Tag Archives: double-helix

The Backstreet Boys sing genetics (not really) but their latest album is called “DNA”

Other that the promotional artwork, cover art and the title, the Backstreet Boys pop band does not seem to have taken science or DNA (deoxyribonucleic acid)/genetics to heart in their latest oeuvre. As for what chickens have to do with it, I I gather this is some sort of humorous nod to a past hit song. Still, I am weirdly fascinated by this January 25, 2019 video news item on Billboard,

Having looked at the list of songs on the DNA album (they’re listed in the Billboard news item where they’ve embedded audio samples), I can’t find anything that suggests an interest in genetics but perhaps you can: Don’t Go Breaking My Heart? Nobody Else? Breathe? New Love? Passionate? Is It Just Me? Chances? No Place? Chateau? The Way It Was? Just Like You Like it? OK? Anyone who can figure out how the songs relate to DNA, please let me know in the Comments.

Frankly, that’s as much analysis as I can offer on the topic. Thankfully, Karen James (an independent educator, researcher, and consultant in molecular biology) has written a February 5, 2019 article (I Want DNA That Way; The Backstreet Boys’ new album and tour features a very old-school depiction of DNA) for slate.com where she unpacks the imagery in the promotional material and on the cover (Note: Links have been removed),

The Backstreet Boys are back. Credit: Dennis Leupold [downloaded from https://slate.com/technology/2019/02/backstreet-boys-dna-album-cover-gene-sequencing.html]

The Backstreet Boys released a new album. I never thought I’d start a science article—or any article—with that sentence, but here we are.

We are here because the promotional artwork for the album (above) is a photograph of the boy band (man band?) lit by a projection of DNA bands. The image, and the album’s title, DNA, jumped out of my Twitter timeline because I’m a geneticist, I work with DNA, and I’ve seen countless images just like it in textbooks and research articles. I’ve even made them myself in the lab.

What struck me as funny (both funny-ha-ha and funny-odd) is that the lab methods that could have produced this image are old—older even than the Backstreet Boys’ first album. One of the methods—called Sanger sequencing—was published in 1977, making it even older than two of the Backstreet Boys themselves, scientist Kristy Lamb pointed out. Genetics is a particularly fast-moving science. New technologies are constantly emerging and eclipsing prior ones. Yet this 40-year-old imagery persists, and not just in the promotional artwork for DNA. Just do a Google image search for “DNA sequencing” and you’ll see plenty of images like this mixed in with the double helices and long GATTACA readouts.

After her description of Sanger sequencing James offers another ‘sequencing’ possibility, almost as old as the Sanger technique,

Careful readers might have noticed that I suggested there was more than one method that produces images like this. At first glance, I thought the projection in the Backstreet Boys’ publicity photo was modified from an image made with Sanger sequencing. But when I looked again in preparation for writing this article, I had second thoughts. Why aren’t the lanes clustered in groups of four? Why are some of the bands in adjacent lanes the same size? (They shouldn’t be if you’re doing Sanger sequencing.) It could be that the photo was heavily modified with individual lanes copied and pasted. Indeed, some of the lanes are even identical to each other (*suppresses fake ivory tower scoff*).

Or it could be that this image was made with another old method: DNA fingerprinting. Made famous in so many crime TV shows, DNA fingerprinting was invented in 1984 by Alec Jeffreys, who, though he did not win a Nobel Prize, was made a knight of the British Empire for his contribution to science, among many other prestigious awards, which is nice.

I suspect the Backstreet Boys weren’t going for a tongue-in-cheek reference to their own advancing age. While today’s DNA sequencing methods produce images that scarcely resemble those produced by Sanger sequencing and DNA fingerprinting, the old-school imagery is still everywhere. The Backstreet Boys’ promotional team probably just went with a stock image that looked compelling and worked well as a projection.

