Tag Archives: metaphors

Artificial intelligence and metaphors

This is a different approach to artificial intelligence. From a June 27, 2017 news item on ScienceDaily,

Ask Siri to find a math tutor to help you “grasp” calculus and she’s likely to respond that your request is beyond her abilities. That’s because metaphors like “grasp” are difficult for Apple’s voice-controlled personal assistant to, well, grasp.

But new UC Berkeley research suggests that Siri and other digital helpers could someday learn the algorithms that humans have used for centuries to create and understand metaphorical language.

Mapping 1,100 years of metaphoric English language, researchers at UC Berkeley and Lehigh University in Pennsylvania have detected patterns in how English speakers have added figurative word meanings to their vocabulary.

The results, published in the journal Cognitive Psychology, demonstrate how throughout history humans have used language that originally described palpable experiences such as “grasping an object” to describe more intangible concepts such as “grasping an idea.”

Unfortunately, this image is not the best quality,

Scientists have created historical maps showing the evolution of metaphoric language. (Image courtesy of Mahesh Srinivasan)

A June 27, 2017 University of California at Berkeley (or UC Berkeley) news release by Yasmin Anwar, which originated the news item,

“The use of concrete language to talk about abstract ideas may unlock mysteries about how we are able to communicate and conceptualize things we can never see or touch,” said study senior author Mahesh Srinivasan, an assistant professor of psychology at UC Berkeley. “Our results may also pave the way for future advances in artificial intelligence.”

The findings provide the first large-scale evidence that the creation of new metaphorical word meanings is systematic, researchers said. They can also inform efforts to design natural language processing systems like Siri to help them understand creativity in human language.

“Although such systems are capable of understanding many words, they are often tripped up by creative uses of words that go beyond their existing, pre-programmed vocabularies,” said study lead author Yang Xu, a postdoctoral researcher in linguistics and cognitive science at UC Berkeley.

“This work brings opportunities toward modeling metaphorical words at a broad scale, ultimately allowing the construction of artificial intelligence systems that are capable of creating and comprehending metaphorical language,” he added.

Srinivasan and Xu conducted the study with Lehigh University psychology professor Barbara Malt.

Using the Metaphor Map of English database, researchers examined more than 5,000 examples from the past millennium in which word meanings from one semantic domain, such as “water,” were extended to another semantic domain, such as “mind.”

Researchers called the original semantic domain the “source domain” and the domain that the metaphorical meaning was extended to, the “target domain.”

More than 1,400 online participants were recruited to rate semantic domains such as “water” or “mind” according to the degree to which they were related to the external world (light, plants), animate things (humans, animals), or intense emotions (excitement, fear).

These ratings were fed into computational models that the researchers had developed to predict which semantic domains had been the sources or targets of metaphorical extension.

In comparing their computational predictions against the actual historical record provided by the Metaphor Map of English, researchers found that their models correctly forecast about 75 percent of recorded metaphorical language mappings over the past millennium.

Furthermore, they found that the degree to which a domain is tied to experience in the external world, such as “grasping a rope,” was the primary predictor of how a word would take on a new metaphorical meaning such as “grasping an idea.”

For example, time and again, researchers found that words associated with textiles, digestive organs, wetness, solidity and plants were more likely to provide sources for metaphorical extension, while mental and emotional states, such as excitement, pride and fear were more likely to be the targets of metaphorical extension.

Scientists have created historical maps showing the evolution of metaphoric language. (Image courtesy of Mahesh Srinivasan)

Here’s a link to and a citation for the paper,

Evolution of word meanings through metaphorical mapping: Systematicity over the past millennium by Yang Xu, Barbara C. Malt, Mahesh Srinivasan. Cognitive Psychology Volume 96, August 2017, Pages 41–53 DOI: https://doi.org/10.1016/j.cogpsych.2017.05.005

The early web version of this paper is behind a paywall.

For anyone interested in the ‘Metaphor Map of English’ database mentioned in the news release, you find it here on the University of Glasgow website. By the way, it also seems to be known as ‘Mapping Metaphor with the Historical Thesaurus‘.

Nanotechnology, math, cancer, and a boxing metaphor

Violent metaphors in medicine are not unusual although the reference is often to war rather than boxing as it is in this news from the University of Waterloo (Canada). Still, it seems counter-intuitive to closely link violence with healing but the practice is well entrenched and it seems attempts to counteract it are a ‘losing battle’ (pun intended).

Credit: Gabriel Picolo "2-in-1 punch." Courtesy: University of Waterloo

Credit: Gabriel Picolo “2-in-1 punch.” Courtesy: University of Waterloo

A June 23, 2016 news item on ScienceDaily describes a new approach to cancer therapy,

Math, biology and nanotechnology are becoming strange, yet effective bed-fellows in the fight against cancer treatment resistance. Researchers at the University of Waterloo and Harvard Medical School have engineered a revolutionary new approach to cancer treatment that pits a lethal combination of drugs together into a single nanoparticle.

Their work, published online on June 3, 2016 in the leading nanotechnology journal ACS Nano, finds a new method of shrinking tumors and prevents resistance in aggressive cancers by activating two drugs within the same cell at the same time.

A June 23, 2016 University of Waterloo news release (also on EurekAlert), which originated the news item, provides more information,

Every year thousands of patients die from recurrent cancers that have become resistant to therapy, resulting in one of the greatest unsolved challenges in cancer treatment. By tracking the fate of individual cancer cells under pressure of chemotherapy, biologists and bioengineers at Harvard Medical School studied a network of signals and molecular pathways that allow the cells to generate resistance over the course of treatment.

Using this information, a team of applied mathematicians led by Professor Mohammad Kohandel at the University of Waterloo, developed a mathematical model that incorporated algorithms that define the phenotypic cell state transitions of cancer cells in real-time while under attack by an anticancer agent. The mathematical simulations enabled them to define the exact molecular behavior and pathway of signals, which allow cancer cells to survive treatment over time.

They discovered that the PI3K/AKT kinase, which is often over-activated in cancers, enables cells to undergo a resistance program when pressured with the cytotoxic chemotherapy known as Taxanes, which are conventionally used to treat aggressive breast cancers. This revolutionary window into the life of a cell reveals that vulnerabilities to small molecule PI3K/AKT kinase inhibitors exist, and can be targeted if they are applied in the right sequence with combinations of other drugs.

