Category Archives: science

Of musical parodies, Despacito, and evolution

What great timing, I just found out about a musical science parody featuring evolution and biology and learned of the latest news about the study of evolution on one of the islands in the Galapagos (where Charles Darwin made some of his observations). Thanks to Stacey Johnson for her November 24, 2017 posting on the Signals blog for featuring Evo-Devo (Despacito Biology Parody), an A Capella Science music video from Tim Blais,

Now, for the latest regarding the Galapagos and evolution (from a November 24, 2017 news item on ScienceDaily),

The arrival 36 years ago of a strange bird to a remote island in the Galapagos archipelago has provided direct genetic evidence of a novel way in which new species arise.

In this week’s issue of the journal Science, researchers from Princeton University and Uppsala University in Sweden report that the newcomer belonging to one species mated with a member of another species resident on the island, giving rise to a new species that today consists of roughly 30 individuals.

The study comes from work conducted on Darwin’s finches, which live on the Galapagos Islands in the Pacific Ocean. The remote location has enabled researchers to study the evolution of biodiversity due to natural selection.

The direct observation of the origin of this new species occurred during field work carried out over the last four decades by B. Rosemary and Peter Grant, two scientists from Princeton, on the small island of Daphne Major.

A November 23, 2017 Princeton University news release on EurekAlert, which originated the news item, provides more detail,

“The novelty of this study is that we can follow the emergence of new species in the wild,” said B. Rosemary Grant, a senior research biologist, emeritus, and a senior biologist in the Department of Ecology and Evolutionary Biology. “Through our work on Daphne Major, we were able to observe the pairing up of two birds from different species and then follow what happened to see how speciation occurred.”

In 1981, a graduate student working with the Grants on Daphne Major noticed the newcomer, a male that sang an unusual song and was much larger in body and beak size than the three resident species of birds on the island.

“We didn’t see him fly in from over the sea, but we noticed him shortly after he arrived. He was so different from the other birds that we knew he did not hatch from an egg on Daphne Major,” said Peter Grant, the Class of 1877 Professor of Zoology, Emeritus, and a professor of ecology and evolutionary biology, emeritus.

The researchers took a blood sample and released the bird, which later bred with a resident medium ground finch of the species Geospiz fortis, initiating a new lineage. The Grants and their research team followed the new “Big Bird lineage” for six generations, taking blood samples for use in genetic analysis.

In the current study, researchers from Uppsala University analyzed DNA collected from the parent birds and their offspring over the years. The investigators discovered that the original male parent was a large cactus finch of the species Geospiza conirostris from Española island, which is more than 100 kilometers (about 62 miles) to the southeast in the archipelago.

The remarkable distance meant that the male finch was not able to return home to mate with a member of his own species and so chose a mate from among the three species already on Daphne Major. This reproductive isolation is considered a critical step in the development of a new species when two separate species interbreed.

The offspring were also reproductively isolated because their song, which is used to attract mates, was unusual and failed to attract females from the resident species. The offspring also differed from the resident species in beak size and shape, which is a major cue for mate choice. As a result, the offspring mated with members of their own lineage, strengthening the development of the new species.

Researchers previously assumed that the formation of a new species takes a very long time, but in the Big Bird lineage it happened in just two generations, according to observations made by the Grants in the field in combination with the genetic studies.

All 18 species of Darwin’s finches derived from a single ancestral species that colonized the Galápagos about one to two million years ago. The finches have since diversified into different species, and changes in beak shape and size have allowed different species to utilize different food sources on the Galápagos. A critical requirement for speciation to occur through hybridization of two distinct species is that the new lineage must be ecologically competitive — that is, good at competing for food and other resources with the other species — and this has been the case for the Big Bird lineage.

“It is very striking that when we compare the size and shape of the Big Bird beaks with the beak morphologies of the other three species inhabiting Daphne Major, the Big Birds occupy their own niche in the beak morphology space,” said Sangeet Lamichhaney, a postdoctoral fellow at Harvard University and the first author on the study. “Thus, the combination of gene variants contributed from the two interbreeding species in combination with natural selection led to the evolution of a beak morphology that was competitive and unique.”