James returns to her theme, why use imagery associated with outdated techniques? (Note: Links have been removed),

But that doesn’t answer the real question: Why is 40-year-old imagery still so ubiquitous? As science writer and editor Stephanie Keep tweeted, one reason may be that, despite its age, the Sanger method is still taught in high school classrooms: “It’s so visual and intuitive.” It’s true. When I teach students about DNA sequencing, I always start with Sanger sequencing and use that as the basis for explaining newer technologies, adding more complexity as I go, following the historical timeline.

Another reason the old imagery is still in use may be that the images produced by newer, so-called next-generation sequencing methods aren’t visually scored by a scientist sitting at a lab bench, but by computers. As such, the images themselves often go unseen by human eyes [emphasis mine], despite their colorful beauty.

Interesting, eh? The latest imagery is not seen by human eyes. So the newest imagery is intended for machines. James presents an example of the ‘new’ imagery,

An image generated using a next-generation DNA sequencing method.. Credit: Illumina [downloaded from https://slate.com/technology/2019/02/backstreet-boys-dna-album-cover-gene-sequencing.html]

According to James, this image was not easily obtained according to one of her tweets. [https://twitter.com/kejames/status/1092888034322845696] So, big thanks to Illumina (there’s also a Wikipedia entry about the company). Getting back to James’ and her article, she asks why the band titled their latest album, DNA,

But why did the Backstreet Boys call their album DNA in the first place? The official RCA Records press release announcing the album says, “BSB analyzed their individual DNA profiles to see what crucial element each member represents in the groups DNA.” It links to a YouTube video that supposedly explains “how their individual strains, when brought together, create the unstoppable and legendary Backstreet Boys.”

The video is a futuristic, spy movie–esque montage, complete with a computerized female voice describing the various characteristics of each Backstreet Boy. Reader, I confess: I cringed. There were so many tropes and misconceptions about DNA packed into the 83-second video, I would have to write a follow-up to this just to explore them. The cringeworthiness doesn’t end there, though. The cover of DNA has each Backstreet Boy on his own spiral staircase.

The staircases are surely meant to evoke the structure of DNA: the famous double helix. But there’s a problem, as the social media account for the journal Genome Biology tweeted: The staircases are spiraling in the wrong direction. DNA is usually right-handed. If you stick out your right thumb, your fingers will naturally curl in a right-handed spiral as you move your hand in the direction your thumb is pointing. The Backstreet Boys’ staircases are left-handed.

Here’s the promotional trailer for DNA,

It’s everything James says it is. As for those wrongly spiraling DNA staircases,

RCA Records [downloaded from https://slate.com/technology/2019/02/backstreet-boys-dna-album-cover-gene-sequencing.html]

Thank you to Karen James for this illuminating article. If you have time, I encourage you to read her piece in its entirety:
I Want DNA That Way; The Backstreet Boys’ new album and tour features a very old-school depiction of DNA.

As for why the Backstreet Boys called their album DNA and you likely guessed. it would seem to be a promotional gimmick meant to leverage the perceived interest in commercial DNA testing by companies such as 23andMe and Ancestry, amongst others.

Movies and science, science, science (Part 1 of 2)

In the last few years, there’s been a veritable plethora of movies (and television shows in Canada and the US) that are about science and technology or have a significant  component or investigate the social impact. The trend does not seem to be slowing.

This first of two parts features the film, *Hidden* Figures, and a play being turned into a film, Photograph 51. The second part features the evolving Theranos story and plans to turn it into a film, The Man Who Knew Infinity, a film about an Indian mathematician, the science of the recent all woman Ghostbusters, and an ezine devoted to science films.

For the following movie tidbits, I have David Bruggeman to thank.

Hidden Figures

From David’s June 21, 2016 post on his Pasco Phronesis blog (Note: A link has been removed),

Hidden Figures is a fictionalized treatment of the book of the same name written by Margot Lee Shetterly (and underwritten by the Sloan Foundation).  Neither the book nor the film are released yet.  The book is scheduled for a September release, and the film currently has a January release date in the U.S.

