The Missing Stuff of Thought

The Stuff of Thought

It would be so easy to latch on to one particular section in cunning linguist Steven Pinker’s new book, The Stuff of Thought. It’s full of expletives, cussing, and good old swear words. There’s a serious point to Pinker’s use of so many taboo words, and it interesting to say the least to hear him using them in interviews and to watch the unprepared interviewer squirm.

But, that’s as maybe. For a blog post aimed at a general audience it would be inappropriate to use some of the more savoury language discussed. Moreover, the post, and potentially the Sciencebase website itself could so easily be tagged as containing adult contact and be filtered out by search engines, proxy servers and nanny software. I could use asterisks to mask off the vowels, but you’d still know what words I was citing and it would look silly. More to the point, while the expletives, their context and usage are fascinating and certainly worthy of close scrutiny, it is the words that Pinker admits do not actually exist that are of most interest.

So what words can we discuss that don’t exist? Well, for instance, why is there no gender-free term for a single member of a herd of cattle in common usage? It sounds wrong to discuss “a cattle”, but on occasions when you do not know the sex of the bovine in question you cannot differentiate between a cow and bull.

And, what about a politically correct word to use instead of the uncomfortable his or her in a sentence where some people might use the grammatically incorrect “their” as a PC alternative. Similarly, there is apparently no emotion-free word for a heterosexual partnership as there is for married couples (spouse) or gay couples (partner). Pinker himself often feels obliged to qualify mention of his own partner as being a woman to save confusion, but suggests that lover is too romantic while, flatmate is not only too unromantic, but is seriously ambiguous, as is the word partner. I’m sure there are many more examples, but Pinker delves into what these missing words (actually the singular cattle is one of my pet peeves) tell us about language and how we think.

You can download a very entertaining interview with Pinker from The Grauniad (mp3 format, 33Mb).

Open Notebook Science

I just listened to Cameron Neylon’s fascinating talk given at Drexel a short time ago, it’s available as a podcast/mp3 via the UsefulChem Blogspot. Neylon has turned to modified blog software to help his team capture their ongoing science and is now opening his laboratory notebooks to the world.

Several things struck me from his talk. First, he points out that grad students are generally reluctant to get involved if it means more work, especially if they are not so hot on keeping a neat paper labbook, but also because their work is suddenly on show to the world. In Neylon’s field there is also the problem of tagging the materials with which his group works – short DNA sequences and proteins. Chemists, of course, have Smiles strings and InChI keys, but there is no single, simple way of tagging a protein like this, that would make it readily searchable across the blogosphere, web or database. This is especially problematic given that many research groups will be working with their own unique sequences.

However, it is the potential power of open notebook science that came across most strongly in Neylon’s talk and it is exemplified by a little anecdote he told in response to a question from the audience at the end of the lecture.

Apparently, one of his students had been struggling with a DNA experiment, finding the heatshock process difficult and not getting the results she expected. Nothing was awry in her procedures until she ran out of sample tubes and Neylon pointed out that the shelves needed restocking. It was at this point that the he and the student realised she had been using a different brand in her experiments to that used in the previously successful runs carried out by other team members.

Of course, the tube brand was not mentioned in anyone’s lab book, it was assumed they were generic components and so brand was irrelevant. Not so. At the scale they are working at, and with highly temperature sensitive materials, a minute difference in tube thickness and precise composition makes all the difference in heat distribution. The students experiments with the other brand failed because this was not taken into account. Industrial chemical engineers would have recognised the problem immediately, I’d assume. Anyway, switching back to the original brand have her almost instantaneous success and results are now being written up.

The point being, that in an open electronic notebook, such problems could be flagged so that group members and supervisor would be alerted. A meta tag in the experiment’s blog post SUCCESS=0,1,NULL could easily be included. Moreover, fields could be added in the equipment section to specify brands so that a failed experiment in which the wrong brand was used might be spotted and a different brand of tube, for instance, used next time. Such information would be archived and available to future generations so that similar mistakes would be circumvented.

Meanwhile, you can listen to the complete talk from Neylon here.