Previously theories of drug resistance have relied on the hypothesis that only certain, “privileged” cells can overcome therapy. The mathematical simulations demonstrate that, under the right conditions and signaling events, any cell can develop a resistance program.

“Only recently have we begun to appreciate how important mathematics and physics are to understanding the biology and evolution of cancer,” said Professor Kohandel. “In fact, there is now increasing synergy between these disciplines, and we are beginning to appreciate how critical this information can be to create the right recipes to treat cancer.”

Although previous studies explored the use of drug combinations to treat cancer, the one-two punch approach is not always successful. In the new study, led by Professor Aaron Goldman, a faculty member in the division of Engineering in Medicine at Brigham and Women’s Hospital, the scientists realized a major shortcoming of the combination therapy approach is that both drugs need to be active in the same cell, something that current delivery methods can’t guarantee.

“We were inspired by the mathematical understanding that a cancer cell rewires the mechanisms of resistance in a very specific order and time-sensitive manner,” said Professor Goldman. “By developing a 2-in-1 nanomedicine, we could ensure the cell that was acquiring this new resistance saw the lethal drug combination, shutting down the survival program and eliminating the evidence of resistance. This approach could redefine how clinicians deliver combinations of drugs in the clinic.”

The approach the bioengineers took was to build a single nanoparticle, inspired by computer models, that exploit a technique known as supramolecular chemistry. This nanotechnology enables scientists to build cholesterol-tethered drugs together from “tetris-like” building blocks that self-assemble, incorporating multiple drugs into stable, individual nano-vehicles that target tumors through the leaky vasculature. This 2-in-1 strategy ensures that resistance to therapy never has a chance to develop, bringing together the right recipe to destroy surviving cancer cells.

Using mouse models of aggressive breast cancer, the scientists confirmed the predictions from the mathematical model that both drugs must be deterministically delivered to the same cell.

Here’s a link to and a citation for the paper,

Rationally Designed 2-in-1 Nanoparticles Can Overcome Adaptive Resistance in Cancer by Aaron Goldman, Ashish Kulkarni, Mohammad Kohandel, Prithvi Pandey, Poornima Rao, Siva Kumar Natarajan, Venkata Sabbisetti, and Shiladitya Sengupta. ACS Nano, Article ASAP DOI: 10.1021/acsnano.6b00320 Publication Date (Web): June 03, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

The researchers have made this illustration of their work available,

Courtesy: American Chemical Society

Courtesy: American Chemical Society

Does the universe have a heartbeat?

It may be a bit fanciful to suggest the universe has a heartbeat but if University of Warwick (UK) researchers can state that dying stars have ‘irregular heartbeats’ then why can’t the universe have a heartbeat of sorts? Getting back to the University of Warwick, their August 26, 2015 press release (also on EurekAlert) has this to say,

Some dying stars suffer from ‘irregular heartbeats’, research led by astronomers at the University of Warwick has discovered.

The research confirms rapid brightening events in otherwise normal pulsating white dwarfs, which are stars in the final stage of their life cycles.

In addition to the regular rhythm from pulsations they expected on the white dwarf PG1149+057, which cause the star to get a few percent brighter and fainter every few minutes, the researchers also observed something completely unexpected every few days: arrhythmic, massive outbursts, which broke the star’s regular pulse and significantly heated up its surface for many hours.

The discovery was made possible by using the planet-hunting spacecraft Kepler, which stares unblinkingly at a small patch of sky, uninterrupted by clouds or sunrises.

Led by Dr JJ Hermes of the University of Warwick’s Astrophysics Group, the astronomers targeted the Kepler spacecraft on a specific star in the constellation Virgo, PG1149+057, which is roughly 120 light years from Earth.

Dr Hermes explains:

“We have essentially found rogue waves in a pulsating star, akin to ‘irregular heartbeats’. These were truly a surprise to see: we have been watching pulsating white dwarfs for more than 50 years now from the ground, and only by being able to stare uninterrupted for months from space have we been able to catch these events.”

The star with the irregular beat, PG1149+057, is a pulsating white dwarf, which is the burnt-out core of an evolved star, an extremely dense star which is almost entirely made up of carbon and oxygen. Our Sun will eventually become a white dwarf in more than six billion years, after it runs out of its nuclear fuel.

White dwarfs have been known to pulsate for decades, and some are exceptional clocks, with pulsations that have kept nearly perfect time for more than 40 years. Pulsations are believed to be a naturally occurring stage when a white dwarf reaches the right temperature to generate a mix of partially ionized hydrogen atoms at its surface.

That mix of excited atoms can store up and then release energy, causing the star to resonate with pulsations characteristically every few minutes. Astronomers can use the regular periods of these pulsations just like seismologists use earthquakes on Earth, to see below the surface of the star into its exotic interior. This was why astronomers targeted PG1149+057 with Kepler, hoping to learn more about its dense core. In the process, they caught a new glimpse at these unexpected outbursts.

“These are highly energetic events, which can raise the star’s overall brightness by more than 15% and its overall temperature by more than 750 degrees in a matter of an hour,” said Dr Hermes. “For context, the Sun will only increase in overall brightness by about 1% over the next 100 million years.”

Interestingly, this is not the only white dwarf to show an irregular pulse. Recently, the Kepler spacecraft witnessed the first example of these strange outbursts while studying another white dwarf, KIC 4552982, which was observed from space for more than 2.5 years.

There is a narrow range of surface temperatures where pulsations can be excited in white dwarfs, and so far irregularities have only been seen in the coolest of those that pulsate. Thus, these irregular outbursts may not be just an oddity; they have the potential to change the way astronomers understand how pulsations, the regular heartbeats, ultimately cease in white dwarfs.

“The theory of stellar pulsations has long failed to explain why pulsations in white dwarfs stop at the temperature we observe them to,” argues Keaton Bell of the University of Texas at Austin, who analysed the first pulsating white dwarf to show an irregular heartbeat, KIC 4552982. “That both stars exhibiting this new outburst phenomenon are right at the temperature where pulsations shut down suggests that the outbursts could be the key to revealing the missing physics in our pulsation theory.”

