Monthly Archives: July 2010

At the atto scale

Earlier this week, a team of Canadian scientists announced that they were able to observe a chemical bond as it broke. From the news item on physorg.com,

Scientists at the National Research Council of Canada (NRC) and the University of Ottawa (uOttawa) enjoyed a bird’s eye view of a chemical bond as it breaks.

The making and breaking of chemical bonds underlie the biochemical processes of life itself. A greater understanding of the quantum processes that lead to chemical reactions may lead to new strategies in the design and control of molecules — ultimately leading to scientific breakthroughs in health care and diagnostic medicine, quantum computing, nanotechnology, environmental science and energy.

The NRC-uOttawa team, led by Dr. David Villeneuve, achieved their feat using a technique developed several years ago at NRC in which an image was obtained of a single electron orbiting a molecule. In the current experiment, which is reported in the July 29th edition of Nature, scientists injected bromine gas into a vacuum chamber. There, an ultra brief ultraviolet light pulse caused the bromine molecules to separate into their individual atoms (a bromine molecule is composed of two bromine atoms).

A few femtoseconds later, an intense infrared laser pulse caused the molecule to emit an attosecond-duration X-ray burst that contained a snapshot of the atom’s position as the molecule fell apart and revealed how the electrons rearranged themselves.

The interference of the x-rays emitted by the two quantum states of the molecule was used to find the location of the atoms and to watch over a period of only 200 femtoseconds as it progressed from being a molecule to being two separate atoms. The experiment reached a precision below 500 zeptoseconds in clocking the emitted x-ray bursts. [emphases mine]

I’ve highlighted the units of measurement because they fascinate me in and of themselves. (I hadn’t encountered zeptos before although I have blogged about attoseconds,  May 13, 2009 posting).

Here are official designations starting with the nanoscale and dropping down to the smallest unit to date (from the US National Institute of Standards and Technology, Technology Services, Weights and Measures page),

nano, (n), meaning 10-9
pico, (p), meaning 10-12
femto, (f), meaning 10-15
atto, (a), meaning 10-18
zepto, (z), meaning 10-21
yocto, (y), meaning 10-24

If nano is the science of small, what will the others be?

Love letter to the British Library

It happened in 2000 and I had no hint of it when I stepped through the doors of the British Library on the last afternoon of my trip to London. A fellow traveler had raved about one of the exhibits (I think it was called 1000 years of English literature) the day before my visit, otherwise I wouldn’t have bothered.

It awoke in me a passion I don’t often share but was roused again when I came across an article on Techdirt (by way of Michael Geist) about the British Library’s latest publication on copyright. From Mike Masnick’s article,

The paper brings together 13 different researchers to all share their opinions, and the general consensus appears to be that copyright today is a serious problem in need of reform (and, no, the “Digital Economy Act” in the UK didn’t help at all). Basically, the key points are that copyright shouldn’t be allowed to get in the way of research activities.

You can download a copy of the paper, Driving UK Research — Is copyright a help or a hindrance?, from Techdirt.

Dame Lynne Brindley, the Chief Executive Officer for the British Library had this to say in her introduction to the paper,

There is a supreme irony that just as technology is allowing greater access to books and other creative works than ever before for education and research, new restrictions threaten to lock away digital content in a way we would never countenance for printed material.

Let’s not wake up in five years’ time and realise we have unwittingly lost a fundamental building block for innovation, education and research in the UK. Who is protecting the public interest in the digital world? We need to redefine copyright in the digital age and find a balance to benefit creators, educators, researchers, the creative industries – and the knowledge economy. (p. 3)

Thirteen researchers and writers discuss how copyright has an impact on all kinds of research (music, theatre, law, the sciences, etc.) and some of the problems associated with using laws designed for print  in a digital world. Dr. Dave Roberts and Vince Smith of the Natural History Museum offer their take on the problems with copyright and scientists along with suggestions for improvements,

For working scientists copyright is at best an irritation and at worst an obstruction. The process of science requires the sharing of results so that both the individual researcher and their institution build reputation and the esteem of their peers through recognition of the quality of their work. Traditionally this has been done by publication on paper and has been characterised as a workflow where scientists, the majority of whom these days are publicly funded, create manuscripts that they submit to publishers, who get other scientists to evaluate and comment on the work (peer review). The publisher sells the result back to the scientists. In the classic model, used to defend copyright, the money made by publishers is apportioned between the creator (author) and the publisher. In science, not only does the author not see any money from their work, but the publisher demands an exclusive right to that income in perpetuity.