Asthma sufferers, don’t hold your breath

TL:DR – If you have asthma, do not fall for quackery, seek professional medical advice and adhere to the qualified recommendations for prescribed medication. By quackery I mean various therapies, crystal healing, homeopathy, chiropractic, osteopathy, acupuncture etc. None of it has any medical validity whatsoever.


As someone who developed exercise-induced bronchospasm (mild asthma) only after coming up to Cambridge in the late 1980s and having never suffered in childhood, I was rather disappointed to find myself on first one inhaler (a reliever) and then a second (preventer). UPDATE: 2020 – The GINA guidelines recommend nobody use Salbutamol these days, much better to be on a preventer with a combined reliever.

Anyway, asthma sufferers everywhere could benefit from breathing exercises that allow them to regain control of their breath, reduce wheezing and breathlessness, and in time cut down on their reliance on inhaled medication. When I mentioned these techniques to my GP during a general checkup, he confessed that before inhalers were available, breathing exercises were all that he and his fellow practitioners could prescribe for mild attacks. What goes around, comes around it seems.

Breathing exercises could be something of a breath of fresh air. Although saying that cold, fresh air is one of the triggers for an asthma episode as fellow sufferers will know.

Across the UK more than 5 million people suffer the potentially debilitating effects of asthma and many millions more around the world. Diagnosis is usually straightforward and most sufferers are prescribed one or both of two kinds of inhaler – an inhaler to reduce symptoms (Salbutamol, for instance, known as a reliever) and another to reduce the underlying inflammation in the lungs (a corticosteroid such as beclomethasone).

Learning to control one’s breath and to breathe through the nose is important for asthma sufferers and something many fail to do, especially when asleep.

Five golden rules for reducing your asthma symptoms:

  1. Breathe through your nose when you can, but never tape up your mouth
  2. Take control of your breathing
  3. Try to avoid nervous or unnecessary coughing
  4. Look after yourself in general
  5. Most importantly, use your prescribed medication properly

You are best advised to talk to your GP about the potential of breathing techniques for you and at the very least to adhere strictly to Rule 5. Whatever you do, do not abandon your medication. Recently, there has been a lot of talk about the Buteyko Method. This is based on a false premise about carbon dioxide levels in the blood being the problem. Don’t follow that route. Breathing exercises may well help you cope, but they will not cure your asthma.

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2007 Weblog Awards

I need your support! Sciencebase got nominated for a 2007 Weblog Award in the Science category, so it would be great if as many of you could vote for the site. This is the link – http://2007.weblogawards.org/polls/best-science-blog-1.php – be sure to pick Sciencebase. I’ve been a bit slow off the mark on this one, and reckon there are probably too many others way ahead of me now to ever catch up, unless all 2604 of today’s Sciencebase’s RSS subscribers vote for me right now and pass the message on!

Never Divide by Zero

There is nothing like a Lego movie to cheer up an overcast day, and it has been a long time since I posted the Newton’s Laws Explained with Lego movie. So let’s get metaphysical and find out what happens when you square infinity or when a bug in the totalityofexistence leads to a universal divide by zero.

I assume everyone spotted that the time – 10:21 – at 1’13” into the movie doesn’t change, it’s still 10:21 at 2’20” in…nice touch or continuity error…or just a lack of another 2 sticker for the Lego clock.

Murine faeces

I’m not sure whether I should admit to the following, but this morning I found little scatterings of murine faeces and could detect a musky yet strong smell of ammonia in the storage area where we keep our dog and cat food. Not nice. In case you haven’t guessed, we got mice.

Odd that these little critters should be so brave as to venture into the part of the house in which the cat spends some of its time and although he is getting on in years, he does still have the legs for a chase (especially when the dog slips her lead and chases him out of the door. Anyway, traps have been bought and placed, droppings have been removed and traces of murine urine have been mopped up (with a cotton bud) and the whole area disinfected.

I got to thinking about that word I used just now. Murine. The “ine” suffix means just means “of”, “like”, or “referring to”, while the “mur” was derived from “mus” then “mur” for mouse in an originating Indo-European language and thence to Latin – “murinus” meaning of mice. The root gives rise to the scientific group name for both mice and rats Muridae or sub-family Murinae. Others words of similar structure include porcine (pigs), bovine (cattle), ursine (bears), ovine (sheep), equine (horses), and of course feline and canine, but not supine.

