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Home » Page 1539

Are physicists a bunch of self-plagiarizers?

By Hamish Johnston

Not exactly, but they are near the top of the league table when it comes to publishing the same paper in two different journals — according to a preprint from sociologists Vincent Lariviere and Yves Gingras at the University of Quebec in Montreal.

The pair combed millions of papers published between 1980-2007 looking for articles with the exactly the same title, first author and number of references. They found nearly 5000 papers that had been published twice — or about 0.05%.

They then compared the abstracts of the duplicate pairs (when available) and found that more than 52% were identical — and the remaining 48% very similar.

So how did physicists make out?

Nearly 0.08% of papers were duplicates, putting physics in second place after “engineering and technology” with over 0.11%.

Lariviere and Gingras point out that the high number in engineering and technology could be related to the large numbers of conference proceedings published in this field. Interestingly, I had a chat about this with a few journals editors here at IOP Publishing and they told me that publishing a paper in a conference proceedings and then a journal seemed to be a common practice for engineers.

Does this duplication matter?

It does if hiring committees or funding bodies simply tote up a candidate’s publications. However, if it’s quality they are looking for, then duplicate papers appear to be rather poor — Lariviere and Gingras show that the average “impact factor” and number of citations of the duplicates is about 65% of the average value for a physics paper.

Are there legitimate reasons for publishing the same thing twice?

I suppose your could make a case if the research cuts across two different disciplines that rarely read each other’s journals.

But in an age when peer-reviewed publications are the currency of success, it does seem like counterfeiting.

Alan Guth bags Isaac Newton medal

The cosmologist Alan Guth has won the 2009 Isaac Newton medal of the Institute of Physics. The American physicist was honoured for “his invention of the inflationary universe model, his recognition that inflation would solve major problems confronting then-standard cosmology, and his calculation, with others, of the spectrum of density fluctuations that gave rise to structure in the universe”.

The Isaac Newton medal includes a £2000 prize and is awarded for “outstanding contributions to physics”. It will be presented at a ceremony in London on 15 October and Guth will deliver the Institute’s 2009 Isaac Newton Lecture on 13 October.

In 1981, Guth introduced the concept of an inflationary universe to address a number of flaws in the conventional big-bang theory of the origin of the universe. According to the inflationary concept, the universe underwent a fantastic burst of hyperexpansion during the first instants after the big bang, stretching unimaginably faster than the conventional picture would predict.

Important questions

This hyperexpansion answered two important questions facing cosmologists at the time: why energy is spread so uniformly throughout the universe and how tiny deviations from perfect uniformity can arise. These deviations eventually led to the formation of galaxies and large-scale structure.

Guth came up with the idea of inflation when he was looking at a phase transition that is believed to have occurred about 10-35 s after the big bang — when the strong force separates from the electroweak force. Grand unified theories had predicted that vast numbers of magnetic monopoles would be created at this time, but there is no observational evidence that this happened.

Working with Henry Tye of Cornell University, Guth realized that theories of particle physics and cosmology could be modified such that a supercooling of the universe occurs at the phase transition — suppressing the production of the monopoles. This supercooling also unleashed a tremendous amount of energy, which accelerated the expansion of the universe in an inflationary period lasting about 10-32 s.

Inflation theory remains an important milestone in the development of cosmology because it showed that the nature of the universe as a whole could be understood in terms of theories derived from particle physics experiments.

Guth, 62, was born in New Jersey and is Victor F Weisskopf Professor of Physics at the Massachusetts Institute of Technology — which he joined in 1980.

Intense X-rays expose Alzheimer’s disease

One way to assess a drug’s effectiveness is to image the changes that it produces in the tissue of patients. But this is very challenging in the case of Alzheimer’s disease, because conventional tools such as magnetic resonance imaging cannot resolve the micrometer-sized changes in the brain that are associated with the illness.

However, these tiny features can now be identified with a version of computed tomography called diffraction-enhanced imaging — according to researchers at Brookhaven National Laboratory and the State University of New York (SUNY), Stony Brook. What’s more, this partnership says that its technique has the potential to deliver early diagnosis of Alzheimer’s disease.

Alzheimer’s disease, a disorder causing dementia in tens of millions of people worldwide, is caused by the build-up of dense areas of protein in the brain. These “plaques” contain a protein called amyloid beta and are just 5-200 μm in size.

Finding individual plaques

The US team identified individual amyloid beta plaques in a mouse brain with the diffraction-enhanced imaging technique that they first developed in 1995. These plaques have previously been observed with the same technique by Japanese researchers, who reported their results in 2006. However, on that occasion the brain tissue was dissected rather than being in a whole brain.