For scientific publishing:

• We urgently need to separate cases where there is substantial loss of income to a content creator though content dissemination (e.g. a professional musician) from those that make no income from dissemination and rely on this as part of their scholarly activities (e.g. a professional scientist). A positive start could be made by removing copyright restrictions on material older than, say, two years from its original publication date.

• Orphan works should be placed in the public domain.

• Making copies for strictly archival purposes should not be subject to copyright control. Libraries in particular should be able to preserve digital copies in perpetuity, which technologically means regularly making copies.

I’m not sure I buy their musician example as someone who suffers from a loss of income as a consequence of content dissemination when many musicians (including some famous ones) are giving away downloads of their music and exploring new business models but the suggestions themselves seem quite reasonable.

Thank you British Library for reminding me how much I love you. (blowing kisses from Canada’s West Coast).

Intersection of philosophy, science policy, and nanotechnology regulation

After coming across a mention of John Rawls in a July 11, 2010 posting by Richard Jones (Soft Machines blog) and his (Rawls’) notions about how people and groups with diverse interests can come to agreements on social norms, I wondered why I hadn’t heard of Rawls before and how his thinking might apply to nanotechnology regulatory frameworks.

Assuming I might not be alone in my ignorance of Rawls’ work, here’s a brief description from a Wikipedia essay,

John Bordley Rawls (February 21, 1921 – November 24, 2002) was an American philosopher and a leading figure in moral and political philosophy. … His magnum opus, A Theory of Justice (1971), is now regarded as “one of the primary texts in political philosophy.”[1] His work in political philosophy, dubbed Rawlsianism,[2] takes as its starting point the argument that “most reasonable principles of justice are those everyone would accept and agree to from a fair position.”[1]

(The footnote details can be found by following the essay link.) I think the idea of people being able to come to agreements when they operate from a fair position is both interesting and seems to be borne out by a recent study in the US that Steffen Foss Hansen has recently published in the Journal of Nanoparticle Research. Michael Berger at Nanowerk has written an in depth article about the study and multicriteria mapping, the technique used to measure and evaluate interviewees’ positions on nanotechnology regulatory frameworks. From the Berger article,

Multicriteria Mapping [MCM] is a computer-based decision analysis technique that provides a way of appraising a series of different potential ways forward on a complex and controversial policy problem. Like other multicriteria approaches, it involves developing a set of criteria, evaluating the performance of each option under each criterion, and weighting each criterion according to its relative importance.

Hansen interviewed 26 stakeholders, including academics, public civil servants, corporate lawyers, [public interest groups,] and representatives from worker unions, industrial companies, and trade association.

One aspect of this research that I thought particularly useful is that the interviews are structured dynamically. From the study,

Once the criteria had been defined, the interviewee was asked to evaluate the relative performance of the different policy options on a numerical scale (0–100) under each of the criteria one-by-one. Zero representing the worst relative performance and a 100 the best. In order to allow for uncertainty in the estimation MCM allows the interviewee to give a range (e.g., 20–30) and to make worst- and best-case assumptions. The lowest values assigned to an option would then reflect the option considered under worst case assumptions whereas the highest would reflect the same option considered under best-case assumptions. Throughout this scoring process the interviewee was asked to explain the value or range assigned to options and assumptions made. One interview had to be terminated at this stage of the interview as the participant realized that he/she had yet to develop a formalized opinion on the most preferred options. Others expressed some dislike with having to put a numerical estimate on something which they normally only discuss in qualitative terms. Others again found it challenging to have to look at all the options through all their criteria scoring and explaining the scoring of up to 72 combinations of policy options and criteria. Normally they would not have to explain their position in such depth.  …  MCM is an iterative process, so interviewees were free to return to review earlier steps of the process at any stage of the interview. (Journal of Nanoparticle Research, vol. 12, p. 1963)

Bravo to the interviewees for going through a demanding process and putting their opinions to the test. Also, I understood from reading the study that MCM captures both quantitative (as the preceding excerpt shows) and qualitative data, an approach I’ve always favoured.