The definition of a species has traditionally included the inability to produce fully fertile progeny from interbreeding species, as is the case for the horse and the donkey, for example. However, in recent years it has become clear that some closely related species, which normally avoid breeding with each other, do indeed produce offspring that can pass genes to subsequent generations. The authors of the study have previously reported that there has been a considerable amount of gene flow among species of Darwin’s finches over the last several thousands of years.

One of the most striking aspects of this study is that hybridization between two distinct species led to the development of a new lineage that after only two generations behaved as any other species of Darwin’s finches, explained Leif Andersson, a professor at Uppsala University who is also affiliated with the Swedish University of Agricultural Sciences and Texas A&M University. “A naturalist who came to Daphne Major without knowing that this lineage arose very recently would have recognized this lineage as one of the four species on the island. This clearly demonstrates the value of long-running field studies,” he said.

It is likely that new lineages like the Big Birds have originated many times during the evolution of Darwin’s finches, according to the authors. The majority of these lineages have gone extinct but some may have led to the evolution of contemporary species. “We have no indication about the long-term survival of the Big Bird lineage, but it has the potential to become a success, and it provides a beautiful example of one way in which speciation occurs,” said Andersson. “Charles Darwin would have been excited to read this paper.”

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

Rapid hybrid speciation in Darwin’s finches by Sangeet Lamichhaney, Fan Han, Matthew T. Webster, Leif Andersson, B. Rosemary Grant, Peter R. Grant. Science 23 Nov 2017: eaao4593 DOI: 10.1126/science.aao4593

This paper is behind a paywall.

Happy weekend! And for those who love their Despacito, there’s this parody featuring three Italians in a small car (thanks again to Stacey Johnson’s blog posting),

A jellyfish chat on November 28, 2017 at Café Scientifique Vancouver get together

Café Scientifique Vancouver sent me an announcement (via email) about their upcoming event,

We are pleased to announce our next café which will happen on TUESDAY,
NOVEMBER 28TH at 7:30PM in the back room of YAGGER'S DOWNTOWN (433 W
Pender).

JELLYFISH – FRIEND, FOE, OR FOOD?

Did you know that in addition to stinging swimmers, jellyfish also cause
extensive damage to fisheries and coastal power plants? As threats such
as overfishing, pollution, and climate change alter the marine
environment, recent media reports are proclaiming that jellyfish are
taking over the oceans. Should we hail to our new jellyfish overlords or
do we need to examine the evidence behind these claims? Join Café
Scientifique on Nov. 28, 2017 to learn everything you ever wanted to
know about jellyfish, and find out if jelly burgers are coming soon to a
menu near you.

Our speaker for the evening will be DR. LUCAS BROTZ, a Postdoctoral
Research Fellow with the Sea Around Us at UBC’s Institute for the
Oceans and Fisheries. Lucas has been studying jellyfish for more than a
decade, and has been called “Canada’s foremost jellyfish
researcher” by CBC Nature of Things host Dr. David Suzuki. Lucas has
participated in numerous international scientific collaborations, and
his research has been featured in more than 100 media outlets including
Nature News, The Washington Post, and The New York Times. He recently
received the Michael A. Bigg award for highly significant student
research as part of the Coastal Ocean Awards at the Vancouver Aquarium.

We hope to see you there!

You can find out more about Lucas Brotz here and about Sea Around Us here.

For anyone who’s curious about the jellyfish ‘issue’, there’s a November 8, 2017 Norwegian University of Science and Technology press release on AlphaGallileo or on EurekAlert, which provides insight into the problems and the possibilities,

Jellyfish could be a resource in producing microplastic filters, fertilizer or fish feed. A new 6 million euro project called GoJelly, funded by the EU and coordinated by the GEOMAR Helmholtz Centre for Ocean Research, Germany and including partners at the Norwegian University of Science and Technology (NTNNU) and SINTEF [headquartered in Trondheim, Norway, is the largest independent research organisation in Scandinavia; more about SINTEF in its Wikipedia entry], hopes to turn jellyfish from a nuisance into a useful product.

