Manes, Brains and Branes

Why the Lion Grew Its ManeI’m playing catch up, after some offline time last week (holidays, families, and illness), so today’s post is a grab-bag of the various items (mainly books) sitting in a large pile on my desk that I thought deserved a quick mention and a link or two for more information.

First up: Why the Lion Grew Its Mane – a big floppy book with a glossy cover and some wonderful nature photography. Author Lewis Smith (a science reporter for The Times (London) describes it as a miscellany of recent scientific discoveries from astronomy to zoology, and that’s pretty much what you get. Somewhat more esoteric is the cosmic book – The Origins of the Universe for Dummies – from Financial Times writer Stephen Pincock and sci-tech writer Mark Frary. Apparently, this is an easy book about a tough question, written at a time when dark energy, dark matter and the validity of the Big Bang are all offering humanity an array of new questions about the nature of reality. Although I didn’t see mention of ‘branes.

My old friend Kyriacos “KC” Nicolaou and colleague T Montagnon are next up. I have written widely about KC’s organic odyssey over the last (almost) two decades of my career as a science writer, having become fascinated by the incredible ways in which he and his team turn simple starting materials into some of the most complex natural products. In Molecules That Changed The World, Nicolaou and Montagnon provide a brief history of the art of chemical synthesis and its impact on society from aspirin and penicillin (sample PDF chapter) to the anticancer compound Taxol.

Nothing is static in the world of health, and as Brian L Syme suggests in Seasonally Fit, improving fitness and health is not just about diet and exercise, it’s about understanding the “rules of the game”. I must confess to agreeing with many of the critics of this book that it is aimed at too wide an audience but fails to hit the spot for any single group – whether health practitioners, academics, or lay people. Nevertheless, there is a nugget of an idea here – that our health is affected by the seasons – and with a decent ghost writer could become a useful book to add to the library of anyone hoping to understand their health more fully.

Also on my desk – Achieving Sustainable Mobility by Erling Holden (a scientific study of the impact of the European Commission’s 1992 motion), Darwin’s Paradox a novel by Nina Munteneanu (about an intelligent virus), Neuromatrix from Morphonix Inc (a PC game based around rogue nanobots, a kind of Lemmings for the 21st Century).

Finally, I’m thoroughly enjoying Brain Rules by John Medina in which he presents 12 principles for surviving and thriving at work, home, and school. This is not just a book, but has an interactive and augmentative website as well as an accompanying DVD to help you get the most out of your brain.

Industrial Organic, Green Fireworks, and Unfolding Proteins

Rolling out OLEDs

I was scanning the commercial world for a change for The Alchemist’s first find this week, and learned that General Electric is hoping to revolutionize OLED (organic light emitting diode) manufacture. A chemical web pioneer is offering a solution making open chemistry commercially viable through the concept of information credits. While firework pollution could go up with a bang if the latest research into eco-friendly pyrotechnics is commercialized. Back down to earth, efforts to inspire girls in science, particularly chemistry, are apparently working, at least during National Girl Scout and National Chemistry weeks. Finally, the FDA is hoping to muscle in on the nanotech world but experts warn that it faces a daunting task with limited resources to approach this burgeoning field.

The Russell Berrie Foundation is the subject of this week’s award, it having donated $28 million to diabetes research with the aim of improving care and perhaps ultimately finding a cure. Find the details in this week’s Alchemist

Also in offsite news, this time in my SpectroscopyNOW.com – more on those green fireworks, how Raman spectroscopy could soon help oncologists predict whether radiotherapy will be successful for treating cervical cancer in different individuals, and the trouble with low-level ozone production.

Video nasties also feature in this week’s SpectroscopyNOW with functional MRI results showing how the brain copes with disgusting images. Apparently, the grin and bear it approach is not nearly as effective as one might think and the method of choice (whether unconscious or conscious) is to reappraise the situation to make what you are seeing not seem so bad.

Finally, two 40-year old stories brought bang up to date as NMR spectroscopy reveals that proteins can shapeshift. This flies in the face of received wisdom concerning protein folding and could lead to a whole new approach to targeting proteins with drugs. Similarly, new X-ray crystallographic evidence finally shows how the anticancer drug bleomycin works. Bleomycin was first isolated from a soil microbe by Japanese chemists in 1965 but its underlying mode of action has remained hidden, until now.

