Tag Archives: analogies

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, 0217 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

Nanotechnology analogies and policy

There’s a two part essay titled, Regulating Nanotechnology Via Analogy (part 1, Feb. 12, 2013 and part 2, Feb. 18, 2013), by Patrick McCray on his Leaping Robot blog that is well worth reading if you are interested in the impact analogies can have on policymaking.

Before launching into the analogies, here’s a bit about Patrick McCray from the Welcome page to his website, (Note: A link has been removed),

As a professor in the History Department of the University of California, Santa Barbara and a co-founder of the Center for Nanotechnology in Society, my work focuses on different technological and scientific communities and their interactions with the public and policy makers. For the past ten years or so, I’ve been especially interested in the historical development of so-called “emerging technologies,” whenever they emerged.

I hope you enjoy wandering around my web site. The section of it that changes most often is my Leaping Robot blog. I update this every few weeks or so with an extended reflection or essay about science and technology, past and future.

In part 1 (Feb. 12, 2013) of the essay, McCray states (Note: Links and footnotes have been removed),

[Blogger’s note: This post is adapted from a talk I gave in March 2012 at the annual Business History Conference; it draws on research done by Roger Eardley-Pryor, an almost-finished graduate student I’m advising at UCSB [University of California at Santa Barbara], and me. I’m posting it here with his permission. This is the first of a two-part essay…some of the images come from slides we put together for the talk.]

Over the last decade, a range of actors – scientists, policy makers, and activists – have used  historical analogies to suggest different ways that risks associated with nanotechnology – especially those concerned with potential environmental implications – might be minimized. Some of these analogies make sense…others, while perhaps effective, are based on a less than ideal reading of history.

Analogies have been used before as tools to evaluate new technologies. In 1965, NASA requested comparisons between the American railroad of the 19th century and the space program. In response, MIT historian Bruce Mazlish wrote a classic article that analyzed the utility and limitations of historical analogies. Analogies, he explained, function as both model and myth. Mythically, they offer meaning and emotional security through an original archetype of familiar knowledge. Analogies also furnish models for understanding by construing either a structural or a functional relationship. As such, analogies function as devices of anticipation which what today is fashionably called “anticipatory governance.”They also can serve as a useful tool for risk experts.

McCray goes on to cover some of the early discourse on nanotechnology, the players, and early analogies. While the focus is on the US, the discourse reflects many if not all of the concerns being expressed internationally.

In part 2 posted on Feb. 18, 2013 McCray mentions four of the main analogies used with regard to nanotechnology and risk (Note: Footnotes have been removed),

Example #1 – Genetically Modified Organisms

In April 2003, Prof. Vicki Colvin testified before Congress. A chemist at Rice University, Colvin also directed that school’s Center for Biological and Environmental Nanotechnology. This “emerging technology,” Colvin said, had a considerable “wow index.” However, Colvin warned, every promising new technology came with concerns that could drive it from “wow into yuck and ultimately into bankrupt.” To make her point, Colvin compared nanotech to recent experiences researchers and industry had experienced with genetically modified organisms. Colvin’s analogy – “wow to yuck” – made an effective sound bite. But it also conflated two very different histories of two specific emerging technologies.

While some lessons from GMOs are appropriate for controlling the development of nanotechnology, the analogy doesn’t prove watertight. Unlike GMOs, nanotechnology does not always involve biological materials. And genetic engineering in general, never enjoyed any sort of unalloyed “wow” period. There was “yuck” from the outset. Criticism accompanied GMOs from the very start. Furthermore, giant agribusiness firms prospered handsomely even after the public’s widespread negative reactions to their products.  Lastly, living organisms – especially those associated with food – designed for broad release into the environment were almost guaranteed to generate concerns and protests. Rhetorically, the GMO analogy was powerful…but a deeper analysis clearly suggests there were more differences than similarities.

McCray offers three more examples of analogies used to describe nanotechnology: asbestos, (radioactive) fallout, and Recombinant DNA which he dissects and concludes are not the best analogies to be using before offering this thought,

So — If historical analogies teach can teach us anything about the potential regulation of nano and other emerging technologies, they indicate the need to take a little risk in forming socially and politically constructed definitions of nano. These definitions should be based not just on science but rather mirror the complex and messy realm of research, policy, and application. No single analogy fits all cases but an ensemble of several (properly chosen, of course) can suggest possible regulatory options.

I recommend reading both parts of McCray’s essay in full. It’s a timely piece especially in light of a Feb. 28, 2013 article by Daniel Hurst for Australian website, theage.com.au, where a union leader raises health fears about nanotechnology by using the response to asbestos health concerns as the analogy,

Union leader Paul Howes has likened nanotechnology to asbestos, calling for more research to ease fears that the growing use of fine particles could endanger manufacturing workers.

”I don’t want to make the mistake that my predecessors made by not worrying about asbestos,” the Australian Workers Union secretary said.

I have covered the topic of carbon nanotubes and asbestos many times, one of the  latest being this Jan. 16, 2013 posting. Not all carbon nanotubes act like asbestos; the long carbon nanotubes present the problems.

