science news

The Seven (deadly) Sins of Science

Professor W. F. v. Gunsteren has written a very interesting essay for Angewandte entitled “The Seven Sins in Academic Behaviour in the Natural Sciences”. In this piece he defines the seven sins as follows (taken from the essay) 

  1.  A poor or incomplete description of the work, for example, publishing pretty pictures instead of evidence of causality.

  2. Failure to perform obvious, cheap tests that could confirm or repudiate a model, theory, or measurement, for example, to detect additional variables or       to show under which conditions a model or theory breaks down.
  3.  Insufficient connection between data and hypothesis or message, leading to lack of support for the message or over-interpretation of data, for example,   rendering the story more sensational or attractive.
  4.  The reporting of only favorable results, for example, reporting positive or desired (hoped for) results while omitting those that are negative.
  5.  Neglect of errors found after publication.

  6.  Plagiarism.

  7. The direct fabrication or falsification of data.

 

Take the incomplete description of the work. Here the scientific journal(s) come in for some criticism; mainly for the restriction of journal space this in turn leading to more date being squeezed into the supplementary material. Interestingly this material is usually freely available while the actual article it corresponds to sits behind a paywall. So in my humble opinion this is a complete waste of time. Either one or the other but not both. The pressure on journal space makes the paper difficult to understand, says Gunsteren. Here I can only agree with him. Actually I wonder just how many referees read the supplementary material. Now you may not believe it, but when I was refereeing papers I always read the stuff that the authors deemed not necessary to put in the paper, and often came across some interesting discrepancies buried deep within and in sometimes in conflict with the actual text in the paper.

It has been said, “A picture is worth a thousand words”. This statement is certainly reflected in today’s publications where colourful diagrams and pictures litter the publication. If this actually helps clarity is open to question. Perhaps the pictures and cartoons should be relegated to the supplementary material and the actual data transposed to the main body of the text.

Moving on to sin number 4 “reporting of favourable results”. Well we all like to have our theories correspond to the observations, placing data in the paper supporting the hypothesis is very helpful in this regard. However, the tendency to omit negative results does not help the cause of science in moving forward. A negative result is also a result, and it’s reporting would actually help other to avoid making the same mistakes. No doubt in these days of fierce competiveness for grant money publishing negative results probably does not help you to obtain funding.

The word plagiarism rears it’s ugly head in sin number 6. This, of course, has recently been the cause of some spectacular events. Here one can think of the two eminent politicians who were discovered to have borrowed results and theorems from others without proper referencing. Self-plagiarism is a contradiction in terms says Prof. Gunsteren. Here I agree with him, how can you steal your own work or written word. You can’t. One recent eminent case makes the point 1-3.

Data fabrication or falsification is certainly the worst offence a scientist can commit. It is a cardinal sin that often ends in tragedy. One just has to be a reader of the Blog Retraction Watch to see just how often this occurs. One notable event in the world of organic chemistry, published in the pages of Angewandte in 2006, was recently retracted by the author of the paper in agreement with the journal editor. You can read all about it here. Over the years there had been several critical remarks about this paper and I’m sure everyone is conversant with the story and I will not go into detail again. But the question(s) remains: Why did it take so long? Why was it only recently initiated? I guess we will never find out, but retracted it was.

Not many members of the lay community are aware of the amount of fabrication that appears to be going on. Research is usually funded from the public domain and it is scandalous to think that this money is being wasted when fabricated data is published. I’m not sure how this can be avoided, as such data can be very difficult to detect. So it is really up to the scientific community working with the journal editors to try and root this out. Not an enviable task. Perhaps a reproduction of these “Seven Sins” on the header page of every journal might jog the memories of the authors. It will be interesting to see if this post receives any useful comments.

References:

  1. R. Breslow, Tetrahedron Lett. 2011, 52, 4228 – 4232.
  2. R. Breslow, Isr. J. Chem. 2011, 51, 990 – 996.
  3. R. Breslow, J. Am. Chem. Soc. 2012, 134, 6887 – 6892.