Global climate change and the human impact on marine ecosystems has led to dramatic decreases in the number of fish in the ocean. It has also had an unforseen side effect: because overfishing decreases the numbers of jellyfish competitors, their blooms are on the rise.

The GoJelly project, coordinated by the GEOMAR Helmholtz Centre for Ocean Research, Germany, would like to transform problematic jellyfish into a resource that can be used to produce microplastic filter, fertilizer or fish feed. The EU has just approved funding of EUR 6 million over 4 years to support the project through its Horizon 2020 programme.

Rising water temperatures, ocean acidification and overfishing seem to favour jellyfish blooms. More and more often, they appear in huge numbers that have already destroyed entire fish farms on European coasts and blocked cooling systems of power stations near the coast. A number of jellyfish species are poisonous, while some tropical species are even among the most toxic animals on earth.

“In Europe alone, the imported American comb jelly has a biomass of one billion tons. While we tend to ignore the jellyfish there must be other solutions,” says Jamileh Javidpour of GEOMAR, initiator and coordinator of the GoJelly project, which is a consortium of 15 scientific institutions from eight countries led by the GEOMAR Helmholtz Centre for Ocean Research in Kiel.

The project will first entail exploring the life cycle of a number of jellyfish species. A lack of knowledge about life cycles makes it is almost impossible to predict when and why a large jellyfish bloom will occur. “This is what we want to change so that large jellyfish swarms can be caught before they reach the coasts,” says Javidpour.

At the same time, the project partners will also try to answer the question of what to do with jellyfish once they have been caught. One idea is to use the jellyfish to battle another, man-made threat.

“Studies have shown that mucus of jellyfish can bind microplastic. Therefore, we want to test whether biofilters can be produced from jellyfish. These biofilters could then be used in sewage treatment plants or in factories where microplastic is produced,” the GoJelly researchers say.

Jellyfish can also be used as fertilizers for agriculture or as aquaculture feed. “Fish in fish farms are currently fed with captured wild fish, which does not reduce the problem of overfishing, but increases it. Jellyfish as feed would be much more sustainable and would protect natural fish stocks,” says the GoJelly team.

Another option is using jellyfish as food for humans. “In some cultures, jellyfish are already on the menu. As long as the end product is no longer slimy, it could also gain greater general acceptance,” said Javidpour. Finally yet importantly, jellyfish contain collagen, a substance very much sought after in the cosmetics industry.

Project partners from the Norwegian University of Science and Technology, led by Nicole Aberle-Malzahn, and SINTEF Ocean, led by Rachel Tiller, will analyse how abiotic (hydrography, temperature), biotic (abundance, biomass, ecology, reproduction) and biochemical parameters (stoichiometry, food quality) affect the initiation of jellyfish blooms.

Based on a comprehensive analysis of triggering mechanisms, origin of seed populations and ecological modelling, the researchers hope to be able to make more reliable predictions on jellyfish bloom formation of specific taxa in the GoJelly target areas. This knowledge will allow sustainable harvesting of jellyfish communities from various Northern and Southern European populations.

This harvest will provide a marine biomass of unknown potential that will be explored by researchers at SINTEF Ocean, among others, to explore the possible ways to use the material.

A team from SINTEF Ocean’s strategic program Clean Ocean will also work with European colleagues on developing a filter from the mucus of the jellyfish that will catch microplastics from household products (which have their source in fleece sweaters, breakdown of plastic products or from cosmetics, for example) and prevent these from entering the marine ecosystem.

Finally, SINTEF Ocean will examine the socio-ecological system and games, where they will explore the potentials of an emerging international management regime for a global effort to mitigate the negative effects of microplastics in the oceans.

“Jellyfish can be used for many purposes. We see this as an opportunity to use the potential of the huge biomass drifting right in front of our front door,” Javidpour said.

You can find out more about GoJelly on their Twitter account.

Colour: an art/science open call for submissions

The submission deadline for this open ‘art/sci’ call is January 17, 2018 (from a November 29, 2017 Art/Science Salon announcement; received via email),

COLOUR: WHAT DO YOU MEAN BY THAT?