Both the film and the book focus on the story of African American women who worked as computers for the government at the Langley National Aeronautic Laboratory in Hampton, Virginia.  The women served as human computers, making the calculations NASA needed during the Space Race.  While the book features four women, the film is focused on three: Katherine Johnson (recipient of the Presidential Medal of Freedom), Dorothy Vaughan, and Mary Jackson.  They are played by, respectively, Taraji P. Henson, Octavia Spencer, and Janelle Monae.  Other actors in the film include Kevin Costner, Kirsten Dunst, Aldis Hodge, and Jim Parsons.  The film is directed by Theodore Melfi, and the script is by Allison Schroeder.

*ETA Oct. 6, 2016: The book ‘Hidden Figures’ is nonfiction while the movie is a fictionalized adaptation  based on a true story.*

According to imdb.com, the movie’s release date is Dec. 25, 2016 (this could change again).

The history for ‘human computers’ stretches back to the 17th century, at least. From the Human Computer entry in Wikipedia (Note: Links have been removed),

The term “computer”, in use from the early 17th century (the first known written reference dates from 1613),[1] meant “one who computes”: a person performing mathematical calculations, before electronic computers became commercially available. “The human computer is supposed to be following fixed rules; he has no authority to deviate from them in any detail.” (Turing, 1950) Teams of people were frequently used to undertake long and often tedious calculations; the work was divided so that this could be done in parallel.

Prior to NASA, a team of women in the 19th century in the US were known as Harvard Computers (from the Wikipedia entry; Note: Links have been removed),

Edward Charles Pickering (director of the Harvard Observatory from 1877 to 1919) decided to hire women as skilled workers to process astronomical data. Among these women were Williamina Fleming, Annie Jump Cannon, Henrietta Swan Leavitt and Antonia Maury. This staff came to be known as “Pickering’s Harem” or, more respectfully, as the Harvard Computers.[1] This was an example of what has been identified as the “harem effect” in the history and sociology of science.

It seems that several factors contributed to Pickering’s decision to hire women instead of men. Among them was the fact that men were paid much more than women, so he could employ more staff with the same budget. This was relevant in a time when the amount of astronomical data was surpassing the capacity of the Observatories to process it.[2]

The first woman hired was Williamina Fleming, who was working as a maid for Pickering. It seems that Pickering was increasingly frustrated with his male assistants and declared that even his maid could do a better job. Apparently he was not mistaken, as Fleming undertook her assigned chores efficiently. When the Harvard Observatory received in 1886 a generous donation from the widow of Henry Draper, Pickering decided to hire more female staff and put Fleming in charge of them.[3]

While it’s not thrilling to find out that Pickering was content to exploit the women he was hiring, he deserves kudos for recognizing that women could do excellent work and acting on that recognition. When you consider the times, Pickering’s was an extraordinary act.

Getting back to Hidden Figures, an Aug.15, 2016 posting by Kathleen for Lainey Gossip celebrates the then newly released trailer for the movie,

If you’ve been watching the Olympics [Rio 2016], you know how much the past 10 days have been an epic display of #BlackGirlMagic. Fittingly, the trailer for Hidden Figures was released last night during Sunday’s Olympic coverage. It’s the story of three brilliant African American women, played by Taraji P Henson, Octavia Spencer and Janelle Monae, who made history by serving as the brains behind the NASA launch of astronaut John Glenn into orbit in 1962.

Three black women helped launch a dude into space in the 60s. AT NASA. Think about how America treated black women in the 60s. As Katherine Johnson, played by Taraji P Henson, jokes in the trailer, they were still sitting at the back of the bus. In 1962 Malcolm X said, “The most disrespected person in America is the Black woman, the most unprotected person in America is the Black woman. The most neglected person in America is the Black woman.” These women had to face that truth every day and they still rose to greatness. I’m obsessed with this story.

Overall, the trailer is good. I like the pace and the performances look strong. …

I’m most excited for Hidden Figures (as Lainey pointed out, this title is THE WORST) because black girls are being celebrated for their brains on screen. That is rare. When the trailer aired, my brother Sam texted me, “WHOA, a smart black girl movie!”