 

By December 9, 2012 3 comments chemical education, opinion, science news

A Bottle a Day keeps the Aging Away

Following on from the tea party where polyphenols reared their (ugly) heads a “highlight” has appeared in Angewandte Chemie English edition1, 2 pointing out the benefits of red wine, i.e. resveratrol. This is a well-known molecule, which has been at the centre of some controversy of late. Resveratrol is chemically trans3,5,4’-trihydroxystilbene:

This compound can be found in many types of fruits and nuts berries AND grapes. Its concentration in red wines varies between 0.1 and 14 mg/L whereby the 3-glycosate achieves levels of 30 mg/L. Frequently associated with this compound is the “French Paradox”, not that the French are a paradox themselves, but that apparently, in spite of consuming large amounts of saturated fats and barrels of red wine, the incidence of heart disease is lower that one might well expect it to be3. Resveratrol has a plethora of biological activities associated with it:

  1. It was originally noticed for its inhibitory effects against the oxidation of lipoproteins, the low-density variety being present at the onset of atherosclerosis4.
  2. Lowering lipid levels5.
  3. Moderate anti-oxidant properties.
  4. Protective for cancer, inhibiting cellular events associated with tumour initiation, promotion and progression6.
  5. It apparently also has a positive effect in diabetes and Alzheimer’s disease.
  6. It is able to activate sirtuin, thus mimicking calorie restriction and hence slowing the aging process.
  7. It also prevents phosphodiesterases from degrading cyclic AMP, also a mechanism of calorie restriction and hence age slowing.

What a list, I wonder what remains to be discovered?

Derek Lowe, at In the Pipeline  has commented extensively on this molecule and I recommend you all to have a read at the following plus the comments from his learned readership;

  1. The Latest Sirtuin Controversy
  2. Resveratrol in Humans: Results of a Controlled Trial
  3. The Sirtuin saga
  4. A resveratrol Research Scandal. Oh, joy
  5. Defending Das’ Resveratrol Research. Oh, Come On.
  6. Would I take resveratrol? Would You?

More about the sirtuins can be found on this page. In detail sirtuin1 information can be found here.

I do not profess to be conversant with all the details surrounding the apparent controversy concerning this compound and its biology. However, there is also big money at stake. GlaxoSmithKline acquired Sirtis, a company founded to discover and develop small molecules with at least some of the seven biological properties listed above. So presumably they are carrying out extensive medicinal chemistry on resveratrol. This won’t be an easy task to pick out one given the multitude of activities associated with this system, perhaps they can bundle 5,6 & 7 together. That is, of course, if there is any money left after paying the rather large fine recently dished out by the US Government. But, there is always the chance of off label indications being discovered!

Well, I shall certainly extend my red wine cellar but there won’t be many bottles in it, as I must take my daily dose of resveratrol by the bottle, especially at my age. Not to mention imbibing in tons of vitamin c and gallons of green tea. So when I drop dead after taking that lot no doubt I shall be considered as “toxic waste” and be treated accordingly.

References:

  1. Quideau, S., Angew Chem Int Ed Engl. 2012, 51(28), 6824-6826.
  2. Quideau, S., Angew Chem Int Ed Engl. 2011, 50(3), 586-621.
  3. S. Renaud, M. de Lorgeril, Lancet 1992, 339, 1523 – 1526.
  4. E. Frankel, A. Waterhouse, J. Kinsella, Lancet 1993, 341, 1103 – 1104.
  5. H. Arichi, Y. Kimura, H. Okuda, K. Baba, M. Kozawa, S. Arichi, Chem. Pharm. Bull. 1982, 30, 1766 – 1770
  6. M. Jang, L. Cai, G. O. Udeani, K. V. Slowing, C. F. Thomas, C. W. W. Becheer, H. H. S. Fong, N. R. Farnsworth, A. D. King- horn, R. G. Mehta, R. C. Moon, J. M. Pezzuto, Science 1997, 275, 218 – 220

Now we can’t drink tea!