Here are the links to my latest science news stories on SpectroscopyNOW.com, live as of April 1: Green Fireworks, Video Nasties, Raman Rates Radiotherapy Results, Protein Shapeshifter, Clear View of Bleomycin, The Highs and Lows of Ozone.

Scientific Sin and Self Plagiarism

Scientific sins

One of the seven deadly sins for scientists I came up with in a previous post on Sciencebase touches on the whole issue of trust. I used the term self-plagiarism, I was alluding to the growing problem of scientists publishing essentially the same paper in two or more journals. Essentially, self-plagiarism is duplication, it’s a kind of cheating. A paper in Nature in January highlighted the problem and explained that it is much more common in China and Japan for whatever reason.

The term – self-plagiarism – caused a little confusion in the comments on my seven sins item, so I asked Jonathan Bailey of Plagiarism Today whether he considered it a useful term.

“I read the article and found the idea interesting,” he told me, “It’s a problem that exists not only in the science arena, but also in the literary and photography one as well. It seems that every field where you can submit multiple copies of a work to different publishers have their own issue with this.”

Bailey added that, “Typically, self-plagiarism refers to the reusing of old writing in new works. For example, an author reusing passages in a new book or a scientist rehashing previously published research as if it were brand new. I’m not sure what the name for this type of problem is, I’ve heard it referred to as “shotgun submissions” or “duplicate submissions” but not really self plagiarism.” So maybe I had coined a quite original phrase but it does not quite fit the crime in question.

However, Bailey’s next comment was quite encouraging, “The term is expanding, it could be a sign of a broader definition of plagiarism,” he told me.

He pointed out that given the inclination of some people to self-plagiarise, the issue is effectively an editorial problem. “Most publications and publishers have rules about these things and, if authors are caught disobeying them, they are reprimanded,” he added, “The problem, of course, is getting caught. Since the majority of
papers are not accepted, the odds of someone being published in two journals are still fairly slim and the odds of it being discovered are even slimmer. Still, much like with traditional plagiarism, the stigma of getting caught is pretty severe and it should deter the good scientists from engaging in this behavior.”

Bailey suggests that probably what is needed is better community policing and enforcement. “That can do far more than anything else,” he says. Perhaps a new form of peer review will enable such policing. How often do physicists see self-plagiarism in the arXiv.org preprint system, for instance.

After this brief email interview, I followed up with Bailey on the Oriental question mentioned in the Nature paper and he had this to say, “I realize that publishing in an English journal and, say, a Japanese journal simultaneously is a faux pas and I can see why, but how serious of an issue is it? How common is it and how major of a slight is it viewed?”

Bailey then pointed out that it might be argued that the scientific community could actually benefit from research that would otherwise be lost in a foreign language journal becoming more accessible because it also gets published in another language. “I don’t agree with that for the same reason I don’t agree with doing it in the literary world,” he emphasises, but it does raise an interesting point not necessarily related to language – Could duplicate publication, self-plagiarism, actually be a good thing, after all?

In science we trust

Why does the public no longer trust science?

In sci we trustThe first response to my question was from user J Pegues, a self-described CEO-level consultant in the US. Pegues, who in one sense ignited the flames, but also emphasised that people do not distrust science, instead they distrust the US government:

Who don’t people trust? Our lame federal government. People don’t even listen any more to what government spokespeople, including the president, say because they have lied to us, instituted policies aligned with their own myopic beliefs, and undermined every ideal the United States has stood for 230 years. Don’t confuse people’s lack of trust in the federal government, its hacks, and policies against the advancement of science with lack of trust in science.

Bryan Webb a marketing consultant in Canada suggested that Pegues is right on target:

We do not believe governments who have their own agenda which in general is not for the good of the people although their words (promises) at election time try to tell us another set of lies.

Uli Hofer, of Owl Database Applications, based in Canada, was the first to respond more directly to my question in the way that I had hoped LinkedIn users would with a point regarding the current media frenzy surrounding almost every scientific paper that appears these days:

A lot of what’s going on in today’s science is way over an average person’s head (astronomy, nuclear science, genetics, etc.). It is not possible to gauge the different points of view in a scientific discussion. The media, in constant pursuit of hot news, report on every scientific paper they can get their hands on. Way too often, these reports are reduced to ‘headlines’. And don’t kid yourself, political correctness governs science too. How often has the public heard about a wonderful new thing that is absolutely safe, that disappeared a short time later because it wasn’t?