Berger’s article goes on to discuss the results from the study,

“Adopting an incremental approach and implementing a new regulatory framework have been evaluated as the best options whereas a complete ban and no additional regulation of nanotechnology were the least favorable” Hansen explains the key findings to Nanowerk.

Participants described their idea of an ‘incremental approach’ as “…launching an incremental process using existing legislative structures—e.g., dangerous substances legislation, classification and labeling, cosmetic legislation, etc.—to the maximum, revisiting them, and, when appropriate only, amending them…” and a ‘new regulatory framework’ as “…launching a comprehensive, in-depth regulatory process specific to nanotechnologies that aims at developing an entirely new legislative framework that tries to take all the widely different nanomaterials and applications into consideration.”

Hansen notes that comparing the ranking of the various options by the stakeholder groups reveals that an incremental approach was ranked highest by a majority of the various stakeholder groups e.g. civil servants, public interest groups, industrial company representatives and corporate lawyers.

Who would have thought that the most extreme ends of opinion as represented by public interest groups that usually favour the precautionary principle and industrial company representatives who argue in favour of little or voluntary regulation could agree on an incremental approach? I suppose it gets back to Rawls and his notion of coming to an agreement from “a fair position.”

More work needs to be done, it’s a single study, only 26 interviews took place, the MCM is a snapshot of a moment in time and may no longer reflect the interviewee’s personal opinions, and the regulatory situation in the US has changed since these interviews took place. Still, with all these caveats, and I’m sure there are others, the study offers encouraging news about diverse groups being able to come to an agreement on the subject of nanotechnology regulatory frameworks.

Two subcultures: science knitters and graffiti knitters, could they come together?

I had no idea that there’s a whole subculture of scientists devoted to knitting. Not just any knitting, science knitting. Thanks to Andrew Maynard at 2020 Science blog (July 25, 2010 posting), I have discovered Woolly Thoughts a website devoted to knitting, crocheting, and mathematics.

In fact, there’s a plethora of websites, blogs, and a subset on Ravelry (social networking for knitters) devoted to science/math knitters, much of which you can find in Andrew’s posting.

One item that particularly my fancy was a piece of ‘illusion knitting’ designed by Alice Bell, a science communication lecturer at the Imperial College of London. Illusion knitting is where the same piece of knitting reveals of one of two different images depending on the angle of sight. Bell’s creation, the Rosalind scarf, can look like stripes from one angle and like a piece of DNA from another angle.

For anyone not familiar with Franklin (from the San Diego Super Computer Center at the University of Southern California web page),

There is probably no other woman scientist with as much controversy surrounding her life and work as Rosalind Franklin. Franklin was responsible for much of the research and discovery work that led to the understanding of the structure of deoxyribonucleic acid, DNA. The story of DNA is a tale of competition and intrigue, told one way in James Watson’s book The Double Helix, and quite another in Anne Sayre’s study, Rosalind Franklin and DNA. James Watson, Francis Crick, and Maurice Wilkins received a Nobel Prize for the double-helix model of DNA in 1962, four years after Franklin’s death at age 37 from ovarian cancer.

Here’s Bell in her Rosalind scarf,

Alice Bell in her Rosalind scarf

This is the angle for the stripes, to see the DNA go to the Feb. 7, 2010 posting on her Slipped Stitch blog or to Andrew’s posting where you can find more goodies like this,

Knitting and crocheting as a means of creating complex geometrical forms has a long and illustrious history. Alan Turing was often seen knitting Möbius strips and other shapes in his lunchtime apparently, according to this 2008 MSNBC [article]. The work of Taimina and others on exploring hyperbolic planes – and their relevance to biology – has been groundbreaking (I know it’s crochet, but Margaret Wertheim’s TED talk on crochet coral and complex math is excellent, [go here]).

Vancouver (Canada) is home to at least two members of another knitting subculture as I found out earlier this year with the publication of a book by two locals, Mandy Moore and Leanne Prain, Yarn Bombing; The Art of Crochet and Knit Graffiti. Their Yarn Bombing blog features projects from around the world. I took a particular liking to Bee Bombs,

Annie's bee bombs in Amsterdam

I wonder if we could get some science yarn bombs going for the 2012 annual meeting of the American Association for the Advancement of Science meeting to take place here in Vancouver?