*ETA Sept. 5, 2016: Aran Shetterly contacted me to say this:

What you may not know is that the term “Hidden Figures” is a specific reference to flight science. It tested a pilot’s ability to pick out a simple figure from a set of more complex, difficult to see images. http://www.militaryaptitudetests.com/afoqt/

Thank you Mr. Shetterly!

Photograph 51 (the Rosalind Franklin story)

Also in David’s June 21, 2016 post is a mention of Photograph 51, a play and soon-to-be film about Rosalind Franklin, the discovery of the double helix, and a science controversy. I first wrote about Photograph 51 in a Jan. 16, 2012 posting (scroll down about 50% of the way) regarding an international script writing competition being held in Dublin, Ireland. At the time, I noted that Anna Ziegler’s play, Photograph 51 had won a previous competition cycle of the screenwriting competition. I wrote again about the play in a Sept. 2, 2015 posting about its London production (Sept. 5 – Nov. 21, 2015) featuring actress Nicole Kidman.

The versions of the Franklin story with which I’m familiar paint her as the wronged party, ignored and unacknowledged by the scientists (Francis, Crick, James Watson, and Maurice Wilkins) who got all the glory and the Nobel Prize. Stephen Curry in a Sept. 16, 2015 posting on the Guardian science blogs suggests the story may not be quite as simple as that (Note: A link has been removed),

Ziegler [Anna Ziegler, playwright] is up front in admitting that she has rearranged facts to suit the drama. This creates some oddities of chronology and motive for those familiar with the history. I know of no suggestion of romantic interest in Franklin from Wilkins, or of a separation of Crick from his wife in the aftermath of his triumph with Watson in solving the DNA structure. There is no mention in the play of the fact that Franklin published her work (and the famous photograph 51) in the journal Nature alongside Watson and Crick’s paper and one by Wilkins. Nor does the audience hear of the international recognition that Franklin enjoyed in her own right between 1953 and her untimely death in 1958, not just for her involvement in DNA, but also for her work on the structure of coal and of viruses.

Published long after her death, The Double Helix is widely thought to treat Franklin unfairly. In the minds of many she remains the wronged woman whose pioneering results were taken by others to solve DNA and win the Nobel prize. But the real story – many elements of which come across strongly in the play – is more complex*.

Franklin is a gifted experimentalist. Her key contributions to the discovery were in improving methods for taking X-ray pictures of and discovering the distinct A and B conformations of DNA. But it becomes clear that her methodical, meticulous approach to data analysis – much to Wilkins’ impotent frustration – eventually allows the Kings ‘team’ to be overtaken by the bolder, intuitive stratagem of Watson and Crick.

Curry’s piece is a good read and provides insight into the ways temperament affects how science is practiced.

Interestingly, there was a 1987 dramatization of the ‘double helix or life story’ (from the Life Story entry on Wikipedia; Note: Links have been removed),

The film tells the story of the rivalries of the two teams of scientists attempting to discover the structure of DNA. Francis Crick and James D. Watson at Cambridge University and Maurice Wilkins and Rosalind Franklin at King’s College London.

The film manages to convey the loneliness and competitiveness of scientific research but also educates the viewer as to how the structure of DNA was discovered. In particular, it explores the tension between the patient, dedicated laboratory work of Franklin and the sometimes uninformed intuitive leaps of Watson and Crick, all played against a background of institutional turf wars, personality conflicts and sexism. In the film Watson jokes, plugging the path of intuition: “Blessed are they who believed before there was any evidence.” The film also shows why Watson and Crick made their discovery, overtaking their competitors in part by reasoning from genetic function to predict chemical structure, thus helping to establish the then still-nascent field of molecular biology.

You can find out more about the stars, crew, and cast here on imdb.com

In addition to Life Story, the dramatization is also sometimes titled as ‘The Race for the Double Helix’ or the ‘Double Helix’.