If you’re a man and you live in Scotland do not drink tea. According to a BBC report  >7 cups a day give you a >50% greater chance of developing prostrate cancer than “normal” tea drinkers. This was the result of a  study over 37 years involving 6000 volunteers aged between 21 & 75 years of age. I’m surprised they didn’t choose whisky and/or beer (they have probably been checked at some point in distant past). This is in direct contrast to a National Cancer Institute report which suggests the opposite, at least for green tea.

What’s next I wonder, coffee is already on the black list, as well as fatty foods smoking, no doubt sex will also rear it’s ugly head in the list of cancer producing agents, water is also dangerous, fish swim in it and you can drown as well.

Wiki tells us the exact opposite to the results reported by the Glasgow study. Tea is actually beneficial for you in all sorts of ways.

So what’s in tea that makes it so harmful or so good for you? Well there is theanine and caffeine, making up about 3% of its dry weight up to 90mg per cup, depending upon the tea. Theanine moves across the blood brain barrier (quite distant from the prostrate) and has a synergistic effect with caffeine, high doses even providing a neuroprotective effect. Caffeine is a stimulant and the author of the Wiki page suggests that it may even have moderately protective effect against certain cancers.

 

There are also things like theobromine (or should it be teaobromine) and theophylline. So those compounds are  probably not the cause of this higher prostrate cancer risk.

What else?

Up to 30% of the dry weight of tea are the catechins. These look like a possible candidates! Some present in green tea are shown below.

 

Just look at all those nasty phenols, they may even have antioxidant properties, but as carcinogens, well,  I think they are not very high on the list.

The tea plant apparently has the capacity to absorb lots of the pollutants we pump out every day, e.g. fluoride and aluminum, the latter  can be present up to 30,000ppm by dry weight! Exactly what the form of the fluoride and aluminum is I don’t know, presumably sodium fluoride, perhaps someone can enlighten me as to the aluminum source.

So everyone, what shall we drink now? How about red wine, with all that reservatrol it must be good for you perhaps the chances of developing cancers will be reduced. It’s like everything we do (apart from working and paying tax), taken in moderation it is very enjoyable, but taken in excess, well I guess we have all suffered a hangover at some time.

Enjoy your tea breaks.

 

Lab Muppet Theory

Quick: What do Pinky and The Brain, Kirk and Spock, Bunsen and Beaker…and your research group all have in common?

Give up? They all subscribe to “Muppet Theory,” a very recent label on a very old phenomenon. As Slate writer Dahlia Lithwick explains, Muppet Theory reprises the age-old struggle between archetypes: Order fighting Chaos, Kermit against Animal, maybe even mustard vs. ketchup.

"Are you thinking what I'm thinking, Pinky?" "I think so, Brain, but isn't Nietzsche a type of cheese?"

Nietzsche formalized this philosophy in 1872 (thanks, NPR!) with his Apollonian (order-seeking) and Dionysian (chaos-loving) personae, stating that true high art comes from the successful fusion of both aspects in one venture.  Well, scientists have argued these points for the last three centuries! Consider the following quotes from two chemistry legends:

“A tidy laboratory means a lazy chemist.” Jöns Jacob Berzelius (1779-1848)

“Fortune favors the prepared mind” – Louis Pasteur (1822-1895)

Right there, you have “Muppet Theory” in action. Lab Order Muppets (Brain, Spock, Bunsen) contribute careful data collection and deep analytical thinking, while the Lab Chaos Muppets (Pinky, Kirk, Beaker) stir the pot, following gut instincts and making wild assumptions. In my experience, Lab Order Muppets are department-builders, sturdy rocks in the storm that can manage conflicts. Lab Chaos Muppets have the devil’s luck, write roguish autobiographies, and often enjoy pop-culture “crossover” success.

So, which Lab Muppet type are you? I’ll disclose my “Muppet type” in the comments, but only after I hear from a few readers.

P.S. While researching this post, I came across this fantastic Agilent ad.