Open Science Summit nears

The July 29 -31, 2010 Open Science Summit is almost upon us (first mentioned here in a June 29, 3010 posting). The summit organizers pose this notion to set the themes for their conference (from the summit’s home page),

Renowned physicist Freeman Dyson identifies two kinds of scientific revolutions, those driven by new concepts (theoretical), and those driven by new tools (technological).

In the last 500 years we’ve witnessed paradigm shattering conceptual shifts associated with names such as Copernicus, Newton, Darwin, and, Einstein. Simultaneously, the evolution of technology drives progress in unpredictable ways—Galileo borrowed principles from the technology of eye-glasses to pioneer the use of the telescope in astronomy, while Watson and Crick relied on Rosalind Franklin’s skill with X-ray diffraction (a tool from physics) to probe the structure of life. (Undoubtedly, Franklin’s contribution would have been more fully recognized under a true Open Science Paradigm.)

To this classification of scientific revolutions, we can now add a third kind, an Organizational Revolution, the advent of a truly “Open Science,” which will profoundly affect the pace and character of subsequent theory and tool-driven paradigm shifts.

Looking at the speakers scheduled, the summit offers an interesting range including Christine Peterson of the Foresight Institute, Special Agent Edward You of the US Federal Bureau of Investigation (FBI)*, Michael Eisen, co-founder of the Public Library of Science (PLoS), David Koepsell, author of Who Owns You?, and more. It does seem to be largely oriented to genomics, bioinformatics, and other biological sciences.

If you can’t attend in person, there will be live streaming by fora.tv, go here.

* The FBI is quite interested in reaching out to scientists as per my posting of  May 25, 2010 about an article in The Scientist titled, SYNTHETIC BIO MEET “Fbio”; You may soon be visited by an FBI agent, or a scientist acting on behalf of one. Here’s why and written by Jill Frommer. The article is now behind a paywall.

A dissolving nanopatch that delivers vaccines without needles

I briefly noted the ‘nanopatch’ last year in an April 22, 2009 posting,

Scientists in Australia are developing a ‘nanopatch’ which would replace the use of needles for vaccinations.

It looks like those Australian scientists have gotten a step closer. According to a news item on Nanowerk,

“What we have been able to show for the first time is that the Nanopatch is completely dissolvable,” Professor [Mark] Kendall {Project Leader, Australian Institute for Bioengineering and Nanotechnology] said.

“That means zero needles, zero sharps, zero opportunity for contamination and zero chance of needle-stick injury.

“The World Health Organisation estimates that 30 percent of vaccinations in Africa are unsafe due to cross contamination caused by needle-stick injury. That’s a healthcare burden of about $25 per administration.”

The Nanopatch is smaller than a postage stamp and is packed with thousands of tiny projections – invisible to the human eye – now dried to include the vaccine itself together with biocompatible excipients.

Research published in journal PLos One [Public Library of Science] in April found that the Nanopatch achieved a protective immune response using an unprecedented one-hundredth of the standard needle and syringe dose.

Professor Kendall said this was 10 times better than any other delivery method.

Congratulations to Professor Kendall and his team.

24 regional nanotechnology centres on the block in UK is old news?

From Siobhan Wagner’s July 23, 2010 article on The Engineer website,

Science minister David Willetts told MPs yesterday it is ‘most unlikely’ the UK’s 24 nanotechnology centres will still be in existence in 18 months time.

In the first public meeting of the House of Commons science and technology committee, Willetts said the UK has too many centres that are ‘sub-critical in size’ and resources are fractionalised by region.

‘We have been getting a strong message that especially when times are tight that people want fewer, stronger centres,’ he said.

Given the budget concerns in the UK, the move can’t be any surprise. From Richard Jones’ (Soft Machines), July 11, 2010 posting (made before this potential cut was announced),

We know that the budget of his [Willetts'] department – Business, Innovation and Skills – will be cut by somewhere between 25%-33%. [emphasis mine] Science accounts for about 15% of this budget, with Universities accounting for another 29% (not counting the cost of student loans and grants, which accounts for another 27%). So, there’s not going to be a lot of room to protect spending on science and on research in Universities.