Astronomers are still trying to settle on an explanation for these never-before-seen outbursts. Given the similarity between the first two stars to show this behaviour, they suspect it might have to do with how the pulsation waves interact with themselves, perhaps via a resonance.

“Ultimately, this may be a new type of nonlinear behaviour that is triggered when the amplitude of a pulsation passes a certain threshold, perhaps similar to rogue waves on the open seas here on Earth, which are massive, spontaneous waves that can be many times larger than average surface waves,” said Dr Hermes. “Still, this is a fresh discovery from observations, and there may be more to these irregular stellar heartbeats than we can imagine yet.”

Here’s a link to and a citation for the paper,

A Second Case of Outbursts in a Pulsating White Dwarf Observed by Kepler by J. J. Hermes, M. H. Montgomery, Keaton J. Bell, P. Chote, B. T. Gänsicke, Steven D. Kawaler, J. C. Clemens, Bart H. Dunlap, D. E. Winget, and D. J. Armstrong.
2015 ApJ 810 L5 (The Astrophysical Journal Letters Volume 810 Number 1). doi:10.1088/2041-8205/810/1/L5
Published 24 August 2015.

© 2015. The American Astronomical Society. All rights reserved.

This paper is behind a paywall but there is an earlier open access version available at arXiv.org,

A second case of outbursts in a pulsating white dwarf observed by Kepler by J. J. Hermes, M. H. Montgomery, Keaton J. Bell, P. Chote, B. T. Gaensicke, Steven D. Kawaler, J. C. Clemens, B. H. Dunlap, D. E. Winget, D. J. Armstrong.  arXiv.org > astro-ph > arXiv:1507.06319

In an attempt to find some live heart beats to illustrate this piece, I found this video from Wake Forest University’s body-on-a-chip program,

The video was released in an April 14, 2015 article by Joe Bargmann for Popular Mechanics,

A groundbreaking program has converted human skin cells into a network of functioning heart cells, and also fused them with lab-grown liver cells using a specialized 3D printer. Researchers at the Wake Forest Baptist Medical Center’s Institute for Regenerative Medicine provided Popular Mechanics with both still and moving images of the cells for a fascinating first look.

“The heart organoid beats because it contains specialized cardiac cells and because those cells are receiving the correct environmental cues,” says Ivy Mead, a Wake Forest graduate student and member of the research team. “We give them a special medium and keep them at the same temperature as the human body, and that makes them beat. We can also stimulate the miniature organ with electrical or chemical cues to alter the beating patterns. Also, when we grow them in three-dimensions it allows for them to interact with each other more easily, as they would in the human body.”

If you’re interested in body-on-a-chip projects, I have several stories here (suggestion: use body-on-a-chip as your search term in the blog search engine) and I encourage you to read Bargmann’s story in its entirety (the video no longer seems to be embedded there).

One final comment, there seems to be some interest in relating large systems to smaller ones. For example, humans and other animals along with white dwarf stars have heartbeats (as in this story) and patterns in a gold nanoparticle of 133 atoms resemble the Milky Way (my April 14, 2015 posting titled: Nature’s patterns reflected in gold nanoparticles).

Singapore as banyan tree, bonsai, and nanotechnology: a truckload of metaphors

There’s a fascinating essay and political analysis by George Yeo (former Foreign Minister of Singapore, etc.) about Singapore’s state of affairs on it’s 50th anniversary in The World Post (a Huffington Post and Berggruen Institute partnership project). From Yeo’s Aug. 3, 2015 essay,

Why Singapore at 50 Is Like a Banyan Tree, a Bonsai and Nanotechnology

Under the late Lee Kuan Yew, Singapore — which this week is celebrating its 50th anniversary as a nation — was unabashedly a hierarchical society. When asked if Singapore was a nanny state, he replied that, if it were one, he was proud to have fostered it. But he also knew that Singapore society was entering a new phase.

In November 1990, Lee Kuan Yew stepped aside to let Goh Chok Tong take over as prime minister. The state retreated a little; controls were carefully loosened; greater diversity was tolerated if not selectively encouraged. As minister for information and the arts, I was happy to push some boundaries — censorship, use of dialects and Singlish, greater emphasis of pre-PAP history and promotion of our diverse ancestral heritage. These were all sensitive issues and I had to manage senior cabinet colleagues artfully. A speech I made about the need to prune the banyan tree in order that civic participation could flourish resonated with many Singaporeans. Pruning the banyan tree means cutting down hierarchy. …

Diversity causes tension. In hierarchical societies, diversity is frowned upon because it makes top-down organization more difficult. Standardization improves efficiency but it also leads to oppression.

Many years ago, the late Cardinal Jan Schotte told me this story about Pope John Paul II, whom he served as the secretary of the Synod of Bishops in the Vatican. Drafting a speech for the Holy Father, Cardinal Schotte inserted a sentence for the pope to say that “despite our differences, we are one.” John Paul II gently chided him and replaced “despite” with “because of.” “Because of our differences, we are one.”

The particularity of the individual is sacrosanct. Each of us is unique; each is ultimately responsible for his own life. The correction by the pope was not of style but of deep principle. Diversity is not to be merely tolerated; it is to be celebrated. For those who believe in God, every human being carries a divine imprint which unites us. For Confucianists and atheists, every human being has a moral core which also makes us one. …

I was most interested in the nanotechnology metaphor and how Yeo relates it to Singapore,

During his first term as chief minister of the southern Indian state of Andhra Pradesh, N. Chandrababu Naidu compared the workings of Singapore to nanotechnology. Yes, we are small but we pack a lot into a tiny space and are able to network Singapore to the entire world.

Singapore is not intelligible in itself. Its economy, culture and politics can only be understood in the context of the region it serves. Singapore is only one node in a dense network of many nodes. Whether the Singapore node grows or shrinks depends on the health of the network and our ability to link up with other nodes and add value. Our diversity is therefore a great strength.

He abandoned the nanotechnology metaphor fairly quickly to talk about diversity, independence, and military preparedness,

Diversity is, however, also our vulnerability. Every channel which connects us to the outside world also brings infection. Maintaining Singapore’s integrity and security is therefore a continuing challenge. Two conditions have to be met for a city-state to be independent.

