Why I retracted my Nature paper: A guest post from David Vaux about correcting the scientific record

Retraction Watch

Last month, Ivan met David Vaux at the 3rd World Conference on Research Integrity in Montreal. David mentioned a retraction he published in Nature, and we thought it would be a great guest post on what it’s like to retract one of your own papers in an attempt to clean up the literature.

In September 1995 Nature asked me to review a manuscript by Bellgrau and co-workers, which subsequently appeared. I was very excited by this paper, as it showed that expression of CD95L on Sertoli cells in allogeneic mismatched testes tissue transplanted under the kidney capsule was able to induce apoptosis of invading cytotoxic T cells, thereby preventing rejection. As I wrote in a News and Views piece, the implications of these findings were enormous – grafts engineered to express CD95L would be able to prevent rejection without generalized immunosuppression.

In fact, I was so…

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Are you on green-coffee bean diet? Forget it, even mice did not lost weight on that either

One thing you may know that a statement is bogus is when it is full of superlatives “A miracle fat burner” as Dr. Oz cited it. What is it? The paleodiet? Noope. Is it the pomegranate diet? Nope either. The green bean coffee diet? Yes and it does not look promising for this diet either according to a study from Mubarrak and colleagues recently published at the Journal of Agricultural and Food Chemistry (http://pubs.acs.org/doi/abs/10.1021/jf400920x) .

Again, this is the same problem again and again. Plants are great chemical plants through their secondary metabolism and provided us with a formidable source of chemicals that are beneficial for us (drugs and medicines) or detrimental if not lethal (poisons).

Among them are a class of molecules that have shown to have various biological properties, most importantly antioxidant activities. However, their effects are best limited to in vivo (animals) studies at worst have been cases of fraudulent cases as the famous Dr. Dipak Das case of 145 scientific frauds in terms of data falsification or fabrication (http://www.npr.org/blogs/health/2012/01/12/145117068/uconn-claims-resveratrol-researcher-falsified-work).

Again, here is the case of chlorogenic acid (one of the many active substance present in coffee beans) that shown poor effects on weight loss in animals. One remarkable aspect of US regulation is the sacro-sanct “FDA approval”. A chemical can claim any therapeutical effect only is it “FDA-approved” and this approval is one of the hardest one to get worldwide, so it gives you the challenges that have every single drug and medicine sold in the US have been through.

Next time, you see a retailer for dietary supplement claiming “fat burner” properties, remember….No FDA approval? No clinical efficact and you may deal with a modern snake oil case.



Weg mit den Speck…but forget the paleodiet on that one

If chemists looked since the age of times to find the “philosophal stone” that would change lead into gold (as Midas was able to change everything into gold), one thing that many of us (especially women before the summer season) is to transform “lard” into “six-packs”. The magic pill, the one that makes out purge the fat and brings you six-inches down.

Everyone would not say no to loose extra pounds without efforts and unfortunately this remains a hopeful dream that we may find a pharmacological switch to transfer the energy contained in our adipose tissue into some other form of energy.
So far no miracles: decrease your intake (decreased carbs intake) and maximize your output (run, sweat…the so-called “no pain, no gain”). There maybe as many diets outside in the wild as I have microbes on my skin but so far no miracles.
However some people outside claim the benefits of the “paleodiet” that our ancestors reluctantly have to live with, getting us back to some hygienist and naturist “utopia” from last centuries.

You may think frugal diet+lot of physical activity=lean? Yes and no. This study brought by NPR showed that our body has a formidable capacity to adapt to food intake and especially energy expenditure. Yes, the “caveman” was lean and have a lot of exercise. Yes, the “caveman” was on a diet. But the “caveman” may have already a well-oiled metabolic system that know how to rewire energy expenditure to keep it optimal for storage.

And this is something that anyone ongoing a diet and weight loss face (including myself): You follow the diet, works great for a couple of months and you are energized….and then you stall on the weight balance for a week, two weeks, a month, a year…..