An exhibition exploring colour as a phenomenon that crosses the
boundaries of the arts and sciences.

Artists and designers revel in, and seek to understand, the visceral,
physical and ephemeral qualities of colour. Sir Isaac Newton began his
scientific experiments with light and prisms as ‘a very pleasing
divertisement, to view the vivid and intense colours produced
thereby’. His investigations ultimately changed our understanding of
the fundamental nature of light and colour. Johann Wolfgang von Goethe
challenged Newton’s understanding as limited, and introduced colour as
an emotionally charged phenomenon. He proposed an alternative
methodological approach based on ’empathic observation’.

COLOUR: WHAT DO YOU MEAN BY THAT? calls for art inspired by, or
questioning, scientific concepts about colour: art that encapsulates
colour knowledge from multiple perspectives.

We are not looking for the merely colourful – rather we look for work
engaging ideas, theories and aspects of colour – both conceptual and
physical – that highlight colour knowledge as richly meaningful across
diverse ways of knowing.

To this end, we invite proposals that present, consider, or respond to
research about colour and colour phenomena. Work may relate to:

* physical colour phenomena, e.g. light sources, interference,
iridescence, scattering, reflection
* chemistry of dyes & pigments
* colour vision / colour perception
* colour renderings of energies outside of the visible spectrum
(ultraviolet, infra-red, etc.)
* colour meanings (cultural, scientific, philosophical)
* cross-sensory colour sensations and understandings
* colour theories
* colour histories

SHOW DATES: MARCH 7-25, 2018.

COLOUR: WHAT DO YOU MEAN BY THAT? is jointly sponsored by Propeller
Gallery and the Colour Research Society of Canada [1]

SHOW LOCATION: Propeller Gallery, 30 Abell St, Toronto, ON, Canada

SUBMISSION DEADLINE: Wed Jan 17, 2018, 11:59pm [which timezone?]

SUBMIT YOUR APPLICATION HERE:
HTTP://HUUTAART.COM/OPENCALLS/COLOUR-WHAT-DO-YOU-MEAN-BY-THAT [2]

SUBMISSION REQUIREMENTS:

You may submit more than one submission, provided the concept is
substantially different for each piece, with a maximum of three
submissions. With each submission, please provide at least one image
(maximum 4 images) relevant to your proposal.

Details about yourself and your work including:

* Name, address, email, phone number, with a brief bio.
* Title of Work, Year, Medium, Size and Value in $CAD.
* A brief written statement about the work, including how the work
deals with, or draws its inspiration from, diverse ways of knowing about
colour (max. 150 words).
* NON-REFUNDABLE SUBMISSION FEE OF $50.00 PER SUBMISSION.

CURATORIAL TEAM MEMBERS: Doreen Balabanoff, Robin Kingsburgh, Janet
Read, Judith Tinkl

ADDITIONAL INFORMATION:

* 25% commission collected on any work sold as a result of this
exhibition.
* For more information visit our website: www.propellerctr.com [3]
* If selected, you agree to allow us to use your submission material,
without compensation, in any potential catalogue/publication for this
exhibition.
* Selected artists will be contacted by email not later than January
31. Delivery instructions will be given at that time.
* An event at the exhibition, related to International Colour Day,
March 21st, will be announced in early 2018.

Please direct inquiries to:

Nathan Heuvingh
Gallery Director
gallery@propellerctr.com
1-416-504-7142

Facebook: https://www.facebook.com/PropellerTO/ [4]
Twitter: @PropellerTO
Instagram: @propellerygallery_to

The co-sponsor for this upcoming exhibition, the Colour Research Society of Canada has a website that proved to be a delightful surprise.

Getting back to COLOUR: WHAT DO YOU MEAN BY THAT?, good luck with your submission, and should it be accepted, good luck with sales!