Cataloguing Innovation

Idea lightbulb

An intriguing paper on the notion of idea generation came to my attention this week. It’s from the International Journal of Management Practice, which might have suggested something rather dry and off topic, but the first named author Roy Woodhead is in the School of Technology, at Oxford Brookes University, UK and researches in the field of “IT service management” while his co-author, M.A. Berawi at the University of Malaya, in Kuala Lumpur, Malaysia, is currently researching value management and innovation in the context of major civil engineering projects.

So, what made this paper stand out? Well, seemingly its main conclusion is that over recent years management-speak has overtaken, perhaps not surprisingly some would say, the actual generation of ideas within an industry, an R&D environment, or elsewhere. So, the whole idea of coming up with something new, inventing, in other words, has become detached from the practical and been lost in the processes of managing information. Common sense, apparently, has once again been usurped by the need to organise.

Management is not wholly to blame for this disjuncture, the researchers hint. In fact, they point out that the reason for the split boils down to an assumption about how our brains work in creative mode. This cognitive theory of creativity holds that ideas are located exclusively within the human brain. This assumption, Woodhead and Berawi suggest has led to a dearth of research into how creativity leads to new ideas because it seems like a problem already solved. This has stifled research into idea generation.

Now, Woodhead and Berawi say it is time to challenge this assumption and to build an alternative view based on the relationship between our intentions and their effects, which could develop new perspectives on idea generation by helping us understand that ideas are not the simply the product of the human mind but are the product of a wide range of information sources and responses to them. It may be obvious, most ideas do not emerge spontaneously from our subconscious, they are seeded and moulded by what we sense and the information we acquire. It may be obvious, but this was apparently not considered part of the theory of idea generation.

The researchers tear into the conventional wisdom of idea generation and the approaches used in management to stimulate R&D and to appraise ideas, they have taken case studies among major technological organisations, predominantly in the oil industry as their raw materials. They emphasise that poor performance among those charged with generating ideas is usually seen as a weakness of the individuals involved, rather than a problem with the assumptions about the standard idea generation techniques employed. As such, the researchers say, under-performance of better idea generation is left unquestioned.

The researchers’ conclusions seem, in retrospect, rather obvious, but they have apparently been ignored for many years because of strongly held belief in a cognitive theory that does not bear closer scrutiny. “We believe our potential to generate new possibilities has been reduced by the view that ideas originate within an individual,” the researchers state. After all, you would not expect a child to be able to design an efficient nuclear power station or devise a recycling system for a metropolis. In this notion lies the key to better idea generation. “Idea generation is something to do with the way external systems work, our knowledge of their workings and an ability to conceive of alternative ways to make things happen.” In other words, our minds can manipulate a new idea, but the new idea emerges not endogenously but from the relationship between mind and world.

Passionate Publisher

My old friend Peter Gölitz this year celebrates a quarter century as Editor-in-Chief of the chemistry journal Angewandte Chemie. When he took over the editorship of the German Chemical Society’s premier chemistry journal in 1982, there were just four other chemists on the editorial staff and the journal published a mere 1000 pages a year. More than 9 out of 10 papers were from Germany. How things have changed.

Angewandte is now a weekly publication, is available online, and has an annual pagecount of 9000 pages. German authors are still the largest group of contributors, but four out of every five articles
published has an international team member. Oh, and Peter has a little more help these days than he did 25 years ago with 18 PhD chemists and 9 other colleagues helping run the show.

Peter is rather proud of the journal’s ISI impact factor, which ha srisen from a little over a “4” in 1982 to better than a 10 this year. It’s even surpassed several of its established competitors in this respect. During my New Scientist years, papers from Angewandte featured prominently in my reporting, partly this was because the journal seemed so much more accessible than the heavier grey tomes from other publishers. More than that though, much of the chemistry published seemed to have at least the potential of immediate applications and often flaunted this with an enticing graphic…perfect for pop science.

Congratulations, Peter, and here’s to the next quarter century ;-)

Grass Comes With Weedkiller

meta-tyrosine

No, it’s not another scare story about the dangers of illicit drugs, even if you don’t inhale. Researchers at Cornell U have discovered that at least one strain of common or garden grass, fescue grass to be precise, produces its own herbicide to prevent weeds growing in your lawn.