Getting back to Photograph 51 (the film), Michael Grandage who directed the stage play will also direct the film. Grandage just made his debut as a film director with ‘Genius’ starring Colin Firth and Jude Law. According to this June 23, 2016 review by Sarah on Laineygossip.com, he stumbled a bit by casting British and Australian actors as Americans,

The first hurdle to clear with Genius, the feature film debut of English theater director Michael Grandage, is that everyone is played by Brits and Aussies, and by “everyone” I mean some of the most towering figures of American literature. You cast the best actor for the role and a good actor can convince you they’re anyone, so it shouldn’t really matter, but there is something profoundly odd about watching a parade of Lit 101 All Stars appear on screen and struggle with American accents. …

That kind of casting should not be a problem with Photograph 51 where the action takes place with British personalities.

Part 2 is here.

*’Human’ corrected to ‘Hidden’ on Sept. 5, 2016.

Taking DNA beyond genetics with living computers and nanobots

You might want to keep a salt shaker with you while reading a June 7, 2016 essay by Matteo Palma (Queen Mary’s University of London) about nanotechnology and DNA on The Conversation website (h/t June 7, 2016 news item on Nanowerk).

This is not a ‘hype’ piece as Palma backs every claim with links to the research while providing a good overview of some very exciting work but the mood is a bit euphoric so you may want to keep the earlier mentioned salt shaker nearby.

Palma offers a very nice beginner introduction especially helpful for someone who only half-remembers their high school biology (from the June 7, 2016 essay)

DNA is one of the most amazing molecules in nature, providing a way to carry the instructions needed to create almost any lifeform on Earth in a microscopic package. Now scientists are finding ways to push DNA even further, using it not just to store information but to create physical components in a range of biological machines.

Deoxyribonucleic acid or “DNA” carries the genetic information that we, and all living organisms, use to function. It typically comes in the form of the famous double-helix shape, made up of two single-stranded DNA molecules folded into a spiral. Each of these is made up of a series of four different types of molecular component: adenine (A), guanine (G), thymine (T), and cytosine (C).

Genes are made up from different sequences of these building block components, and the order in which they appear in a strand of DNA is what encodes genetic information. But by precisely designing different A,G,T and C sequences, scientists have recently been able to develop new ways of folding DNA into different origami shapes, beyond the conventional double helix.

This approach has opened up new possibilities of using DNA beyond its genetic and biological purpose, turning it into a Lego-like material for building objects that are just a few billionths of a metre in diameter (nanoscale). DNA-based materials are now being used for a variety of applications, ranging from templates for electronic nano-devices, to ways of precisely carrying drugs to diseased cells.

He highlights some Canadian work,

Designing electronic devices that are just nanometres in size opens up all sorts of possible applications but makes it harder to spot defects. As a way of dealing with this, researchers at the University of Montreal have used DNA to create ultrasensitive nanoscale thermometers that could help find minuscule hotspots in nanodevices (which would indicate a defect). They could also be used to monitor the temperature inside living cells.

The nanothermometers are made using loops of DNA that act as switches, folding or unfolding in response to temperature changes. This movement can be detected by attaching optical probes to the DNA. The researchers now want to build these nanothermometers into larger DNA devices that can work inside the human body.

He also mentions the nanobots that will heal your body (according to many works of fiction),

Researchers at Harvard Medical School have used DNA to design and build a nanosized robot that acts as a drug delivery vehicle to target specific cells. The nanorobot comes in the form of an open barrel made of DNA, whose two halves are connected by a hinge held shut by special DNA handles. These handles can recognise combinations of specific proteins present on the surface of cells, including ones associated with diseases.

When the robot comes into contact with the right cells, it opens the container and delivers its cargo. When applied to a mixture of healthy and cancerous human blood cells, these robots showed the ability to target and kill half of the cancer cells, while the healthy cells were left unharmed.

Palma is describing a very exciting development and there are many teams worldwide working on ways to make drugs more effective and less side effect-ridden. However there does seem to be a bit of a problem with targeted drug delivery as noted in my April 27, 2016 posting,

According to an April 27, 2016 news item on Nanowerk researchers at the University of Toronto (Canada) along with their collaborators in the US (Harvard Medical School) and Japan (University of Tokyo) have determined that less than 1% of nanoparticle-based drugs reach their intended destination …

Less than 1%? Admittedly, nanoparticles are not the same as nanobots but the problem is in the delivery, from my April 27, 2016 posting,

… the authors argue that, in order to increase nanoparticle delivery efficiency, a systematic and coordinated long-term strategy is necessary. To build a strong foundation for the field of cancer nanomedicine, researchers will need to understand a lot more about the interactions between nanoparticles and the body’s various organs than they do today. …

I imagine nanobots will suffer a similar fate since the actual delivery mechanism to a targeted cell is still a mystery.