First, its foreign policy has to be nimble to adjust to a shifting external balance of power. Second, the citizenry must be united in its common defense against external subversion and aggression. The external and internal equations have to be solved simultaneously. Only when Singaporeans feel secure about their own place at home can they turn outwards and do big things together. I spent 16 years as a soldier, first in the Army, then the Air Force and, finally, in the Joint Staff. The Singapore Armed Forces is a well-equipped and well-trained militia. Its fighting ability is completely dependent on the unity of diverse Singaporeans and their commitment to a common, righteous cause. By being prepared for war, we are more likely to have peace. It is better not to be put to the test.

If we can maintain peace in Asia for another 10 to 20 years, the region will be transformed beyond recognition and become a powerhouse of the global economy. While trials of strength are inevitable, Sino-U.S. relations are unlikely to deteriorate too badly. Even when China’s economy overtakes that of the U.S. in size, the U.S. will remain the dominant military and political power in the world for decades to come. American popular culture has already taken over the world.

Unlike the U.S., China is not a missionary power. So long as it is able to maintain its own political and cultural universe within, China has no ambition to compete with the U.S. for global supremacy without. If China is also a missionary power, like the former Soviet Union, another hot or cold war is inevitable. Happily, China is not and a titanic clash between the U.S. and China is not inevitable.

Between China and India, they are more likely to cooperate than to fight. Except for a minor border war in 1962, which has been largely forgotten in China, the long history of contact between them has been peaceful. Each recognizes the other as an ancient people.

Yeo provides a very interesting perspective, that of an insider intimately involved in Singapore’s evolution as a city-state.  I don’t entirely agree with his analysis about China. While they may not have the ‘missioinary’ society he sees in the US, China has been expansionist in the past and are currently busy absorbing Tibet.

You can find out more about George Yeo Yong-Boon here. As I think the Huffington Post is sufficiently well known that a description is unnecessary, I don’t think the same can said of the Berggruen Institute, so here goes. From the Berggruen Institute home page,

The Berggruen Institute is dedicated to the design and implementation of new ideas of good governance — drawing from practices in both East and West — that can be brought to bear on the common challenges of globalization in the 21st century.

We are an independent, non-partisan “think and action tank” that engages cutting edge entrepreneurs, global thinkers and political leaders from around the world as key participants in our projects.

The great transition of our time is from American-led globalization 1.0 to the interdependence of plural identities that characterizes globalization 2.0 as the dominance of the West recedes with the rise of the rest. A political and cultural awakening, amplified by social media, is part and parcel of this shift, and good governance must respond by devolving power and involving citizens more meaningfully in governing their communities. At the same time, we believe that accountable institutions must be created that can competently manage the global links of interdependence.

In another life, I was quite interested in diversity and viewpoints that contrast with my own from a cultural perspective. This foray, given the essay title, was a surprise and a delightful one at that.

Metaphors in a brief overview of the nanomedicine scene circa August 2014

An Aug. 1, 2014 article by Guizhi Zhu (University of Florida), Lei Mei ((Hunan University; China), and Weihong Tan (University of Florida) for The Scientist provides an overview of the latest and greatest regarding nanomedicine while underscoring the persistence of certain medical metaphors. This overview features a prediction and a relatively benign (pun intended) metaphor,

Both the academic community and the pharmaceutical industry are making increasing investments of time and money in nanotherapeutics. Nearly 50 biomedical products incorporating nanoparticles are already on the market, and many more are moving through the pipeline, with dozens in Phase 2 or Phase 3 clinical trials. Drugmakers are well on their way to realizing the prediction of Christopher Guiffre, chief business officer at the Cambridge, Massachusetts–based nanotherapeutics company Cerulean Pharma, who last November forecast, “Five years from now every pharma will have a nano program.”

Technologies that enable improved cancer detection are constantly racing against the diseases they aim to diagnose, and when survival depends on early intervention, losing this race can be fatal. [emphasis mine] While detecting cancer biomarkers is the key to early diagnosis, the number of bona fide biomarkers that reliably reveal the presence of cancerous cells is low. To overcome this challenge, researchers are developing functional nanomaterials for more sensitive detection of intracellular metabolites, tumor cell–membrane proteins, and even cancer cells that are circulating in the bloodstream. (See “Fighting Cancer with Nanomedicine,” The Scientist, April 2014.)

So, the first metaphor ‘racing’ gives the reader a sense of urgency, the next ones, including “fighting cancer’, provoke a somewhat different state of mind,

Eye on the target

The prototype of targeted drug delivery can be traced back to the concept of a “magic bullet,” proposed by chemotherapy pioneer and 1908 Nobel laureate Paul Ehrlich. [emphasis mine] E[hrlich envisioned a drug that could selectively target a disease-causing organism or diseased cells, leaving healthy tissue unharmed. A century later, researchers are developing many types of nanoscale “magic bullets” that can specifically deliver drugs into target cells or tissues.

It would seem we might be in a state of war as you ‘fight cancer’ with your ‘eyes on the target’ as you ‘shoot magic bullets’ in time to celebrate the 100th anniversary of the start to World War I.

Kostas Kostarelos wrote a Nov. 29, 2013 posting for the Guardian Science Blogs where he (professor of nanomedicine at the University of Manchester and director of the university’s Nanomedicine Lab) discussed war metaphors in medicine and possible unintended consequences (Note: A link has been removed). Here’s his discussion about the metaphors,

Almost every night I have watched the news these past few months my senses have been assaulted by unpleasant, at times distressing, images of war: missiles, killings and chemical bombs in Syria, Kenya, the USA. I wake up the next morning, trying to forget what I watched the night before, and going to work with our researchers to develop the next potential high-tech cure for cancer, thinking: “does what we do matter at all … ?”

So I was intrigued by an article that will be published in one of the scientific journals in our field entitled: “Nanomedicine metaphors: from war to care”. The next lab meeting we had was very awkward, because I was constantly thinking that indeed a lot of the words we were using to communicate our science were directly imported from the language of war. Targeting, stealth nanoparticle, smart bomb, elimination, triggered release, cell death. I struggled to find alternative language.

… Hollywood analogies and simplistic interpretations about “good” and “bad” may be inaccurate, but they do seem appropriate and convincing.

