is where, instead of rattling off small blog entries of mundane thoughts, I coalesce them into one. Ergo, I only waste a fraction of your time!

1. Debating a AAAS membership. I don't really need a subscription (hard-copy or online) of Science, but their new t-shirt (Ways to Demonstrate Science) is really cool. Can't find a picture of it online yet, but if I do soon, I'll link to it here.

2. According to Google Analytics, I've had 14,434 (~40/day) pageviews in the past year. As a standalone amateur blogger, I'll take that as some good numbers.

3. My tri-society has informed me that I have been a member for five years. I guess if I sit down and do the math I have been in the field for roughly that period of time now. I didn't think it had been that long. I guess time flies when you're having fun?

4. If you think agriculture is contributing to global warming, think again.
The study included carbon dioxide and other gases such as methane emitted by rice paddies. It found that, overall, the intensification of farming helped keep the equivalent of 600 billion tonnes of CO2 out of the atmosphere – roughly a third of all human greenhouse-gas emissions between 1850 and 2005.

5. I think I'd like one of these for Christmas. However I don't live in a drought-ridden area. At least not most years.
The Waterboxx, invented by Pieter Hoff, is a low cost device that can help plants to survive in drought-ridden areas.

6. To everything there is a season. At least that is what the verse in Ecclesiastes (3:1) says. Then why do we and our medical community spend so much money delaying the inevitable?
Americans increasingly are treated to death, spending more time in hospitals in their final days, trying last-ditch treatments that often buy only weeks of time, and racking up bills that have made medical care a leading cause of bankruptcies.

Tuesday, September 28, 2010

Watch this space ...

... I have some news I'll reveal in the upcoming days.

Monday, September 27, 2010

Writing Reviews

A couple of weeks back an interesting discussion was had (well, it appears to be over) at DrugMonkey's Scientopia page, on the issue of citation practices. I chimed in with my own practice ... I don't give a rats patooie what journal the manuscript is in, as long as it was good science. And that would have been it, had not someone uttered something I found completely unfathomable.
I do not have adequate time to do all of the fact-checking myself for every reference in my 200-reference review article.
Excuse me? I responded here ...
Say what? You include references into an article without fact-checking them yourself? I can understand going through the abstract, skimming the R&D, and reading the conclusions … but if you can’t be bothered to read the damn article, why are you citing it?!
... and here ...
Yah … I’m following up my own reply. If by fact-checking you mean subsequent articles which support and/or refute said article … IMNSHO, if it’s important enough to cite, then it’s important enough to know the history behind the article and how it was received IN THE FIELD YOU’RE WRITING A REVIEW ARTICLE IN. If you don’t know the history behind the literature in said field, let someone else write the review article.
I also said ...
What I said is that if you’re in a field you should at least know the relevant literature, especially if you’re writing a review on said literature. Cold-citing an article? Piss poor.
I continue to stand by those comments. Why would anyone cite an article without taking a look at and understanding said article? How would you even know where to begin, to properly cite the article, when you have no idea what was contained within the manuscript and/or how it was perceived post-publication? Taking someone else's word for it? Sure, but how do you know they got it right?

I was damn sure then, and I remain damn sure now, that if you can't bother to pick up the manuscript yourself, read at the very least the Abstract, Results & Discussion, and Conclusions (if your journal has them) yourself ... skim them at the very least ... you have no business reporting on that article in your own article/review. I don't care if you have one week to write the article, or one year. You should have at least a passing familiarity with the work in order to cite it.

But hey, I was just being argumentative, right?

But wait, it gets better. I then find a blog entry on the discussion. Stumbled across it really. It does its very best to completely misconstrue the entire point of my comments over at DM's blog ...
There have been implications on the interwebz that I totally cannot do a good job of this if I am a non-expert and if I do not spend infinity bajillion hours researching Mango Skin Allergies. That I will do the world of science a serious injustice if I do not provide the very best reference for every point in my article. That it takes a real expert to know the field, the history of the field, to put all of the confusing shit in the context of the field, appreciate the field, take the field out for some lobster, and try to put the moves on the field after dinner.

Bulls**t indeed Candid Enginner. Bulls**t that for someone with a graduate degree your reading comprehension is abysmal. No one, not me, nor anyone else at DM's blog stated that you must spend countless hours on the review (though a week really is crap IMNSHO) or that you must provide the very best reference, or that you must be a real expert to know the field, or know every minute detail of the history of field. I did say that ... you should understand the damn papers you are going to cite! And yes, you should also know how those papers relate to the field. Now, since she didn't clarify what she meant by "fact check" I suppose we can't truly understand what she was trying to say, but honestly I think a fairly reasonable conclusion is that "fact checking" meant (at least in part) how the manuscript fits in the "big picture" of the entire field.