World heritage music stored in DNA

It seems a Swiss team from the École Polytechnique de Lausanne (EPFL) have collaborated with American companies Twist Bioscience and Microsoft, as well as, the University of Washington (state) to preserve two iconic jazz pieces on DNA (deoxyribonucleic acid) according to a Sept. 29, 2017 news item on phys.org,,

Thanks to an innovative technology for encoding data in DNA strands, two items of world heritage – songs recorded at the Montreux Jazz Festival [held in Switzerland] and digitized by EPFL – have been safeguarded for eternity. This marks the first time that cultural artifacts granted UNESCO heritage status have been saved in such a manner, ensuring they are preserved for thousands of years. The method was developed by US company Twist Bioscience and is being unveiled today in a demonstrator created at the EPFL+ECAL Lab.

“Tutu” by Miles Davis and “Smoke on the Water” by Deep Purple have already made their mark on music history. Now they have entered the annals of science, for eternity. Recordings of these two legendary songs were digitized by the Ecole Polytechnique Fédérale de Lausanne (EPFL) as part of the Montreux Jazz Digital Project, and they are the first to be stored in the form of a DNA sequence that can be subsequently decoded and listened to without any reduction in quality.

A Sept. 29, 2017 EPFL press release by Emmanuel Barraud, which originated the news item, provides more details,

This feat was achieved by US company Twist Bioscience working in association with Microsoft Research and the University of Washington. The pioneering technology is actually based on a mechanism that has been at work on Earth for billions of years: storing information in the form of DNA strands. This fundamental process is what has allowed all living species, plants and animals alike, to live on from generation to generation.

The entire world wide web in a shoe box

All electronic data storage involves encoding data in binary format – a series of zeros and ones – and then recording it on a physical medium. DNA works in a similar way, but is composed of long strands of series of four nucleotides (A, T, C and G) that make up a “code.” While the basic principle may be the same, the two methods differ greatly in terms of efficiency: if all the information currently on the internet was stored in the form of DNA, it would fit in a shoe box!

Recent advances in biotechnology now make it possible for humans to do what Mother Nature has always done. Today’s scientists can create artificial DNA strands, “record” any kind of genetic code on them and then analyze them using a sequencer to reconstruct the original data. What’s more, DNA is extraordinarily stable, as evidenced by prehistoric fragments that have been preserved in amber. Artificial strands created by scientists and carefully encapsulated should likewise last for millennia.

To help demonstrate the feasibility of this new method, EPFL’s Metamedia Center provided recordings of two famous songs played at the Montreux Jazz Festival: “Tutu” by Miles Davis, and “Smoke on the Water” by Deep Purple. Twist Bioscience and its research partners encoded the recordings, transformed them into DNA strands and then sequenced and decoded them and played them again – without any reduction in quality.

The amount of artificial DNA strands needed to record the two songs is invisible to the naked eye, and the amount needed to record all 50 years of the Festival’s archives, which have been included in UNESCO’s [United Nations Educational, Scientific and Cultural Organization] Memory of the World Register, would be equal in size to a grain of sand. “Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”

A new concept of time

At EPFL’s first-ever ArtTech forum, attendees got to hear the two songs played after being stored in DNA, using a demonstrator developed at the EPFL+ECAL Lab. The system shows that being able to store data for thousands of years is a revolutionary breakthrough that can completely change our relationship with data, memory and time. “For us, it means looking into radically new ways of interacting with cultural heritage that can potentially cut across civilizations,” says Nicolas Henchoz, head of the EPFL+ECAL Lab.

Quincy Jones, a longstanding Festival supporter, is particularly enthusiastic about this technological breakthrough: “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access… So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and their partners are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA! I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.

A Sept. 29, 2017 Twist Bioscience news release is repetitive in some ways but interesting nonetheless,