I must say, however, that even in pathology, modern medicine increasingly considers the disease to be part of our body, often leading to successful treatment not by “eradication” and “elimination” but by holistic management of a chronic condition. The case of HIV therapeutics is perhaps the brightest example of such revisionist thinking, which has transformed the disease from a “death sentence” in the early years after its discovery to a nonlethal chronic infection today.

Kostarelos then contrasts the less warlike ‘modern medicine’ metaphors with nanomedicine,

In nanomedicine, which is the application of nanotechnologies and nanomaterials to design medical treatments, the war imagery is even more prevalent. Two of the most clinically successful and intensively studied technologies that operate at the nanoscale are “stealth” and “targeted” medicines. “Stealth” refers to a hydrophilic (water-loving) shield built around a molecule or nanoparticle, made from polymers, that minimises its recognition by the body’s defence mechanisms. “Targeting” refers to the specific binding of certain molecules (such as antibodies, peptides and others) to receptors (or other proteins) present only at the surface of diseased cells. The literature in nanomedicine is abundant with both “stealthing”, “targeting” and combinations thereof.

Kostarelos then asks this question,

The question I keep asking myself since I read the article about war metaphors in nanomedicine has been whether we are using terminology in a simplistic, single-minded manner that could stifle creative and out-of-the-box thinking.

Intriguing unintended consequences, yes?

Getting back to The Scientist article, which I found quite informative and interesting, its ‘war metaphors’ seem to extend even to some of the artwork accompanying the article,

[downloaded from http://www.the-scientist.com/?articles.view/articleNo/40598/title/Nanomedicine/]

[downloaded from http://www.the-scientist.com/?articles.view/articleNo/40598/title/Nanomedicine/]

Is that a capsule or a bullet? Regardless, this * article provides a good overview of the research.

* The word ‘a’ was removed on Aug. 8, 2014.

Whose Electric Brain? the video

After a few fits and starts, the video of my March 15, 2012 presentation to the Canadian Academy of Independent Scholars at Simon Fraser University has been uploaded to Vimeo. Unfortunately the original recording was fuzzy (camera issues) so we (camera operator, director, and editor, Sama Shodjai [samashodjai@gmail.com]) and I rerecorded the presentation and this second version is the one we’ve uploaded.

Whose Electric Brain? (Presentation) from Maryse de la Giroday on Vimeo.

I’ve come across a few errors; at one point, I refer to Buckminster Fuller as Buckminster Fullerene and I state that the opening image visualizes a neuron from someone with Parkinson’s disease, I should have said Huntingdon’s disease. Perhaps, you’ll come across more, please do let me know. If this should become a viral sensation (no doubt feeding a pent up demand for grey-haired women talking about memristors and brains), it’s important that corrections be added.

Finally, a big thank you to Mark Dwor who provides my introduction at the beginning, the Canadian Academy of Independent Scholars whose grant made the video possible, and Simon Fraser University.

ETA March 29, 2012: This is an updated version of the presentation I was hoping to give at ISEA (International Symposium on Electronic Arts) 2011 in Istanbul. Sadly, I was never able to raise all of the funds I needed for that venture. The funds I raised separately from the CAIS grant are being held until I can find another suitable opportunity to present my work.

Nanodiagnostics: a roundtable at Kavli and new report from Cientifica

The Kavli Foundation, based in California, held a roundtable discussion on ‘Fighting Cancer with Nanotechnology‘ which focused largely on diagnostics and drug delivery. According to a March 14, 2012 news item on Nanowerk, the four participants were:

  • Anna Barker – Former Deputy Director of the National Cancer Institute (NCI) and current Director of Arizona State University’s Transformative Healthcare Networks;
  • Mark E. Davis – Professor of Chemical Engineering at the California Institute of Technology (Caltech), and a member of the Experimental Therapeutics Program of the Comprehensive Cancer Center at the City of Hope;
  • James Heath – Professor of Chemistry at Caltech and a founding Board member of Caltech’s Kavli Nanoscience Institute;
  • Michael Phelps – Norton Simon Professor, and Chair of Molecular and Medical Pharmacology at the University of California Los Angeles.

The researchers discussed how nanotechnology holds the promise of revolutionizing the way medicine wages war against cancer, from providing new ways to combine drugs to delivering gene-silencing therapeutics for cancer cells. [emphasis mine]

Yet again, war has been used as a metaphor for healing. I particularly appreciate the way ‘revolution’, which resonates with US audiences in a very particular way, has been introduced.

The discussion features diagnostics,

JAMES HEATH: That is certainly an important application. A typical diagnostic test measures only a single protein. But the nature of cancer—even a single cancer type—is that it can vary significantly from patient to patient. The implication is that there is probably not a single protein biomarker that can distinguish between such patient variations. Even to confidently address a single diagnostic question may take measuring several protein biomarkers. Discovering the right biomarkers is extremely challenging—you might have 300 candidate biomarkers from which you want to choose just six, but you will likely have to test all 300 on a very large patient pool to determine the best six. That’s tough to do with existing technologies because each protein measurement requires a large sample of blood or tumor tissue, and each measurement is time-consuming, labor intensive and expensive. With some of the emerging nanotechnologies, a large panel of candidate protein biomarkers can be rapidly measured from just a pinprick of blood, or a tissue sample as small as a single cell. This allows one to accelerate the development of conventional diagnostic tests, but it also opens up the possibilities for fundamentally new diagnostic approaches. These are opportunities that nanotech is bringing into play that simply weren’t there before.

Here’s one of my favourite comments,

MICHAEL PHELPS: Yes. All of us developing therapeutics want to have a transparent patient—to see where the drug goes throughout all tissues of the body, whether it hits the disease target in a sufficient dose to induce the desired therapeutic effect on the target, and where else the drug goes in the body regarding side effects. [emphasis mine] PET [positron emission tomography ‘scan’] can reveal all this. For this reason almost all drug companies now use PET in their discovery and development processes.

I suspect Phelps was a bit over enthused and spoke without thinking. I’m sure most doctors and researchers would agree that what they want is to heal without harm and not transparent patients. That’s why they’re so excited about nanotechnology and therapeutics, they’re trying to eliminate or, at least, lessen harm in the healing process. It would be nice though if they get past the ‘war’ metaphors and dreams of transparent patients.