What I found particularly interesting in this posting is Willetts’ reference to a philosopher in his speech made July 9, 2010 and Jones’ discussion of what this reference might mean as the UK government grapples with science research, budget cuts, and finding common ground within a coalition that shares the rights and responsibilities of ruling,

More broadly, as society becomes more diverse and cultural traditions increasingly fractured, I see the scientific way of thinking – empiricism – becoming more and more important for binding us together. Increasingly, we have to abide by John Rawls’s standard for public reason – justifying a particular position by arguments that people from different moral or political backgrounds can accept. And coalition, I believe, is good for government and for science, given the premium now attached to reason and evidence. [Jones' excerpt of Willetts' speech]

The American political philosopher John Rawls was very concerned about how, in a pluralistic society, one could agree on a common set of moral norms. He rejected the idea that you could construct morality on entirely scientific grounds, as consequentialist ethical systems like utilitarianism try to, instead looking for a principles based morality; but he recognised that this was problematic in a society where Catholics, Methodists, Atheists and Muslims all had their different sets of principles. Hence the idea of trying to find moral principles that everyone in society can agree on, even though the grounds on which they approve of these principles may differ from group to group. In a coalition uniting parties including people as different as Evan Harris and Philippa Stroud [I assume one is a conservative and the other a liberal democrat in the UK's coalition government] one can see why Willetts might want to call in Rawls for help.

Jones’ posting provides other insights into Willett’s perspective. (BTW, If you do check out the blog, be sure to read the comments.) As for what this perspective might mean relative to the proposed cut, I don’t know. Unfortunately, I have to wait for a future Jones’ posting where he will discuss,

The other significant aspect of Willetts’s speech was a wholesale rejection of the “linear model” of science and innovation, but this needs another post to discuss in detail.

In the meantime, Tim Harper, prinicipal of Cientifica (a nanotechnology consulting firm), and TNT blogger notes,

The lack of any reaction to Fridays announcement that many of the UKs nanotech centres would be unlikely to survive is because it is old news.

He goes on to speculate that the government is gradually preparing the public for the really big cuts due in October 2010. He also provides a brief history of the centres and some of the peculiar circumstances of their existence.

Who do you write like? and other writing bits

I write like
Cory Doctorow

I Write Like by Mémoires, Mac journal software. Analyze your writing!

I found this ‘analyse my writing style’ game thanks to The Shebeen Club. (It’s very easy to play, just copy and  paste some of your writing into a submission box and hit submit. A minute or so later you get your answer. (Btw, I’m thrilled with my result.)

As for other ‘writery’ things, Dave at The Black Hole offers advice, links and practical information for people who want to become science writers,

Throughout the course of my own training, I have encountered a number of fellow trainees that have a passion for science writing and they live amongst a sea of those that do not. For those considering a career shift toward this passion, I think the first critical step is to figure out what kind of science writing you are interested in… loosely I’ve broken it up into three categories:

Popular

Feeding the brains of the public

Technical

Accurately explaining scientific protocols and/or information

Editorial

Consolidating or shifting a scientific field, making policy, designing programs, lobbying for change

While Dave is addressing science trainees, his advice is applicable to anyone who’s interested in science writing but without a science background, you will have different challenges.

I’ll make one addition to Dave’s list of organizations you might want to check out, the Society for Technical Communication. I’ve belonged to it for a number of years and they provide a lot of valuable information if you’re interested in the field.

Finally, there’s this interesting article at Fast Company by Rachel Arendt about Tin House and some new rules for submitting manuscripts to them,

A crafty new submissions policy from Tin House Books is reminding writers to be readers—and consumers.

The book press and quarterly literary magazine’s recent call for manuscripts welcomes unsolicited submissions but comes with a caveat: Each submission must include a receipt for a book purchased at a bookstore. As for those who can’t afford to buy books or get to a bookstore, Tin House asks for a haiku or under-100-word sentence explaining why. Writers who prefer their words in e-ink can send similar explanations for their turn away from bookstores and analog reading.

Arendt goes on the describe the publisher and the thinking behind this initiative.