Twist Bioscience, a company accelerating science and innovation through rapid, high-quality DNA synthesis, today announced that, working with Microsoft and University of Washington researchers, they have successfully stored archival-quality audio recordings of two important music performances from the archives of the world-renowned Montreux Jazz Festival.
These selections are encoded and stored in nature’s preferred storage medium, DNA, for the first time. These tiny specks of DNA will preserve a part of UNESCO’s Memory of the World Archive, where valuable cultural heritage collections are recorded. This is the first time DNA has been used as a long-term archival-quality storage medium.
Quincy Jones, world-renowned Entertainment Executive, Music Composer and Arranger, Musician and Music Producer said, “With advancements in nanotechnology, I believe we can expect to see people living prolonged lives, and with that, we can also expect to see more developments in the enhancement of how we live. For me, life is all about learning where you came from in order to get where you want to go, but in order to do so, you need access to history! And with the unreliability of how archives are often stored, I sometimes worry that our future generations will be left without such access…So, it absolutely makes my soul smile to know that EPFL, Twist Bioscience and others are coming together to preserve the beauty and history of the Montreux Jazz Festival for our future generations, on DNA!…I’ve been a part of this festival for decades and it truly is a magnificent representation of what happens when different cultures unite for the sake of music. Absolute magic. And I’m proud to know that the memory of this special place will never be lost.”
“Our partnership with EPFL in digitizing our archives aims not only at their positive exploration, but also at their preservation for the next generations,” says Thierry Amsallem, president of the Claude Nobs Foundation. “By taking part in this pioneering experiment which writes the songs into DNA strands, we can be certain that they will be saved on a medium that will never become obsolete!”
The Montreux Jazz Digital Project is a collaboration between the Claude Nobs Foundation, curator of the Montreux Jazz Festival audio-visual collection and the École Polytechnique Fédérale de Lausanne (EPFL) to digitize, enrich, store, show, and preserve this notable legacy created by Claude Nobs, the Festival’s founder.
In this proof-of-principle project, two quintessential music performances from the Montreux Jazz Festival – Smoke on the Water, performed by Deep Purple and Tutu, performed by Miles Davis – have been encoded onto DNA and read back with 100 percent accuracy. After being decoded, the songs were played on September 29th [2017] at the ArtTech Forum (see below) in Lausanne, Switzerland. Smoke on the Water was selected as a tribute to Claude Nobs, the Montreux Jazz Festival’s founder. The song memorializes a fire and Funky Claude’s rescue efforts at the Casino Barrière de Montreux during a Frank Zappa concert promoted by Claude Nobs. Miles Davis’ Tutu was selected for the role he played in music history and the Montreux Jazz Festival’s success. Miles Davis died in 1991.
“We archived two magical musical pieces on DNA of this historic collection, equating to 140MB of stored data in DNA,” said Karin Strauss, Ph.D., a Senior Researcher at Microsoft, and one of the project’s leaders.  “The amount of DNA used to store these songs is much smaller than one grain of sand. Amazingly, storing the entire six petabyte Montreux Jazz Festival’s collection would result in DNA smaller than one grain of rice.”
Luis Ceze, Ph.D., a professor in the Paul G. Allen School of Computer Science & Engineering at the University of Washington, said, “DNA, nature’s preferred information storage medium, is an ideal fit for digital archives because of its durability, density and eternal relevance. Storing items from the Montreux Jazz Festival is a perfect way to show how fast DNA digital data storage is becoming real.”
Nature’s Preferred Storage Medium
Nature selected DNA as its hard drive billions of years ago to encode all the genetic instructions necessary for life. These instructions include all the information necessary for survival. DNA molecules encode information with sequences of discrete units. In computers, these discrete units are the 0s and 1s of “binary code,” whereas in DNA molecules, the units are the four distinct nucleotide bases: adenine (A), cytosine (C), guanine (G) and thymine (T).
“DNA is a remarkably efficient molecule that can remain stable for millennia,” said Bill Peck, Ph.D., chief technology officer of Twist Bioscience.  “This is a very exciting project: we are now in an age where we can use the remarkable efficiencies of nature to archive master copies of our cultural heritage in DNA.   As we develop the economies of this process new performances can be added any time.  Unlike current storage technologies, nature’s media will not change and will remain readable through time. There will be no new technology to replace DNA, nature has already optimized the format.”
DNA: Far More Efficient Than a Computer 