I found the comments about the US FDA (Food and Drug Administration), pharmaceutical companies and biotech startups quite interesting,

ANNA BARKER: These challenges are mostly related to perception and having the tools to demonstrate that the agent does what you say it does. It’s more difficult for nanotherapeutics than for other drugs because they employ a new set of technologies that the FDA is more guarded about approving. The FDA is responsible for the health of the American public, so they are very careful about putting anything new into the population. So the challenges have to do with showing you can deliver what you said you were going to deliver to the target, and that the toxicity and distribution of the agent in the body is what you predicted. You have to have different measures than what is included in the classic toxicology testing packages we use for potential drugs.

MARK DAVIS: There’s so much cool science that people want to do, but you’re limited in what you can do in patients for a number of reasons. One is financial. This area is not being pushed forward by big Pharma, but by biotech companies, and they have limited resources. Secondly, the FDA is still learning about these innovations, they can limit what you are allowed to do in a clinical trial. For example, when we did the first clinical trial with a nanoparticle that had a targeting agent enabling it to latch onto a specific receptor on cancer cells and a gene silencing payload, we realized it would be important to know if patients have this receptor and the gene target of the payload to begin with. Prebiopsies from patients before testing the nanotherapeutic on them to see if the tumor cells had this receptor and gene target in abundance would have been helpful. However, in this first-in-man trial, the FDA did not allow required biopsies, and they were performed on a volunteer-basis only.

It is a fascinating discussion as it provides insight into the field of nanotherapeutics and into the some of the researchers.

On the topic of nanodiagnostics but this time focusing on the business end of things, a new report has been released by Cientifica. From the March 13, 2012 press release,

Nanodiagnostics will be a $50-billion market by 2021; Cientifica’s “Nanotechnology for Medical Diagnostics” looks at emerging nanoscale technologies

Following on from Cientifica’s Nanotechnology for Drug Delivery report series, “Nanotechnology for Medical Diagnostics,” a 237-page report, takes a comprehensive look at current and emerging nanoscale technologies used for medical diagnostics.

Areas examined include quantum dots, gold nanoparticles, exosomes, nanoporous silica, nanowires, micro- and nanocantilever arrays, carbon nanotubes, ion channel switch nanobiosensors, and many more.

Cientifica estimates medical imaging is the sector showing the highest growth and impact of nanomaterials. Already a $1.7-billion market, with gold nanoparticle applications accounting for $959 million, imaging will continue to be the largest nanodiagnostics sector, with gold nanoparticles, quantum dots and nanobiosensors all easily exceeding $10 billion.

“Getting onboard with the right technology at the right time is crucial,” said Harper [Tim Harper, Cientifica’s Chief Executive Officer]. “The use of exosomes in diagnosis, for instance, a relatively new technique and a tiny market, is set to reach close to half a billion dollars by 2021.”

You can find out more and/or purchase the report here.

I have written about Cientifica’s  Nanotechnology for Drug Delivery (NDD) white paper here and have published an interview with Tim Harper about global nanotechnology funding and economic impacts here.

Rail system and choreography metaphors in a couple of science articles

If you are going to use a metaphor/analogy when you’re writing about a science topic  because you want to reach beyond an audience that’s expert on the topic you’re covering or you want to grab attention from an audience that’s inundated with material, or you want to play (for writers, this can be a form of play [for this writer, anyway]), I think you need to remain true to your metaphor. I realize that’s a lot tougher than it sounds.

I’ve got examples of the use of metaphors/analogies in two recent pieces of science writing.

First, here’s the title for a Jan. 23, 2012 article by Samantha Chan for The Asian Scientist,

Scientists Build DNA Rail System For Nanomotors, Complete With Tracks & Switches

Then, there’s the text where the analogy/metaphor of a railway system with tracks and switchers is developed further and abandoned for origami tiles,

Expanding on previous work with engines traveling on straight tracks, a team of researchers at Kyoto University and the University of Oxford have used DNA building blocks to construct a motor capable of navigating a programmable network of tracks with multiple switches.

In this latest effort, the scientists built a network of tracks and switches atop DNA origami tiles, which made it possible for motor molecules to travel along these rail systems.

Sometimes, the material at hand is the issue. ‘DNA origami tiles’ is a term in this field so Chan can’t change it to ‘DNA origami ties’ which would fit with the railway analogy. By the way, the analogy itself comes from (or was influenced by) the title the scientists chose for their published paper in Nature Nanotechnology (it’s behind a paywall),

A DNA-based molecular motor that can navigate a network of tracks

All in all, this was a skillful attempt to get the most out of a metaphor/analogy.

For my second example, I’m using a Jan. 12, 2012 news release by John Sullivan for Princeton University which was published in Jan. 12, 2012 news item on Nanowerk. Here’s the headline from Princeton,

Ten-second dance of electrons is step toward exotic new computers

This sets up the text for the first few paragraphs (found in both the Princeton news release and the Nanowerk news item),

In the basement of Hoyt Laboratory at Princeton University, Alexei Tyryshkin clicked a computer mouse and sent a burst of microwaves washing across a silicon crystal suspended in a frozen cylinder of stainless steel.

The waves pulsed like distant music across the crystal and deep within its heart, billions of electrons started spinning to their beat.

Reaching into the silicon crystal and choreographing the dance of 100 billion infinitesimal particles is an impressive achievement on its own, but it is also a stride toward developing the technology for powerful machines known as quantum computers.

Sullivan has written some very appealing text for an audience who may or may not know about quantum computers.

Somebody on Nanowerk changed the headline to this,

Choreographing dance of electrons offers promise in pursuit of quantum computers

Here, the title has been skilfully reworded for an audience that knows more quantum computers while retaining the metaphor. Nicely done.

Sullivan’s text goes on to provide a fine explanation of an issue in quantum computing, maintaining coherence, for an audience not expert in quantum computing. The one niggle I do have is a shift in the metaphor,

To understand why it is so hard, imagine circus performers spinning plates on the top of sticks. Now imagine a strong wind blasting across the performance space, upending the plates and sending them crashing to the ground. In the subatomic realm, that wind is magnetism, and much of the effort in the experiment goes to minimizing its effect. By using a magnetically calm material like silicon-28, the researchers are able to keep the electrons spinning together for much longer.