Frank Schroeder of the Boyce Thompson Institute for Plant Research at Cornell has identified an amino acid, meta-tyrosine, or m-tyrosine, produced by these lawn grasses and exuded from their roots in large quantities, which act as natural herbicides. It was colleague Cecile Bertin now research director for PharmAfrican, a Montreal-based biopharmaceuticals company, who made the initial discovery that fescue grasses inhibit plants from growing around them. The identification of m-tyrosine could lead to novel natural product garden herbicides. While m-tyrosine itself is too water soluble to be applied directly as a herbicide a less hydrophilic analog might be developed that could keep your lawn weed free, naturally.

In our household, lawn weeds are the least of our worries and I wish they would engineer a new strain of grass that prevents labrador puppies from urinating on the grass and leaving brown patches of dead turf.

InChI=1/C9H11NO3/c10-8(9(12)13)5-6-2-1-3-7(11)4-6/h1-4,8,11H,5,10H2,(H,12,13)/f/h12H

Back to Fundamentals

Buckminsterfullerene

Is there any justification for spending public money on fundamental scientific research for which there is no obvious potential for technological application, wealth creation, or any obvious purpose other than the advancement of human knowledge? If the decision were left to the short-sighted or those with no appreciation of what it is to see the wider horizon of blue skies research then it is unlikely that budgets would ever be stretched beyond funding the kind of research that provides almost instantaneous gratification, immediate payback, and obvious applications.

Jean-Jacques Salomon emeritus Professor of Technology and Society and the Director of the Centre Science, Technologie et Société, Conservatoire National des Arts et Métiers (CNAM), in Paris, France, explains that there is no way to measure the pay-off of basic research activities. He suggests that the reason governments deem to spend taxpayers’ money in this area is actually quite ideological rather than bearing the stamp of economic common sense.

Writing in the International Journal of Technological Learning, Innovation and Development (2007, 1, 125-135), he explains that even in times of privatisation, liberalisation, and reduced state intervention, there are good reasons for such public investments. But, how much is enough and how much would be too much?

Many of those in the world of commercial science would perhaps see any spending on fundamental science as untenable unless there were at least some vague opportunity for commercial exploitation of the results within a reasonable timeframe. In contrast the scientists in academia carrying out fundamental research see it as an essential part of any nation’s science base. They often cite the case of the molecule that fell to earth, buckminsterfullerene. The discovery of the all-carbon C60 molecule emerged from fundamental science that went even beyond blue skies into interstellar chemistry. Surely, this area of research could have no earthly application?

Well, yes and no. Buckminsterfullerene itself is yet to demonstrate any potent commercial viability, but on the other hand, without the discovery of that unique molecule we may not have seen the development of the so-called buckytubes, the elongated cousins of buckminsterfullerene known more formally as carbon nanotubes.

Fundamental, basic, or pure research is a fuzzy concept. There are of course, free-floating ideas that are perhaps nothing more than the rhetorical quests of scientists given the freedom to explore fully, but there are also designer labs that work on esoteric concepts, maverick hypotheses, and bizarre theoretical notions, purely with the aim of converting their outputs into something more tangible. That’s not to say they are commercially driven, just that they know that if only they can meld the right ingredients in the right proportions then something useful must emerge.

As Harvey Brooks said, ‘Basic science per se, contributes to culture, it contributes to our social well-being, including national defence, and public health; to our economic well-being, and it is an essential element of the education not only of scientists, but also of the population as a whole.’ Can you put a price on that? Well, governments must, Brooks is on record as suggesting that a 15% annual increase is minimal in order to cope with the forecast population of graduates students and faculty. But, Salomon points out that there is no fixed ratio between the amount of resources to which basic research can aspire and those devoted to other research activities.

In terms of fundamentals in Europe, Salomon suggests that the new European Research Council will be in a position to contribute to improvement of basic science. He asks whether assessing R&D indicators should therefore be part of the default responsibilities of any assessment of how well pure science should be funded.

Research Blogging IconSalomon, J. (2007). Why sustain fundamental research? International Journal of Technological Learning, Innovation and Development, 2 (1) DOI: 10.1504/IJTLID.2007.015400