To which I say ... if you personally don't know how the manuscript truly fits into the big picture of the field (because you didn't check for yourself, because you're busy writing super-important-review) ... how the heck are you writing a review on it?


Now, I'm willing to be educated on this issue. It's possible that I may have overlooked an argument which really makes sense on this issue, but so far I haven't. Not really.

Oh, and by the way ... when writing a review, it helps to keep the people who are going to take credit/blame on said review in the loop. Otherwise you wind up wasting tons of time. Telling a field they don't know how to do their work in the field is going to make so many enemies for your PostDoc adviser that it's irresponsible to even consider writing such a treatise. It's one thing to play fast and loose with your own career. It should be a crime to play fast and loose with someone elses.

Wednesday, September 22, 2010

Scientific Misconduct

The Genomic Repairman has a blog entry up asking about scientific misconduct. He found an instance of two journal articles from the same group that used an identical figure in a set of 2008 and 2010 reports. Is this scientific misconduct? If they didn't cite it, you betcha ... and even if they did cite it, they could be butting their heads up against copyright issues with the 2008 journal. Any way you cut it, if you can't be bothered to change things up, like oh I dunno redoing the experiment to generate a new figure, you deserve to be hoisted up by your own petard.

I have a similar tale as a graduate student, but this one didn't involve me stumbling across two publications of a science enemy. Instead, I came across the scientific misconduct of one of my departments professors.

I came across this misconduct early on in my journey as a graduate student. It was before my second year was completed and a friend and I were studying for our general exam. We would alternate between the building he worked in, the building I worked in, and the campus library. This day we were in his building and we had taken a break. I was in the hall looking at the lab posters and came across the work of Professor M. Professor M had several of their papers tacked to the board as well and I was leafing through them.

Something caught my eye.

I noticed that in two papers on the same subject, published back-to-back (but in different journals), looked awfully similar. In Manuscript A, there were several tables. In Manuscript B, there were several figures. I took note of it and went back to studying. Later that evening I went to the library and printed out the two manuscripts ... and began lining up the tables and figures.

They matched.

Whiskey. Tango. Foxtrot. I slept on it and then brought the evidence to my adviser the next morning. He was not pleased, but there was no denying it. This was a clear cut case of double publishing. My adviser said he'd take care of it, and took the evidence I collected. That was the last I heard of it. Now, there were several other instances of moral turpitude concerning Professor M, the combination of which forced him out of our department and university altogether. I'm not sure what role his double publishing played, and to be honest I have never looked for a retraction of either paper. I suppose I could go and check now (check back for an ETA). I don't know if Professor M rues the time spent at our university, but I do know what the immediate consequences of Professor M's actions were ...

Department Chair at a different university.

ETA: Both publications still exist in the literature, with neither ever being retracted.

Wednesday Micro Hits

One. It's definitely misconduct.

Two. I feel naked when I don't wear an undershirt underneath my polo.

Three. Let the poor guy die in peace. Quit asking him if he's going to convert on his deathbed. Honestly, he's already on his deathbed so asking him is silly.

Four. The Archaea are the next great frontier in microbiology. If anyone wants to carve out their niche in microbiology, seriously consider this line of research. There is so much about the Archaea that we don't know, but we do know that they contribute A LOT to environmental processes.

Five. This twitter thing is pretty interesting. Don't know if I'll stick with it, but so far it's been fun and a bit of a time hog.

Six. I love my new Streetcars shoes. Got the Carerra's (#5703) and they're as comfortable as my Ecco's.

Tuesday, September 21, 2010

Joyful Video Tuesday ...

... because the alternative sucks.

Caught in the crossfire

Humans suffer collateral damage as microbes battle it out. Guess we've become the microbe's turf eh?
When S. pneumoniae is forced to share space with Haemophilus influenzae, another common and ordinarily asymptomatic bacterium, the two begin a tussle for space. But H. influenzae has an extra trick up its sleeve, calling on our immune system to help get rid of its competitor by recruiting white blood cells called neutrophils, which surround and attack the S. pneumoniae bacteria.
This of course forces S. pneumoniae to respond ...
Many strains of S. pneumoniae exist, each coated with a thick sugar capsule. In some strains, the capsule is particularly protective, and appears to act as armour against the host's immune response. This allows the bacterium to enter the blood stream where it can go on to replicate and cause serious diseases such as pneumonia, bacteraemia (blood infection), septicaemia and meningitis.