The diffraction enhanced imaging tool used by the US researchers employs X-rays generated from Brookhaven’s National Synchrotron Light Source (NSLS) synchrotron source. As this monochromatic beam passes through the sample, X-rays scatter and refract at different angles, depending on the tissue’s characteristics. These differences are amplified with an analyzer crystal.

This crystal has a very narrow reflectivity profile and it produces a peak reflectance for X-rays unaffected by transmission through the sample. For deviations of just a few microradians, reflectivity drops to nearly zero. Thanks to the steep slope associated with this reflectivity profile, angular changes in the transmitted beam are converted into changes in intensity that are recorded on a detector array. By repeating this process over a wide variety of incident angles, it is possible to construct a 3D image.

Mapping changes in density

“With our technique, the 3D data set represents a map of the changes in density,” explains team member Dean Connor, a former researcher at Brookhaven who has recently moved to the University of North Carolina. “Anywhere where there is an interface between two materials, there will be a dark or light spot in the 3D data,” he explains.

The superior resolving power of team’s diffraction enhanced imaging tool stems from a thousand-fold increase in the intensity of the X-ray beam compared to that used for conventional tomography. “While diffraction-enhanced imaging does not have improved spatial resolution compared to normal X-ray imaging, it does generate significantly more contrast for soft tissue features,” says Connor. “This allows smaller soft tissue features to be seen.”

Using their imaging tool, Connor and his co-workers have identified amyloid beta plaques with a diameter of less than 30 μm. These had a difference in density from the surrounding brain tissue of just 2%.

The team compared these results with those that it obtained by staining slices of brain tissue, and identifying the plaques under a microscope. Good agreement was observed when comparing the size distribution of the plaques, and their density.

Alternative imaging techniques

Magnetic resonance imaging (MRI) can also image tissue, but its produces an inferior spatial resolution. “While MRI can allow for exquisite soft tissue contrast, even high-field, high-resolution small-animal imaging systems have a resolution of 20-30 μm,” explains Connor. In comparison, diffraction enhanced imaging has a theoretical resolution of just 2 μm, although this would require a dose that exceeds the limit that can be given to patient.

However, a synchrotron source is a large and very expensive facility not suitable for clinical use. Connor points out that if diffraction enhanced imaging is to screen humans for Alzheimer’s disease, then it will have to be implemented with a conventional X-ray tube. A spin-off company called NextRay is working towards this.

The Brookhaven-SUNY partnership also want to improve to the imaging system, so that it can reveal amyloid beta plaques through a mouse skull. In addition, this team wants to develop new high-throughput, high-resolution imaging system that will be implemented at NSLS II, which is being built at Brookhaven and should offer a much brighter X-ray beam by 2015.

Benefits and obstacles

Alessandro Olivo, a researcher at University College London with expertise in computed tomography, is very supportive of the work of Connor and his colleagues: “X-ray images have properties — primarily of resolution — which are not accessible by any other imaging technique.”

However, he points out that there are many obstacles to overcome before X-rays can be used to screen humans for Alzheimer’s disease.

This includes the development of a new generation of detectors that combine high-resolution with high-efficiency, to ultimately limit the dose given to the patient. “This resolution level also poses a problem in terms of data volumes, and data analysis. This would have to be dealt with if a human brain is imagined, instead of that of a mouse.”

The research is published in the journal NeuroImage.

Old news under embargo

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What did Phoenix see?

By Hamish Johnston

In September 2008, planetary scientists told the world that the Phoenix Mars Lander had made several interesting discoveries on Mars — you can read all about it here on the NASA website.

This was duly reported by the BBC and other popular news outlets.

The scientists also wrote several scientific papers about their findings and submitted them to a prestigious journal — which now has the cheek to “embargo” the story until the papers are published!

That means that if I report on the papers before they are published I could lose my access to the journal’s embargoed preprints. Also, if a scientist had spoken to me about their paper while it was being peer-reviewed — and I had written about it — the paper could have been be dropped by the prestigious journal. Which is bad news for the researchers.

But I won’t be reporting on it because you already know what Phoenix saw on Mars

So what is the point of the embargo? Is the journal simply going through the motions of its embargo policy — or is this a cynical ploy to get this story back into the news?

I’m not the only one wondering about the point of embargo policies — Julianne over at Cosmic Variance started a good discussion earlier this month — and of course our very own Jon Cartwright looked into the practice last year.