Wasn’t there a way to stay with dance? You could have had dancers spinning props or perhaps the dancers themselves being blown off course and avoided the circus performers. Yes, the circus is more colourful and appealing but, in this instance, I would have worked to maintain the metaphor first introduced, assuming I’d noticed that I’d switched metaphors.

So, I think I can safely say that using metaphors is tougher than it looks.

Fuel cells and iron veins and Ballard Power Systems

The iron ‘veins’ are an idea from the researchers at the US National Institute of Standards and Technology (NIST) that might make fuel cells a standard piece of equipment in a car. From the August 31, 2011 news item on Nanowerk,

With a nod to biology, scientists at the National Institute of Standards and Technology (NIST) have a new approach to the problem of safely storing hydrogen in future fuel-cell-powered cars. Their idea: molecular scale “veins” of iron permeating grains of magnesium like a network of capillaries. The iron veins may transform magnesium from a promising candidate for hydrogen storage into a real-world winner (“Thermodynamics, kinetics and microstructural evolution during hydrogenation of iron-doped magnesium thin films”).

Hydrogen has been touted as a clean and efficient alternative to gasoline, but it has one big drawback: the lack of a safe, fast way to store it onboard a vehicle. According to NIST materials scientist Leo Bendersky, iron-veined magnesium could overcome this hurdle. The combination of lightweight magnesium laced with iron could rapidly absorb—and just as importantly, rapidly release—sufficient quantities of hydrogen so that grains made from the two metals could form the fuel tank for hydrogen-powered vehicles.

There are more technical details in the Nanowerk news item.

Since Ballard Power Systems, known for its fuel cell powered buses, is located in the Vancouver area (the region where I live) I was curious as the why this NIST advance is considered so wonderful. After all, fuel cells are already being used commercially. From the Ballard website page on buses,

Ballard designs and manufactures fully-integrated FC velocity®-HD6 fuel cell modules delivering 75 kW or 150 kW of power for use in the bus market. Ballard’s leading-edge fuel cell technology combined with our customer’s advanced hybrid bus system designs have demonstrated improved vehicle performance, durability and lower cost. All of which has created a path to commercialization for the fuel cell hybrid bus.

Zero-emission fuel cell-powered buses deliver economic, operational as well as environmental benefits, when compared to traditional diesel or diesel hybrid systems. Economic benefits are a direct result of increased fuel cell efficiency and reliability. And fuel cell buses emit only water vapour, eliminating air pollutants such as nitrogen oxides, sulphur oxides and particulate matter. Fuel cell buses can also significantly reduce greenhouse gas emissions on a “well-to-wheel” basis, when compared to conventional technologies.

I note Ballard has a hybrid system so perhaps the NIST researchers are working on a 100% fuel cell system? I did check one more thing while I was on the Ballard website, the technical specifications for the fuel cells used to power the buses. The weight for the smaller 75w fuel cell is 350 kg or 772 lbs. and its dimensions are 1530 x 871 x 495 mm or 50 x 34 x 12 in. With that weight and those dimensions, I imagine that’s why we haven’t been hearing about hybrid fuel cell cars. I now better understand why the NIST researchers are excited.

Graphene, IBM’s first graphene-based integrated circuit, and the European Union’s pathfinder programme in information technologies

A flat layer of carbon atoms packed into a two-dimensional honeycomb arrangement, graphene is being touted as a miracle (it seems)  material which will enable new kinds of electronic products. Recently, there have been a number of news items and articles featuring graphene research.

Here’s my roundup of the latest and greatest graphene news. I’m starting with an application that is the closest to commercialization: IBM recently announced the creation of the first graphene-based integrated circuit. From the Bob Yirka article dated June 10, 2011 on physorg.com,

Taking a giant step forward in the creation and production of graphene based integrated circuits, IBM has announced in Science, the fabrication of a graphene based integrated circuit [IC] on a single chip. The demonstration chip, known as a radio frequency “mixer” is capable of producing frequencies up to 10 GHz, and demonstrates that it is possible to overcome the adhesion problems that have stymied researchers efforts in creating graphene based IC’s that can be used in analog applications such as cell phones or more likely military communications.

The graphene circuits were started by growing a two or three layer graphene film on a silicon surface which was then heated to 1400°C. The graphene IC was then fabricated by employing top gated, dual fingered graphene FET’s (field-effect transistors) which were then integrated with inductors. The active channels were made by spin-coating the wafer with a thin polymer and then applying a layer of hydrogen silsequioxane. The channels were then carved by e-beam lithography. Next, the excess graphene was removed with an oxygen plasma laser, and then the whole works was cleaned with acetone. The result is an integrated circuit that is less than 1mm2 in total size.

Meanwhile, there’s a graphene research project in contention for a major research prize in Europe. Worth 1B Euros, the European Union’s 2011 pathfinder programme (Future and Emerging Technologies [Fet11]) in information technology) will select two from six pilot actions currently under way to be awarded a Flagship Initiative prize.  From the Fet11 flagships project page,

FET Flagships are large-scale, science-driven and mission oriented initiatives that aim to achieve a visionary technological goal. The scale of ambition is over 10 years of coordinated effort, and a budget of up to one billion Euro for each Flagship. They initiatives are coordinated between national and EU programmes and present global dimensions to foster European leadership and excellence in frontier research.

To prepare the launch of the FET Flagships, 6 Pilot Actions are funded for a 12-month period starting in May 2011. In the second half of 2012 two of the Pilots will be selected and launched as full FET Flagship Initiatives in 2013.

Here’s the description of the Graphene Science and technology for ICT and beyond pilot action,

Graphene, a new substance from the world of atomic and molecular scale manipulation of matter, could be the wonder material of the 21st century. Discovering just how important this material will be for Information and Communication Technologies is the long term focus of the Flagship Initiative, simply called, GRAPHENE. This aims to explore revolutionary potentials, in terms of both conventional as well as radically new fields of Information and Communication Technologies applications.

Bringing together multiple disciplines and addressing research across a whole range of issues, from fundamental understandings of material properties to Graphene production, the Flagship will provide the platform for establishing European scientific and technological leadership in the application of Graphene to Information and Communication Technologies. The proposed research includes coverage of electronics, spintronics, photonics, plasmonics and mechanics, all based on Graphene.