Geoff Charlwood of Clinical Informatics at Pharmaceutical Profiles Ltd of Nottingham, England, suggested that there is something in the science and government issue and claimed that people do on the whole trust the government Chief Scientist of the day, in much the same way that they trust the Bank of England on interest rates and trust reports coming from the Chief Inspector of Prisons. Even though they may make mistakes, they are usually honest ones, he says:

They demonstrably maintain their independence from political considerations. On the occasions when such people overtly bring an agenda to their job, trust declines.

Walt Wallgren, a partner at Solid Ground Investments in San Francisco, had a fairly contrary view in that he believes the problem lies not with science but with scientists themselves:

If the scientific method is rigidly applied and results are unemotionally reported, science and scientists are on a firm footing.

He points out that scientists are people too. “They all have their own beliefs and ideas and they hate to be wrong just like everybody else. There are just as many pre-conceived beliefs in the scientific world today as there are in the pulpit. And, I believe that many of them are opposite to what religion teaches just to try to prove religion wrong.” He adds several examples from nutrition and health, global warming and even fundamental physics:

The distrust of science comes from too many purported scientists trying to get the data to fit the hypothesis and selling the idea to the general public. If you don’t like the answer, change the question make the answer fit your position. After all, studies have proven that you can prove anything with studies.

Software architect Brian Conner from the Greater San Diego area admits his gut feelings pertain only to US residents:

I doubt that much of the public understands and respects scientific principles. Though the basics of the scientific method is taught in school in the US I don’t know many people who really understand its importance. Lack of understanding leads to a situation where the public cannot distinguish between “good science” and “bad science.”

David Evans, a Multimedia Designer at the Science Museum of Minnesota, on the other hand, suggests that science will always be used to promote greed, and that is what breaks the promise that the big word Science has to offer.

Universities are always looking at how the results of scientific inquiry can be adapted to profitable results in the Real World. Scientific inquiry gets steered to businesses that copyright the results, and charge money for the opportunity to use the results, even after the public has paid for the scientific inquiry through grants based on taxes. How can you trust greed?

Graduate student Herman Van Wietmarschen of Leiden University also emphasises that science is not as neutral as one might believe, adding that scientific work has many social, ethical and often also economic aspects closely interwoven with it:

No scientific finding ever finds its uses to the public without a widespread network of other actors. Usually money needs to be found to develop the technology, interest of some companies needs to be found.

Robert Poulk, a network troubleshooter based in Seattle also points out that what happens between scientific discovery and their presentation:

We live in an advertising-driven world; content is presented not based on the public’s need to understand but on the advertisers’ need to get our attention, and they get it using classic bait-and-switch.

Information manager Christopher Goh suggested that my initial question gives in to the cynics and adds that there has never been more need of good science as there is today:

Science has come a long way from Copernicus and even Mendel, and those who want to seek out fact can do the right due diligence and sort through the raft of opinions quite easily. That pursuit of truth has and will always remain critical to man kind, and as long as science remains true to that pursuit, then all we can do is hope the right educational policies and frameworks will create a generation of people willing to seek it.

There were many other excellent responses to my initial question and follow-up qualification, which can all be read in their entirety on the LinkedIn site, here. You can also link up with any of the members who responded.

I posted the question above on the business and networking site LinkedIn as a test. It was a deliberately naïve and heavily loaded question, which I hoped would inspire fellow LinkedIn users to respond in depth, but on reflection I probably committed at least one of the seven deadly sins for scientists. It turned out to be quite a controversial question and inspired, if not quite hate mail, then quite a few flames, which I discussed in an earlier post about LinkedIn questions.

So, yes, you might say it has quite an inherent bias, suggesting as it does that the public is some kind of entity beyond science and that in this divide there is some obvious distrust.

Pricing Petrochemical Know-how

An informatics approach to pricing petrochemical products has been devised by scientists at the Market Research Department of the Research Institute of Petroleum Industry (RIPI) in Tehran, Iran. Their model puts a price on “know-how”, which is the most complicated activity of the commercialization stage.

Writing in the International Journal of Technology, Policy and Management, (2008, 8, 279-297), Reza Bandarian, Ahmad Mousaei, Abbasali Ghadirian and Maham Tabatabaei explain their approach. “The RIPI has a mission to bring ideas to market in terms of developing new technologies and new products,” they say, “Commercialization is one of the critical stages in this process.” Their model examines three pricing scenarios – optimistic, pessimistic and actual – for selling technology and was validate against historical data of various RIPI petrochemical products.