I suppose I’m particularly ticked-off about embargoes because last week I came across two papers on the arXiv preprint server that would have made for a fantastic news story. I spent an hour or so doing background research and then asked a freelance journalist to cover the papers. He invested more time…but guess what, both papers had been submitted to prestigious journals and the authors wouldn’t talk.

So instead of being rewarded with a scoop for my daily scouring of the arXiv, our story will be published at the same time as those who simply waited for the press release.

It’s soul destroying!

So, what do you think?

Cancer and scientific risk-taking

By Margaret Harris

How do you dramatize the obscure process of funding scientific research for a public audience? If you’re a general-interest publication like The New York Times, one answer is to use cancer as an example.

A thought-provoking article published at the weekend describes how the tendency to dole out grant monies to projects that are limited in scope — and therefore quite likely to succeed within their allotted few-year period — is hurting cancer research. “Playing It Safe in Cancer Research” cites as examples a study of whether people who really like food have trouble following diets (funded), and research that led to the development of herceptin, a ground-breaking treatment for certain types of breast cancer (rejected by mainstream agencies, funded by a special grant from a cosmetics firm).

It occurred to me while I was reading the article that these issues are far from unique to cancer research. Scientists in all disciplines have long complained about how the process of applying for and receiving grants seems to reward “incrementalist” research, and “You have to say what you’ll find before they’ll pay you to look for it” is a common refrain.

It seems I wasn’t alone in thinking the problem could be relevant to physics. Today’s letters section in the NY Times includes one from Lee Smolin of the Perimeter Institute for Theoretical Physics, in which he suggests a “scientific venture capital” fund that would support high-risk, high-reward research using 10 percent of the existing US science budget. Another writer, neurologist Michael Rogawski, suggests funding researchers based on what they’ve already done, not what they’re proposing to do.

What do physicsworld.com readers think of these ideas? Any other suggestions for how we should be rewarding risk-taking research?

What is a quantum computer…

By Hamish Johnston

…and how do we build one?

That’s the title of a paper posted by Carlos Perez-Delgado and Pieter Kok on arXiv.

The two physicists — based at the University of Sheffield — have proposed an updated version of David Di Vincenzo’s checklist for what makes a system suitable for quantum computing.

According to Di Vincenzo it must:

1. Be a scalable physical system with well-defined qubits
2. Be initializable to a simple fiducial state such as |000…>
3. Have decoherence times much longer than gate operation times
4. Have a universal set of quantum gates
5. Permit high quantum efficiency, qubit-specific measurements
6. Have the ability to interconvert stationary and flying qubits
7. Have the ability to faithfully transmit flying qubits between specific locations

The first five were proposed in 1996 and then updated in 2000 to include the distinction between stationary and “flying” qubits — the latter referring to a photon or other such particle that can transfer quantum information.

In their paper, Perez-Delgado and Kok argue that the above criteria are not general enough to evaluate the various “paradigms” for quantum computing that have emerged since 2000.

They suggest the following criteria that must be met to create a “scalable and fault-tolerant quantum computer”.

1. Any quantum computer must have a quantum memory.
2. Any quantum computer must facilitate a controlled quantum evolution of the quantum memory.
3. Any quantum computer must include a method for cooling the quantum memory.
4. Any quantum computer must provide a readout mechanism for (non-empty) subsets of the quantum memory.

1, 2 and 4 seem reasonable — but what do they mean by “cooling”?

By cooling they mean the removal of entropy (or randomness) in the context of information theory.

Entropy will leak into a quantum memory as the memory interacts in unwanted and uncontrollable ways with its surroundings. Also, entropy is generated when a quantum memory is “erased” so that the next computation can begin.

Although this cooling could be split into “error correction” and “initialization” respectively, they argue that there is a certain “fuzziness” between the two processes. I believe this is because initialization can often be a multi-step process that must involve error correction.

I’m not a quantum-computing expert, but I’m guessing that criterion 3 will be the most difficult to satisfy…

Diamond targets biological threats

A firm in the US is drawing up plans for a badge–sized, wearable sensor that can detect in real time the presence of E. coli, anthrax, salmonella and other biological threats. The sensor, which contains tiny diamond cantilevers, is being developed by Advanced Diamond Technologies (ADT) in Illinois. The company is currently six months into a three-year research programme and hopes to have prototype devices available by the end of 2011.