[Project Team:]

Andrea Ferrari, Cambridge University, UK
Jari Kinaret, Chalmers University, Sweden
Vladimir Falko, Lancaster University, UK
Jani Kivioja, NOKIA, Finland [emphases mine]

Not so coincidentally (given one member of the team is associated with Nokia and another is associated with Cambridge University), the Nokia Research Centre jointly with Cambridge University issued a May 4, 2011 news release (I highlighted it in my May 6, 2011 posting [scroll down past the theatre project information]) about the Morph concept (a rigid, flexible, and stretchable phone/blood pressure cuff/calculator/and  other electronic devices in one product) which they have been publicizing for years now. The news release concerned itself with how graphene would enable the researchers to take the Morph from idea to actuality. The webpage for the Graphene Pilot Action is here.

There’s something breathtaking when there is no guarantee of success about the willingness to invest up to 1B Euros in a project that spans 10 years. We’ll have to wait until 2013 before learning whether the graphene project will be one of the two selected as Flagship Initiatives.

I must say the timing for the 2010 Nobel Prize for Physics which went to two scientists (Andre Geim and Konstantin Novoselov) for their groundbreaking work with graphene sems interesting (featured in my Oct. 7, 2010 posting) in light of this graphene activity.

The rest of these graphene items are about research that could lay the groundwork for future commercialization.

Friday, June 13, 2011 there was a news item about foaming graphene on Nanowerk (from the news item),

Hui-Ming Cheng and co-workers from the Chinese Academy of Sciences’ Institute of Metal Research at Shenyang have now devised a chemical vapor deposition (CVD) method for turning graphene sheets into porous three-dimensional ‘foams’ with extremely high conductivity (“Three-dimensional flexible and conductive interconnected graphene networks grown by chemical vapour deposition” [published in Nature Materials 10, 424–428 (2011) doi:10.1038/nmat3001 Published online 10 April 2011]). By permeating this foam with a siloxane-based polymer, the researchers have produced a composite that can be twisted, stretched and bent without harming its electrical or mechanical properties.

Here’s an image from the Nature Publishing Group (NPG) of both the vapour and the bendable, twistable, stretchable composite (downloaded from the news item on Nanowerk where you can find a larger version of the image),

A scanning electron microscopy image of the net-like structure of graphene foam (left), and a photograph of a highly conductive elastic conductor produced from the foam. (© 2011 NPG)

The ‘elastic’ conductor (image to the right) reminds me of the ‘paper’ phone which I wrote about May 8, 2011 and May 12, 2011. (It’s a project where teams from Queen’s University [in Ontario] and Arizona State University are working to create flexible screens that give you telephony, music playing and other capabilities  much like the Morph concept.)

Researchers in Singapore have developed a graphene quantum dot using a C60 (a buckminster fullerene). From the June 13, 2011 news item (Graphene: from spheres to perfect dots) on Nanowerk,

An electron trapped in a space of just a few nanometers across behaves very differently to one that is free. Structures that confine electrons in all three dimensions can produce some useful optical and electronic effects. Known as quantum dots, such structures are being widely investigated for use in new types of optical and electronics technologies, but because they are so small it is difficult to fabricate quantum dots reproducibly in terms of shape and size. Researchers from the National University of Singapore (NUS) and A*STAR have now developed a technique that enables graphene quantum dots of a known size to be created repeatedly and quickly (“Transforming C60 molecules into graphene quantum dots” [published in Nature Nanotechnology 6, 247–252 (2011) doi:10.1038/nnano.2011.30 Published online 20 March 2011]).

This final bit is about a nano PacMan that allows for more precise patterning from a June 13, 2011 article written by Michael Berger,

A widely discussed method for the patterning of graphene is the channelling of graphite by metal nanoparticles in oxidizing or reducing environments (see for instance: “Nanotechnology PacMan cuts straight graphene edges”).

“All previous studies of channelling behavior have been limited by the need to perform the experiment ex situ, i.e. comparing single ‘before’ and ‘after’ images,” Peter Bøggild, an associate professor at DTU [Danish Technical University] Nanotech, explains to Nanowerk. “In these and other ex situ experiments the dynamic behavior must be inferred from the length of channels and heating time after completion of the experiment, with the rate of formation of the channel assumed to be consistent over the course of the experiment.”

In new work, reported in the June 9, 2011 advance online edition of Nano Letters (“Discrete dynamics of nanoparticle channelling in suspended graphene” [published in Nano Letters, Article ASAP, DOI: 10.1021/nl200928k, Publication Date (Web): June 9, 2011]), Bøggild and his team report the nanoscale observation of this channelling process by silver nanoparticles in an oxygen atmosphere in-situ on suspended mono- and bilayer graphene in an environmental transmission electron microscope, enabling direct concurrent observation of the process, impossible in ex-situ experiments.

Personally, I love the youtube video I’ve included here largely because it features blobs (as many of these videos do) where they’ve added music and titles (many of these videos do not) so you can better appreciate the excitement,

From the article by Michael Berger,

As a result of watching this process occur live in a transmission electron microscope, the researchers say they have seen many details that were hidden before, and video really brings the “nano pacman” behavior to life …

There’s a reason why they’re so interested in cutting graphene,

“With a deeper understanding of the fine details we hope to one day use this nanoscale channelling behavior to directly cut desired patterns out of suspended graphene sheets, with a resolution and accuracy that isn’t achievable with any other technique,” says Bøggild. “A critical advantage here is that the graphene crystal structure guides the patterning, and in our case all of the cut edges of the graphene are ‘zigzag’ edges.”

So there you have it. IBM creates the first integrated graphene-based circuit, there’s the prospect of a huge cash prize for a 10-year project on graphene so they could produce the long awaited Morph concept and other graphene-based electronics products while a number of research teams around the world continue teasing out its secrets with graphene ‘foam’ projects, graphene quantum dots, and nano PacMen who cut graphene’s zigzag edges with precision.

ETA June 16, 2011: For those interested in the business end of things, i.e. market value of graphene-based products, Cameron Chai features a report, Graphene: Technologies, Applications, and Markets, in his June 16, 2011 news item on Azonano.