Quantum kind of day: metaphors, language and nanotechnology

I had a bonanza day on the Nanowerk website yesterday as I picked up three items, all of which featured the word ‘quantum’ in the title and some kind of word play or metaphor.

From the news item, Quantum dots go with the flow,

Quantum dots may be small. But they usually don’t let anyone push them around. Now, however, JQI [Joint Quantum Institute] Fellow Edo Waks and colleagues have devised a self-adjusting remote-control system that can place a dot 6 nanometers long to within 45 nm of any desired location. That’s the equivalent of picking up golf balls around a living room and putting them on a coffee table – automatically, from 100 miles away.

There’s a lot of detail in this item which gives you more insight (although the golf ball analogy does that job very well) into just how difficult it is to move a quantum dot and some of the problems that had to be solved.

Next, A quantum leap for cryptography,

To create random number lists for encryption purposes, cryptographers usually use mathematical algorithms called ‘pseudo random number generators’. But these are never entirely ‘random’ as the creators cannot be certain that any sequence of numbers isn’t predictable in some way.

Now a team of experimental physicists has made a breakthrough in random number generation by applying the principles of quantum mechanics to produce a string of numbers that is truly random.

‘Classical physics simply does not permit genuine randomness in the strict sense,’ explained research team leader Chris Monroe from the Joint Quantum Institute (JQI) at the University of Maryland in the US. ‘That is, the outcome of any classical physical process can ultimately be determined with enough information about initial conditions. Only quantum processes can be truly random — and even then, we must trust the device is indeed quantum and has no remnant of classical physics in it.’

This is a drier piece (I suspect that’s due to the project itself) so the language or word play is in the headline. I immediately thought of a US tv series titled, Quantum Leap where, for five seasons, a scientist’s personality/intellect/spirit is leaping into people’s bodies, randomly through time. There are, according to Wikipedia, two other associations, a scientific phenomenon and a 1980s era computer. You can go here to pursue links for the other two associations. This is very clever in that you don’t need to have any associations to understand the base concept in the headline but having one or more association adds a level or more of engagement.

The final item, Scientists climb the quantum ladder,

An EU [European Union]-funded team of scientists from Cardiff University in the UK has successfully fired photons (light particles) into a small tower of semiconducting material. The work could eventually lead to the development of faster computers. …

The scientists, from the university’s School of Physics and Astronomy, said a photon collides with an electron confined in a smaller structure within the tower. Before the light particles re-emerge, they oscillate for a short time between the states of light and matter.

While I find this business of particles oscillating between two different states, light and matter, quite fascinating this particular language play is the least successful. I think most people will do what I did and miss the relationship between the ‘tower’ in the news item’s first paragraph and the ‘ladder’ in the headline. I cannot find any other attempt to play with either linguistic image elsewhere in the item.

Given that I’m  a writer I’m going to argue that analogies, metaphors, and word play are essential when trying to explain concepts to audiences that may not have your expertise and that audience can include other scientists. Here’s an earlier posting about some work by a cognitive psychologist, Kevin Dunbar, who investigates how scientists think and communicate.

Responsible science communication and magic bullets; lego and pasta analogies; sing about physics

Cancer’s ‘magic bullet],  a term which has been around for decades, is falling into disuse and deservedly. So it’s disturbing to see it used by someone in McGill University’s (Montreal, Canada) communications department for a recent breakthrough by their researchers.

The reason ‘magic bullet for cancer’ has been falling into is disuse because it does not function well as a metaphor with what we now know about biology. (The term itself dates from the 19th century and chemist, Paul Erlich.) It continues to exist because it’s an easy (and lazy) way to get attention and headlines. Unfortunately, hyperbolic writing of this type obscures the extraordinary and exciting work that researchers are accomplishing. From the news release on the McGill website (also available on Nanowerk here),

A team of McGill Chemistry Department researchers led by Dr. Hanadi Sleiman has achieved a major breakthrough in the development of nanotubes – tiny “magic bullets” that could one day deliver drugs to specific diseased cells.

The lead researcher seems less inclined to irresponsible hyperbole,

One of the possible future applications for this discovery is cancer treatment. However, Sleiman cautions, “we are still far from being able to treat diseases using this technology; this is only a step in that direction. Researchers need to learn how to take these DNA nanostructures, such as the nanotubes here, and bring them back to biology to solve problems in nanomedicine, from drug delivery, to tissue engineering to sensors,” she said.

You’ll notice that the researcher says these ‘DNA nanotubes’ have to be brought “back to biology.” This comment brought to mind a recent post on 2020 Science (Andrew Maynard’s blog) about noted chemist and nanoscientist’s, George Whitesides, concerns/doubts about the direction for cancer and nanotechnology research. From Andrew’s post,

Cancer treatment has been a poster-child for nanotechnology for almost as long as I’ve been involved with the field. As far back as in 1999, a brochure on nanotechnology published by the US government described future “synthetic anti-body-like nanoscale drugs or devices that might seek out and destroy malignant cells wherever they might be in the body.”