I quite enjoyed Palma’s essay and appreciated the links he provided. My only proviso, keep a salt shaker nearby. That rosy future is going take a while to get here.

What is Dr. Who’s sonic screwdriver?

Dr. Who, a British Broadcasting Corporation science fiction television programme, has an enormous following worldwide. I am not one of those followers as you might have guessed from the headline, which means I didn’t understand this pop culture reference, from the April 23, 2012 news item on Nanowerk,

For fans of the hit series Doctor Who, the Sonic Screwdriver will be a familiar device. But now an international team of EU-funded researchers has taken equipment designed for magnetic resonance imaging (MRI)-guided focused ultrasound surgery and demonstrated a real Sonic Screwdriver, lifting and spinning a free-floating 10 cm-diameter rubber disk with an ultrasound beam.

I’m going to concentrate on the project first since this EU (European Union) funded project has a somewhat confusing configuration, which I’ll try to tease apart later in this posting. From the news item,

Dr Mike MacDonald, of the Institute for Medical Science and Technology (IMSAT) in the [University of Dundee, Scotland] United Kingdom, comments: ‘This experiment not only confirms a fundamental physics theory but also demonstrates a new level of control over ultrasound beams which can also be applied to non-invasive ultrasound surgery, targeted drug delivery and ultrasonic manipulation of cells.’

The theory the team were testing had not previously been proved in a single experiment; it is valid for both sound and light, and is used in fields like quantum communications and biophotonics. The theory states that the ratio of angular momentum to energy in a vortex beam is equal to the ratio of the number of intertwined helices to the frequency of the beam.

Dr Christine Demore from IMSAT comments: ‘For the first time, our experimental results confirm directly the validity of this fundamental theory. Previously this ratio could only be assumed from theory as the angular momentum and power in a beam had only ever been measured independently.’

The ultrasound beam generated by the researchers resembles the ‘double-helix’ structure of DNA but with many more twisted strands, or helices. This vortex beam generates a rotating, angular component of momentum that can exert torque on an object. In the recent publication, they showed how they could generate vortex beams with many intertwined helices, using a 1 000-element ultrasound transducer array as an acoustic hologram. These beams are so powerful they can levitate and spin the 90 g-disk made of ultrasonic absorber in water.

Here’s a 30 secs. video of the ‘sonic screwdriver’,

Ray Walters in his April 20, 2012 article  for Geek.com offers a description using measurements that are more commonly used in Canada and the US for what we’re seeing in the video [I have removed a link from the following passage],

Depicted in the video above, the “Sonotweezers” [aka, sonic screwdriver] project as it’s officially known, uses an ultrasound beam that is structured like a strand of DNA. The difference being that there are many more twisted strands that can be used to bring torque to bear on objects for movement. The team has used its device to levitate and spin a 3.17 ounce, 10cm diameter rubber disk that was suspended in water.

To make this happen, the research team used a 1000-element ultrasound transducer array to create what’s called an acoustic hologram.

The project known as ‘Sonotweezers’ at the University of Dundee,  is part of a larger European Union project, Nanoporation, which is investigating drug delivery to cancer cell using MRI (magnetic resonance imaging) and guided focused ultrasound. The larger project includes a couple of Israeli teams, neither of which seem to be involved with the Sonotweezers/sonic screwdriver project. I gather some of the funding for the Sonotweezers project comes from the UK’s Engineering and Physical Sciences Ressearch Council (EPSRC). You can find out more about the Scottish team at the University of Dundee, Sonotweezers, and EPSRC in the April 19, 2012 press release on the University of Dundee website.