There are increasing demands on companies, not just in the petrochemicals sector but across the commercial spectrum. The marketplace needs better, faster and cheaper technology and products, while intellectual property, once simply seen as an expense has become an important source of revenue. Indeed, many of the problems seen in modern business hinge purely on IP rather than solid, hands-on extracted or manufactured resources. IP provides a critical competitive advantage for the firms that hold it but a serious disadvantage for those that do not.

Bandarian and colleagues point out that companies can no longer rely on the incremental innovation, i.e., improving on what has already been done, to compete and survive. Today it seems that “radical innovation” and “breakthrough products” are essential to long-term commercial sustenance. Even governments are beginning to recognize this in their wealth creation programs. The US National Science Foundation (NSF), which funds a huge amount of academic research in the USA not only demands that research projects are interesting, good quality and important scientifically, but that they also demonstrate the solution to a societal need or goal, which might be in constant flux.

The bottom line is that: “What customers want today, they will not want tomorrow, says the team. They point out that almost half the major corporations that existed in 1975 no longer trade. This is probably best explained by the fact that those corporations failing to grasp this simple tenet.

“One of the explanations for this dismal record is that companies are still trying to link emerging technologies with existing markets when they should be linking emerging technologies with emerging markets.”

In Iran and other countries of the Middle East, the researchers explain electronics, medicines and chemicals are major imports, while Iran’s national income comes essentially from oil production. Unfortunately, this resource has been used for wealth creation rather than technology creation. “Traditionally, the oil industry has improved in engineering maintenance while based on technology limitation; we have been kept behind that of developed countries, and the gap has increased.

This is perhaps the most important reason why Iran is the market leader in basic petrochemical products, but in high-value products, we have lost the market against developed countries,” the researchers add. They present a model that could allow innovation to seep, if not surge, through, by using know-how to evaluate and price innovative products, it is based on the low-cost and speed of current pricing models -experiential and mathematical – and side-steps their disadvantages of being untimely, requiring too much pre-market testing, and being highly skills dependent.

The researchers incorporate various factors into their model – the life cycle of know-how, annual market size, raw material and total production cost, selling price, net profit, earned income during investment, risk-free rate of return, know-how investment required, know-how return in its life cycle, know-how annual return in its life cycle, present value of know-how return in its life cycle.

Other factors can be fed into the model depending on the specific characteristics of the product in question. Indeed, “Our comprehensive framework of the commercialization of new technologies in the petroleum industry that can be used with some modification for other industries,” the researchers say. They tested their model retrospectively against RIPI product data and demonstrated an accuracy of around 97%.

Soft Option for Hard Water

Hard water

Well, after a week of sinning, today’s post is more straightforward science news. First up, a soft test for hard water. Researchers in Spain have developed an inexpensive, reusable, and portable hard water sensor based on a fluorescing strand of DNA that could preclude the need for time-consuming titration and or laboratory-bound atomic absorption spectroscopy methods and so be used in the field.

Also this week, aqueous nanovalves. Researchers in the US have developed a new type of molecular nanovalve that can control the flow of small molecules trapped within porous silica spheres. the device could be used as a novel drug-delivery agent as it operates in aqueous conditions and responds to changes in pH.

Finally, in my spectroscopynow column, I discussed the cloudiness of ouzo, pernod, pastis, and related beverages. Now, the mechanism of the cloud formation has been revealed but I am still curious as to why those who imbibe such aniseed-based drinks get a second hit the morning after the night before, when they have a drink water. Anyone who understands what that is all about should leave their thoughts in the comments below.

Dexamethasone Banned Substance

Dexamethasone structureRussian biathlete Tatiana Moiseeva tested positive for the banned drug dexamethasone (dex), according to a recent report from news agency Allsport. The news was followed up by CNN, which mentioned little of the drug’s activity.

Dexamethasone is a fluorinated corticosteroid (11b,16a)-9-fluoro-11,17,21-trihydroxy-
16-methylpregna-1,4-diene-3,20-dione, to be precise. It acts as an antiinflammatory and an immunosuppressant and as such is used in rheumatoid arthritis, in surgery to prevent rejection of artificial components, and in oncology to ameliorate the effects of chemotherapy. It also has efficacy in altitude sickness. In sport, it’s antiinflammatory action, of course, allows athletes to train harder and work through injuries faster.

Moiseeva meanwhile, is holding out hope that her “B” sample will show negative and that the result reported on her “A” sample was a false positive.

Drinking Softened Water

A Chemspy reader sent me an email asking about the best way to fix their water softener.

