Tag Archives: metaphors

viral symphOny: an electronic soundwork à propos during a pandemic

Artist Joseph Nechvatal has a longstanding interest in viruses, i.e., computer viruses and that work seems strangely apt as we cope with the COVID-19 pandemic. He very kindly sent me some à propos information (received via an April 5, 2020 email),

I wanted to let you know that _viral symphOny_ (2006-2008), my 1 hour 40 minute collaborative electronic noise music symphony, created using custom artificial life C++ software based on the viral phenomenon model, is available to the world for free here:

https://archive.org/details/ViralSymphony

Before you click the link and dive in you might find these bits of information interesting. BTW, I do provide the link again at the end of this post.

Origin of and concept behind the term ‘computer virus’

As I’ve learned to expect, there are two and possibly more origin stories for the term ‘computer virus’. Refreshingly, there is near universal agreement in the material I’ve consulted about John von Neuman’s role as the originator of the concept. After that, it gets more complicated; Wikipedia credits a writer for christening the term (Note: Links have been removed),

The first academic work on the theory of self-replicating computer programs[17] was done in 1949 by John von Neumann who gave lectures at the University of Illinois about the “Theory and Organization of Complicated Automata”. The work of von Neumann was later published as the “Theory of self-reproducing automata”. In his essay von Neumann described how a computer program could be designed to reproduce itself.[18] Von Neumann’s design for a self-reproducing computer program is considered the world’s first computer virus, and he is considered to be the theoretical “father” of computer virology.[19] In 1972, Veith Risak directly building on von Neumann’s work on self-replication, published his article “Selbstreproduzierende Automaten mit minimaler Informationsübertragung” (Self-reproducing automata with minimal information exchange).[20] The article describes a fully functional virus written in assembler programming language for a SIEMENS 4004/35 computer system. In 1980 Jürgen Kraus wrote his diplom thesis “Selbstreproduktion bei Programmen” (Self-reproduction of programs) at the University of Dortmund.[21] In his work Kraus postulated that computer programs can behave in a way similar to biological viruses.

Science fiction

The first known description of a self-reproducing program in a short story occurs in 1970 in The Scarred Man by Gregory Benford [emphasis mine] which describes a computer program called VIRUS which, when installed on a computer with telephone modem dialing capability, randomly dials phone numbers until it hit a modem that is answered by another computer. It then attempts to program the answering computer with its own program, so that the second computer will also begin dialing random numbers, in search of yet another computer to program. The program rapidly spreads exponentially through susceptible computers and can only be countered by a second program called VACCINE.[22]

The idea was explored further in two 1972 novels, When HARLIE Was One by David Gerrold and The Terminal Man by Michael Crichton, and became a major theme of the 1975 novel The Shockwave Rider by John Brunner.[23]

The 1973 Michael Crichton sci-fi movie Westworld made an early mention of the concept of a computer virus, being a central plot theme that causes androids to run amok.[24] Alan Oppenheimer’s character summarizes the problem by stating that “…there’s a clear pattern here which suggests an analogy to an infectious disease process, spreading from one…area to the next.” To which the replies are stated: “Perhaps there are superficial similarities to disease” and, “I must confess I find it difficult to believe in a disease of machinery.”[25]

Scientific American has an October 19, 2001 article citing four different experts’ answer to the question “When did the term ‘computer virus’ arise?” Three of the experts cite academics as the source for the term (usually Fred Cohen). One of the experts does mention writers (for the most part, not the same writers cited in the Wikipedia entry quotation in the above).

One expert discusses the concept behind the term and confirms what most people will suspect. Interestingly, this expert’s origin story varies somewhat from the other three.

Computer virus concept

From “When did the term ‘computer virus’ arise?” (Joseph Motola response),

The concept behind the first malicious computer programs was described years ago in the Computer Recreations column of Scientific American. The metaphor of the “computer virus” was adopted because of the similarity in form, function and consequence with biological viruses that attack the human system. Computer viruses can insert themselves in another program, taking over control or adversely affecting the function of the program.

Like their biological counterparts, computer viruses can spread rapidly and self-replicate systematically. They also mimic living viruses in the way they must adapt through mutation [emphases mine] to the development of resistance within a system: the author of a computer virus must upgrade his creation in order to overcome the resistance (antiviral programs) or to take advantage of new weakness or loophole within the system.