Diamond is well known for being exceptionally hard and a good conductor of heat. But it also has other properties that make it useful as a biosensor. In particular, the surface of diamond is covered with strong hydrogen–carbon bonds, which means that it is stable in water, unlike other sensor materials like silicon. Moreover, the hydrogen atoms can be stripped off and replaced with antibody molecules that can bond, like a lock and key, with a target biomolecule like E. coli.

The new device consists of diving–board-shaped cantilevers, each about 100 μm long, mounted on a semiconductor chip. Each diamond cantilever is highly uniform and consists of nanocrystalline grains, each about 2–5 nm in diameter, deposited using chemical–vapour deposition. Any biomolecule landing on the surface of the cantilever changes the device’s vibrational frequency, which can be converted into an electrical signal through the piezoelectric response of the cantilever.

Detecting 100 cells

To ensure that the signal is strong enough, ADT is planning to incorporate as many as 50 individual cantilevers in each sensor. One challenge will be to concentrate the pathogenic agents so that even tiny amounts can be detected — the initial target is to detect 100 cells in 100 μl of fluid. The sensor could even be used to detect a range of different target molecules by simply attaching different antibodies to each cantilever.

“We want to miniaturize the sensor so that it can be worn as a badge or around the neck,” says lead investigator John Carlisle. The final device will also have to communicate its signal wirelessly so that, say, a firefighter wearing the sensor is aware of potentially hazardous conditions in a building and also that information is sent to a centralized response team.

Although the project is being fully funded by a $4.8m contract from the US Defense Threat Reduction Agency, the firm says the sensor could have non-military applications such as determining whether, say, water is safe to drink. Carlisle even wants to adapt the sensor so that it can detect not just water–based biomolecules but those that are air-borne too. “There are very sizeable opportunities,” he says.

Taking strings to the masses

By Edwin Cartlidge in Rome

Whether string theory can tell us anything about reality is a moot point. In the last two or three years this purported “theory of everything” – in principle unifying gravity with the three other forces in nature – has been given a kicking by certain scientists who see it as a kind of intellectual play thing that makes no testable predictions. See What Gina says.. for a taste of that debate.

Certainly the names of some of the talks at the world’s leading string-theory conference, Strings 2009, held in Rome this past week, were on the abstract side. “Holography and the S-Matrix”, “Superconducting black holes”, and “Stringy instantons and duality” give some flavour of the discussions held among the roughly 500 participants at the five-day conference. The fact that the meeting was held at the Pontifical University of Saint Thomas Aquinas only seemed to reinforce its other-worldliness.

But help was on hand for outsiders wanting to try and understand what on Earth this all means. Earlier today, particle physicist grandee Nicola Cabibbo introduced the curious of Rome to two of the big names of string theory – Edward Witten and Brian Greene. Witten, widely regarded as the leading figure in string theory, introduced himself with a few words of Italian and then told the audience what physicists hope to discover when they finally, hopefully, switch on the Large Hadron Collider at the CERN laboratory in Geneva this autumn.

In addition to the expected Higgs boson, the endower of all mass, Witten said that within the debris of particle collisions at the LHC might also be evidence of dark matter and of supersymmetry, which says that a whole slew of new fundamental particles must exist for there to be balance in the subatomic world. And one of the intriguing things about supersymmetry is that it could provide some kind of evidence for string theory.

It was at this point that Witten handed the baton to Greene. Greene is well known for his popularization of science, and with good reason. With some snazzy graphics and his flair for performing, he told us why it is so hard to come up with a theory of quantum gravity, explaining that the smooth variation of space-time as described by general relativity “runs headlong” into the turbulent, chaotic world of quantum mechanics. Postulating that the ultimate constituents of matter are tiny lengths of string, whose different modes of vibration correspond to different fundamental particles, is one way of resolving this problem, he went on, because such strings are like spread-out points that smooth the wild undulations at the smallest scale.

This model, however, has some very odd implications. Greene pointed out that string theory requires an extra 6 (or 7) dimensions of space in addition to the three that we are aware of. Helpfully, these dimensions are so small that we can’t see them, but unhelpfully there are rather a lot of ways of curling these extra dimensions up – some 10500 different ways as it turns out. And we would have to study all 10500 if we want to find out whether or not string theory describes the real world.

For Greene, all is not lost, however. He pointed out that 10500 is somewhat bigger than 10120, and that’s a measure of how much we don’t understand dark energy. In a nutshell he argued that if we happen to live in one of the few of the 10500 universes where conditions are just right for us to exist then there’s a damn good chance that we could have such an apparently statistically unlikely dark energy. For Greene, this suggests we might be on the right lines with string theory. Others may be less convinced.