So I was somewhat surprised to see the eminent chemist and nano-scientist George Whitesides questioning how much progress we’ve made in developing nanotechnology-based cancer treatments, in an article published in the Columbia Chronicle.

Whitesides comments are quite illuminating (from the article, Microscopic particles have huge possibilites [sic], by Ivana Susic,

George Whitesides, professor of chemistry and chemical biology at Harvard University, said that while the technology sounds impressive, he thinks the focus should be on using nanoparticles in imaging and diagnosing, not treatment.

The problem lies in being able to deliver the treatment to the right cells, and Whitesides said this has proven difficult.

“Cancer cells are abnormal cells, but they’re still us,” he said. [emphasis is mine]

The nanoparticles sent in to destroy the cancer cells may also destroy unaffected cells, because they can sometimes have cancer markers even if they’re healthy. Tumors have also been known to be “genetically flexible” and mutate around several different therapies, Whitesides explained. This keeps them from getting recognized by the therapeutic drugs.

The other problem with targeting cancer cells is the likelihood that only large tumors will be targeted, missing smaller clumps of developing tumors.

“We need something that finds isolated [cancer] clumps that’s somewhere else in the tissue … it’s not a tumor, it’s a whole bunch of tumors,” Whitesides said.

The upside to the treatment possibilities is that they buy the patient time, he said, which is very important to many cancer patients.

“It’s easy to say that one is going to have a particle that’s going to recognize the tumor once it gets there and will do something that triggers the death of the cell, it’s just that we don’t know how to do either one of these parts,” he said.

There is no simple solution. The more scientists learn about biology the more complicated it becomes, not less. [emphasis is mine] Whitesides said one effective way to deal with cancer is to reduce the risk of getting it by reducing the environmental factors that lead to cancer.

It’s a biology problem, not a particle problem,” he said. [emphasis is mine]

If you are interested , do read Andrew’s post and the comments that follow as well as the article that includes Whitesides’ comments and quotes from Andrew in his guise as Chief Science Advisor for the Project on Emerging Nanotechnologies.

All of this discussion follows on yesterday’s (Mar.17.10) post about how confusing inaccurate science reporting can be.

Moving onwards to two analogies, lego and pasta. Researchers at the University of Glasgow have ‘built’ inorganic (not carbon-based) molecular structures which could potentionally be used as more energy efficient and environmentally friendly catalysts for industrial purposes. From the news item on Nanowerk,

Researchers within the Department of Chemistry created hollow cube-based frameworks from polyoxometalates (POMs) – complex compounds made from metal and oxygen atoms – which stick together like LEGO bricks meaning a whole range of well-defined architectures can be developed with great ease.

The molecular sensing aspects of this new material are related to the potassium and lithium ions, which sit loosely in cavities in the framework. These can be displaced by other positively charged ions such as transition metals or small organic molecules while at the same time leaving the framework intact.

These characteristics highlight some of the many potential uses and applications of POM frameworks, but their principle application is their use as catalysts – a molecule used to start or speed-up a chemical reaction making it more efficient, cost-effective and environmentally friendly.

Moving from lego to pasta with a short stop at the movies, we have MIT researchers describing how they and their team have found a way to ‘imprint’ computer chips by using a new electron-beam lithography process to encourage copolymers to self-assemble on the chip. (Currently, manufacturers use light lasers in a photolithographic process which is becoming less effective as chips grow ever smaller and light waves become too large to use.) From the news item on Nanowerk,

The new technique uses “copolymers” made of two different types of polymer. Berggren [Karl] compares a copolymer molecule to the characters played by Robert De Niro and Charles Grodin in the movie Midnight Run, a bounty hunter and a white-collar criminal who are handcuffed together but can’t stand each other. Ross [Caroline] prefers a homelier analogy: “You can think of it like a piece of spaghetti joined to a piece of tagliatelle,” she says. “These two chains don’t like to mix. So given the choice, all the spaghetti ends would go here, and all the tagliatelle ends would go there, but they can’t, because they’re joined together.” In their attempts to segregate themselves, the different types of polymer chain arrange themselves into predictable patterns. By varying the length of the chains, the proportions of the two polymers, and the shape and location of the silicon hitching posts, Ross, Berggren, and their colleagues were able to produce a wide range of patterns useful in circuit design.

ETA (March 18,2010): Dexter Johnson at Nanoclast continues with his his posts (maybe these will form a series?) about more accuracy in reporting, specifically the news item I’ve just highlighted. Check it out here.

To finish on a completely different note (pun intended), I have a link (courtesy of Dave Bruggeman of the Pasco Phronesis blog by way of the Science Cheerleader blog) to a website eponymously (not sure that’s the right term) named physicssongs.org. Do enjoy such titles as: I got Physics; Snel’s Law – Macarena Style!; and much, much more.

Tomorrow: I’m not sure if I’ll have time to do much more than link to it and point to some commentary but the UK’s Nanotechnologies Strategy has just been been released today.