Hi, I have a water softener. I met a local repair service, not affiliated with the manufacturer in any way, who can rebuild my broken unit with better quality after-market parts. Sounds like a good plan to me.

So far so good…the reader goes on…

The repair guy proposes to add some good quality resin to the tank to “top it up” if needed, and to add charcoal to the resin tank as well, as a filter enhancement. He claims the charcoal will get cleaned when the resin goes through the water softener’s normal recharge.

Again, sounds reasonable to me, although I suspect that the efficiency of a unit will depend on the quality of the components and presumably the actual fault and how that has been repaired. But, it was the final sentence of the email that made my heart skip a beat.

I only know charcoal filters as something you put inline, and replace before it poisons the drinker with its collected contaminants. Could the charcoal really be recharged and have the same useful lifetime the resin has?

Can you spot the potentially fatal flaw in what this Chemspy reader is doing with his water softener? I can and I’ve emailed him to tell him to cease and desist with immediate effect or suffer the consequences…your thoughts in the comments below would be appreciated.

Basic Chemistry Resources

Intute provides links and tutorials for educators and researchers in a wide range of disciplines. Part of their efforts involves hosting 雷竞技官网 ’s monthly Spotlight column in the sciences section. The organisation also publishes a range of booklets that provide fast and direct access to a stack of useful resources.

The 12-page chemistry booklet is now available in HTML and PDF formats for access online, with live and updating links. The page comes out of the MyIntute system which means it gets updated when information about a site is changed in the Intute database, although no new sites will be added to the booklet, the Intute database provides additional access to the latest resources.

  • Bibliographic databases
  • Data collections and databanks
  • Journals
  • E-prints
  • Web directories
  • Professional societies, institutes and associations
  • Mailing lists
  • Educational resources
  • Chemical nomenclature

You can access all of the above via the intute chemistry booklet, online now.

Sciencebase Seedier Side

Censored elephant

Anyone would think Sciencebase resided in one of the seedier corners of the internet. Because of all the recent fuss about the new seven deadly sins, I was just checking out the visitor traffic using Google Webmaster Tools and found some quite worrying search queries that bring you, dear readers, to this cybershore.

Apparently, 4% of the searches on Google Images this week brought you looking for the periodic table of sex!

Well, I have to admit, there is a thumbnail graphic of said item on the site, mentioned in a post Periodic Post, from August 2006. And, Sciencebase ranks #7 in Google for that phrase, so it’s perhaps not surprising. Slightly more worrying is what people were searching for who reached my post Giving Good Headline, which was about the subject of press releases and the best approach to headline writing. Then there are the dozens of visitors looking for Girly Games who found my article on the psychology of video game addiction and how it apparently differs between males and females.

I’m loathe to list some of the other terms people are searching for on Google Images for that brings them to Sciencebase, oh go on then, you twisted my arm: erectile dysfunction, premature ejaculation, seven deadly sins, erotic, and several I’d blush even to type.

Sexy search queries

Now, Sciencebase, for one reason or another (and it’s not because, it’s that kind of site) somehow ranks quite highly for several of those terms. However, there are a few others that bring visitors to the site for which the site ranks way, way down the search engine results pages (SERPs), and I don’t just mean the bottom of page 1, or page 2 even, I mean bottom of page 73. Now, that reveals true search diligence, I’d suggest. Whoever works their way through 72 pages of results to get to that one item?

Most visitors are not after smut, thankfully, they’re after the site’s hard-hitting science news and views with a cynical bite. Unfortunately, as I was writing this post, I realised that posting it in its original form was unlikely to reduce the tide of filth, in fact it might simply encourage more of those seedier searches, so I’ve removed a few of the less choice keywords, just to make it safe for work and to prevent the site from getting slapped with an adult-filtering ban.

Afters I’d put the finishing touches to this piece, I checked the site’s top searches in GWMT again, just to see if there had been any additional phrases of interest. I discovered that Sciencebase is now ranking for “polar bears willie soon” in blog searching. Asa search phrase that has to be pretty unique. I assumed it was from someone in the UK urgently tracking down Arctic bestiality sites, or Inuit innuendo, until I realised it’s actually two phrases – Polar Bears (the Arctic beast in question) and Willie Soon (the climate change skeptic) – both of which I mentioned in my CO2 refusenik post recently. It seems that Sciencebase is not quite the quagmire of filth some of the site’s visitors had hoped after all.