This is were we are and maybe why we face our modern problem. Our body is hardwired for preventing starvation and has evolved to prioritize storage and reduce the energy expenditure. Now add to it our brain wiring for sweet and fatty food (also great form of storage around our belly).

My take on this article? Dont let the paleodiet dictate your life, because you will get depressed and you will crave on comfort foods (that are rich in carbs and fat). Know that you will never face a size 0 and know you are genetically defined to have a certain shape. But keep on exercising everyday (I hit the treadmill everyday, thanks to Anytime Fitness) and know your BMR and manage your food intake as you manage your account balance.

Would you pay $37 to find out that a publisher had mistakenly printed an article twice?

Retraction Watch

clinicalgerontologistDo you have a spare $37 that’s just burning a hole in your pocket?

If so, today is your lucky day. You can plunk down your hard-earned cash for a chance to read a retraction notice in Clinical Gerontologist that resulted from a goof by its publisher, Taylor & Francis.

Here’s the notice for “Does Social Desirability Confound the Assessment of Self-Reported Measures of Well-Being and Metacognitive Efficiency in Young and Older Adults?”

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Forbidden fruit: apple pomace paper retracted for plagiarism

Retraction Watch

foodbioprodprocThe journal Food and Bioproducts Processinghas retracted a 2012 article on apple pomace — the remnants of a pressed fruit — by a group from India.

The reason? Turns out the paper “Utility of apple pomace as a substrate for various products: A review,” fell a little to close to the tree.

Here’s the retraction notice:

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Supreme Court: Natural DNA is not patentable (but cDNA is)

The recent decision of the Supreme Court is a big relief for scientists like me, following the battle engaged between Myriad (the company behind the BRCA test and Angelina Jolie’s story). It clearly stipulates that natural DNA cannot be patented, but artificial (cDNA) can.
What are the differences and how it would impact us? Lets take the BRCA gene as an example.

Mutations in the BRCA genes (BRCA1 and BRCA2) are linked to increased risk in breast and ovarian cancer (thus explaining Angelina’s decision for the double mastectomy that I would argue against but this not the topic of this blog). Before the decision, Myriad had the exclusivity of the BRCA gene including the gene product (protein), thus making the development of detection kit and assays exclusive to Myriad (at least in the US). The problems of this test? Very expensive ($3000-6000 per screening) and not 100% reliable. On the other side of the Atalantic Sea, French have also a BRCA kit that is slightly cheaper than the US one but also more reliable. Thus, we can clearly understand that having the open access to the genome would help the development of new technologies and at the end decrease the cost of this kit, good for your health and your wallet.

The proof of my reasoning? Look at the cost of DNA sequencing. You even have a company called “23 and Me” that sequence your genome for $100 (but also opens another genie contained in the bottle).

In the other hand, artificial DNA is still under patent. What does it mean? For the general public not much but for scientist, that means now virtually everyone can patent any cDNA or recombinant DNA (for example someone that created a hybrid of the BRCA gene fused with a green-fluorescent protein contained in a plasmid could apply a patent on it). That can be a no-problem for scientists (as patents most of the time protect the intellectual property by the scientist that formulated that cDNA and you have to acknowledge them in your publications at minimum) but may become a hassle for all these companies like Affymetrix, Illumina or Agilent that heavily rely on cDNA for the DNA microarray analysis (the next BIG THING is personnalized medicine). So let’s how things are going in that direction….


Glaxo asks Nature Medicine to retract paper by fired company scientist

Retraction Watch

natmedcoverIn what could be a significant blow to a major pharmaceutical company, Nature Medicine is reportedly set to retract a 2010 article by a group of researchers affiliated with a Chinese arm of the drug giant GlaxoSmithKline.

We’re not the first to report the news — you can read coverage of it on In the Pipeline and Pharmalot, for starters — which includes the revelation that Glaxo has fired Jingwu Zang, a co-author of the suspect paper and former senior vice president and head of research and development at the Shanghai facility: in other words, a big fish. (Big enough to have a profile in, well, Nature Reviews Drug Discovery.)

Pharmalot has quoted a Glaxo spokeswoman:

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