'No Laughing Antimatter'

angels 4.jpg

By Hamish Johnston

When the film Angels and Demons was released last month, physicists around the world were inspired to give lectures about the “science” behind the film.

Now, someone has gathered a selection of videos and slides of these lectures in one place for your viewing pleasure.

My favourite title is The Science Behind ‘Angels and Demons’ is No Laughing Antimatter by Rolf Heuer, Boris Kayser and Leon Lederman.

Grab some popcorn and enjoy!

UK physics hit by new cuts

One of the UK’s leading research councils has announced today that it is to slash funding for a number of key national facilities. The Science and Technology Facilities Council (STFC) says that its £491m programme for 2009–10 will include a cut in support for the Diamond Light Source as well as “reductions in facility operations” at the ISIS neutron source and the Central Laser Facility. STFC chief executive Keith Mason blames the cuts on “the impact of the international financial situation”, which has led to a 15.1% rise in its subscriptions to CERN and other international facilities from £214.9m last year to £247.3m in 2009–10.

The STFC says it will make “significant internal savings” to re-invest in the science programme, including cuts in staff numbers by restricting recruitment, travel and use of external consultants. The council also plans to review its five neutron and light-source facilities that it funds “to ensure maximum cost effectiveness of these investments for UK science”. Mason promises, however, that funding for standard and rolling grants will be maintained at the level previously forecast.

Two other projects will see funding reduced: the Cambridge Astronomical Survey Unit (CASU) and the Wide-Field Astronomy Unit (WAFU) at Edinburgh. Meanwhile, the UK’s contribution to the Nuclear Structure, Astrophysics and Reaction (Nustar) project at the FAIR facility in Germany, and a research effort, dubbed SPIDER, into a generic particle-physics detector, will not now get any cash until April 2010 — a year later than planned. An upgrade to the VULCAN laser at the Rutherford Appleton Laboratory will also be deferred by a year.

Neutron reductions

Neutron scatterers in the UK will be particularly affected by the £2.3m cut to the ISIS facility, which has only just opened a £148m “second target station”. Uschi Steigenberger, ISIS operations director, told physicsworld.com that ISIS can now only be used for a maximum 120 days this year — a fifth fewer than last year. Indeed, a similar budget cut last year had already reduced the number of days that ISIS is used from 180 to 150.

“Other neutron-scattering labs, such as the Institut Laue-Langevin in France, typically operate for 220 days per year, which is the level recommended by the National Audit Office for an optimum operation and usage of ISIS,” she says. “ISIS serves over 1100 scientists and nearly half of the science programme carried out here is in areas like energy, environment, health and IT that map directly onto the UK government’s research priorities and have a strong economic impact. These programmes will be directly affected by the drastic reduction in operating time.”

The problems at ISIS and elsewhere stem from the 15.1% rise in the STFC’s international subscriptions. These have forced the council to fork out an extra £19.3m for its subscription to the European Space Agency, which has risen by 23% to £103.2m, as well an extra £5.5m for CERN, which has gone up by 6.9% to £85.6m. There are also increases to the membership fees of the European Southern Observatory (up 13.9% to £29.3m), the ILL (up 10.7% to £18.4m) and the European Synchrotron Radiation Facility (up 25.7% to £10.7m).

’Short-term and penny-pinching’

Robert Kirby-Harris, chief executive of the Institute of Physics, which publishes physicsworld.com, calls the STFC cuts “an ill omen”. Although he blames the problems on the “unique structure of STFC and the effects of a falling pound”, he thinks that the newly created Department for Business, Innovation and Skills, which sets the STFC’s budget, needs to do more to protect science.

“We would like to see the government match its verbal commitment to science and technology with funding to maintain the UK’s scientific stature, at the very least,” says Kirby-Harris. “Given President Obama has significantly increased the US science budget and the big Asian economies are doing likewise, our strategy appears very short term and penny-pinching. Further threats to the amount of scientific research being undertaken next year by STFC raise alarm bells and there appears to be no end of bad news in sight for this particular research council.”

Brian Foster, a particle physicist at Oxford University, who was highly critical of an earlier £80m STFC funding shortfall that opened up in late 2007, says that the council’s reaction this time has been “generally very sensible in that they have managed to avoid any more ‘blood on the floor'”. However, Foster is worried about next year, when he thinks the STFC will face a major shortfall unless the government steps in to help by protecting the STFC from currency fluctuations. “Otherwise it will be impossible for STFC to engage in sensible long-term planning,” he says.

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