Computer viruses also act like biologics [emphasis mine] in the way they can be set off: they can be virulent from the outset of the infection, or they can be activated by a specific event (logic bomb). But computer viruses can also be triggered at a specific time (time bomb). Most viruses act innocuous towards a system until their specific condition is met.

The computer industry has expanded the metaphor to now include terms like inoculation, disinfection, quarantine and sanitation [emphases mine]. Now if your system gets infected by a computer virus you can quarantine it until you can call the “virus doctor” who can direct you to the appropriate “virus clinic” where your system can be inoculated and disinfected and an anti-virus program can be prescribed.

More about Joseph Nechvatal and his work on viruses

The similarities between computer and biological viruses are striking and with that in mind, here’s a clip featuring part of viral symphOny,

Before giving you a second link to Nechvatal’s entire viral symphOny, here’s some context about him and his work, from the Joseph Nechvatal Wikipedia entry, (Note: Links have been removed),

He began using computers to make “paintings” in 1986 [11] and later, in his signature work, began to employ computer viruses. These “collaborations” with viral systems positioned his work as an early contribution to what is increasingly referred to as a post-human aesthetic.[12][13]

From 1991–1993 he was artist-in-residence at the Louis Pasteur Atelier in Arbois, France and at the Saline Royale/Ledoux Foundation’s computer lab. There he worked on The Computer Virus Project, which was an artistic experiment with computer viruses and computer animation.[14] He exhibited at Documenta 8 in 1987.[15][16]

In 1999 Nechvatal obtained his Ph.D. in the philosophy of art and new technology concerning immersive virtual reality at Roy Ascott’s Centre for Advanced Inquiry in the Interactive Arts (CAiiA), University of Wales College, Newport, UK (now the Planetary Collegium at the University of Plymouth). There he developed his concept of viractualism, a conceptual art idea that strives “to create an interface between the biological and the technological.”[17] According to Nechvatal, this is a new topological space.[18]

In 2002 he extended his experimentation into viral artificial life through a collaboration with the programmer Stephane Sikora of music2eye in a work called the Computer Virus Project II,[19] inspired by the a-life work of John Horton Conway (particularly Conway’s Game of Life), by the general cellular automata work of John von Neumann, by the genetic programming algorithms of John Koza and the auto-destructive art of Gustav Metzger.[20]

In 2005 he exhibited Computer Virus Project II works (digital paintings, digital prints, a digital audio installation and two live electronic virus-attack art installations)[21] in a solo show called cOntaminatiOns at Château de Linardié in Senouillac, France. In 2006 Nechvatal received a retrospective exhibition entitled Contaminations at the Butler Institute of American Art’s Beecher Center for Arts and Technology.[4]

Dr. Nechvatal has also contributed to digital audio work with his noise music viral symphOny [emphasis mine], a collaborative sound symphony created by using his computer virus software at the Institute for Electronic Arts at Alfred University.[22][23] viral symphOny was presented as a part of nOise anusmOs in New York in 2012.[24]

Here’s a link to the complete viral symphOny with his website here and his blog here.

ETA April 7, 2020 at 1135 PT: Joseph Nechvatal’s book review of Gustav Metzger’s collected writings (1953–2016) has just (April 2020) dropped at The Brooklyn Rail here:  https://brooklynrail.org/2020/04/art_books/Gustav-Metzgers-Writings.

CRISPR (clustered regularly interspaced short palindromic repeats) has a metaphor issue?

Elinor Hortie at the University of Sydney (Australia) has written a very interesting essay about CRISPR ‘scissors’, a metaphor she find misleading. From Hortie’s July 4, 2019 essay on The Conversation,

Last week I read an article about CRISPR, the latest tool scientists are using to edit DNA. It was a great piece – well researched, beautifully written, factually accurate. It covered some of the amazing projects scientist are working on using CRISPR, like bringing animals back from extinction and curing diseases. It also gave me the heebies, but not for the reason you might expect.

Take CRISPR. It’s most often described as a pair of molecular scissors that can be used to modify DNA, the blueprint for life. And when we read that, I think most of us start imagining something like a child with her Lego bricks strewn in front of her, instruction booklet in one hand, scissors in the other. One set of pictograms, one model; one gene, one disease; one snip, one cure. We’re there in a blink. CRISPR seems like it can work miracles.

I want to stress that the molecular scissors metaphor is pretty damn accurate as far as it goes. But in focusing on the relatively simple relationship between CRISPR and DNA, we miss the far more complicated relationship between DNA and the rest of the body. This metaphor ignores an entire ecosystem of moving parts that are crucial for understanding the awe-inspiring, absolutely insane thing scientists are trying to do when they attempt gene editing.

Hortie proposes a different metaphor,

In my research I use CRISPR from time to time. To design experiments and interpret results effectively, I need a solid way to conceptualise what it can (and can’t) do. I do not think of CRISPR as molecular scissors.

Instead I imagine a city. The greater metropolis represents the body, the suburbs are organs, the buildings are cells, the people are proteins, and the internet is DNA.

In this metaphor CRISPR is malware. More precisely, CRISPR is malware that can search for any chosen 20-character line of code and corrupt it. This is not a perfect metaphor by any stretch, but it gets me closer to understanding than almost anything else.

Hortie offers an example from her own work demonstrating how a CRISPR ‘malware’ metaphor/analogy more accurately represents the experience of using the gene-editing system,

As an example, let’s look at Alzheimer’s, one of the diseases CRISPR is being touted to cure. The headlines are usually some variation of “CRISPR to correct Alzheimer’s gene!”, and the molecular scissors analogy is never far behind.

It seems reasonable to me that someone could read those words and assume that chopping away the disease-gene with the DNA-shears should be relatively simple. When the cure doesn’t appear within five years, I can understand why that same person would come to ask me why Big Pharma is holding out (this has happened to me more than once).

Now let’s see how it looks using the malware metaphor. The consensus is that Alzheimer’s manifests when a specific protein goes rogue, causing damage to cells and thereby stopping things from working properly inside the brain. It might have a genetic cause, but it’s complicated. In our allegorical city, what would that look like?

I think riots would come close. Rampaging humans (proteins) destroying houses and property (cells), thereby seriously derailing the normal functioning of a specific suburb (the brain).

And you want to fix that with malware?

It’s hard to predict the domino effect

Can you imagine for a second trying to stop soccer hooligans smashing things on the streets of Buenos Aires by corrupting roughly three words in the FIFA by-laws with what’s essentially a jazzed-up command-F function?

I’m not saying it’s not possible – it absolutely is.

But think of all the prior knowledge you need, and all the pieces that have to fall in place for that to work. You’d have to know that the riots are caused by football fans. You’d have to understand which rule was bothering them (heaven help you if it’s more than one), and if that rule causes drama at every game. You’d have to find a 20-character phrase that, when corrupted, would change how the rule was read, rather than just making a trivial typo.

You’d have to know that the relevant footballers have access to the updated rule book, and you’d have to know there were no other regulations making your chosen rule redundant. You’d have to know there aren’t any similar 20-character phrases anywhere on the internet that might get corrupted at the same time (like in the rules for presidential succession say, or in the nuclear warhead codes). Even then you’d still be rolling the dice.

Even if you stop the riots successfully, which of us really know the long-term consequences of changing the World Game forever?

That’s stretching the metaphor as Hortie notes herself later in the essay. And, she’s not the only one concerned about metaphors and CRISPR. There’s a December 8, 2017* article by Rebecca Robbins for STAT news which covers ten analogies/metaphors ranked from worst to best,

… Some of these analogies are better than others. To compile the definitive ranking, I sat down with STAT’s senior science writer Sharon Begley, a wordsmith who has herself compared CRISPR to “1,000 monkeys editing a Word document” and the kind of dog “you can train to retrieve everything from Frisbees to slippers to a cold beer.”

Sharon and I evaluated each of the metaphors we found by considering these three questions: Is it creative? Is it clear? And is it accurate? Below, our rankings of CRISPR analogies, ordered from worst to best:

0. A knockout punch


9. The hand of God


8. A bomb removal squad

It’s a very interesting list with a description of why each does and doesn’t work as an analogy. By the way, ‘scissors’ was not the top analogy. The number one spot went to ‘A Swiss army knife’.

There are many more essays than I would have believed concerning CRISPR and metaphors/analogies. I’m glad to see them as the language we use to describe our work and our world helps us understand it and can constrain us in unexpected ways. Critiques such as Hortie’s and the others can help us to refine the language and to recognize its limitations.

h/t July 4, 2019 news item on phys.org

*”December 8, 0217′ corrected to ‘December 8, 2017’ on Jan.20.21

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.