Each cell within the human body contains approximately three billion base pairs of DNA. With 75 trillion cells in the human body, this equates to the storage of 150 zettabytes (1021) of information within each body. By comparison, the largest data centers can be hundreds of thousands to even millions of square feet to hold a comparable amount of stored data.
The Elegance of DNA as a Storage Medium
Like music, which can be widely varied with a finite number of notes, DNA encodes individuality with only four different letters in varied combinations. When using DNA as a storage medium, there are several advantages in addition to the universality of the format and incredible storage density. DNA can be stable for thousands of years when stored in a cool dry place and is easy to copy using polymerase chain reaction to create back-up copies of archived material. In addition, because of PCR, small data sets can be targeted and recovered quickly from a large dataset without needing to read the entire file.
How to Store Digital Data in DNA
To encode the music performances into archival storage copies in DNA, Twist Bioscience worked with Microsoft and University of Washington researchers to complete four steps: Coding, synthesis/storage, retrieval and decoding. First, the digital files were converted from the binary code using 0s and 1s into sequences of A, C, T and G. For purposes of the example, 00 represents A, 10 represents C, 01 represents G and 11 represents T. Twist Bioscience then synthesizes the DNA in short segments in the sequence order provided. The short DNA segments each contain about 12 bytes of data as well as a sequence number to indicate their place within the overall sequence. This is the process of storage. And finally, to ensure that the file is stored accurately, the sequence is read back to ensure 100 percent accuracy, and then decoded from A, C, T or G into a two-digit binary representation.
Importantly, to encapsulate and preserve encoded DNA, the collaborators are working with Professor Dr. Robert Grass of ETH Zurich. Grass has developed an innovative technology inspired by preservation of DNA within prehistoric fossils.  With this technology, digital data encoded in DNA remains preserved for millennia.
About UNESCO’s Memory of the World Register
UNESCO established the Memory of the World Register in 1992 in response to a growing awareness of the perilous state of preservation of, and access to, documentary heritage in various parts of the world.  Through its National Commissions, UNESCO prepared a list of endangered library and archive holdings and a world list of national cinematic heritage.
A range of pilot projects employing contemporary technology to reproduce original documentary heritage on other media began. These included, for example, a CD-ROM of the 13th Century Radzivill Chronicle, tracing the origins of the peoples of Europe, and Memoria de Iberoamerica, a joint newspaper microfilming project involving seven Latin American countries. These projects enhanced access to this documentary heritage and contributed to its preservation.
“We are incredibly proud to be a part of this momentous event, with the first archived songs placed into the UNESCO Memory of the World Register,” said Emily Leproust, Ph.D., CEO of Twist Bioscience.
About ArtTech
The ArtTech Foundation, created by renowned scientists and dignitaries from Crans-Montana, Switzerland, wishes to stimulate reflection and support pioneering and innovative projects beyond the known boundaries of culture and science.
Benefitting from the establishment of a favorable environment for the creation of technology companies, the Foundation aims to position itself as key promoter of ideas and innovative endeavors within a landscape of “Culture and Science” that is still being shaped.
Several initiatives, including our annual global platform launched in the spring of 2017, are helping to create a community that brings together researchers, celebrities in the world of culture and the arts, as well as investors and entrepreneurs from Switzerland and across the globe.
 
About EPFL
EPFL, one of the two Swiss Federal Institutes of Technology, based in Lausanne, is Europe’s most cosmopolitan technical university with students, professors and staff from over 120 nations. A dynamic environment, open to Switzerland and the world, EPFL is centered on its three missions: teaching, research and technology transfer. EPFL works together with an extensive network of partners including other universities and institutes of technology, developing and emerging countries, secondary schools and colleges, industry and economy, political circles and the general public, to bring about real impact for society.
About Twist Bioscience
At Twist Bioscience, our expertise is accelerating science and innovation by leveraging the power of scale. We have developed a proprietary semiconductor-based synthetic DNA manufacturing process featuring a high throughput silicon platform capable of producing synthetic biology tools, including genes, oligonucleotide pools and variant libraries. By synthesizing DNA on silicon instead of on traditional 96-well plastic plates, our platform overcomes the current inefficiencies of synthetic DNA production, and enables cost-effective, rapid, high-quality and high throughput synthetic gene production, which in turn, expedites the design, build and test cycle to enable personalized medicines, pharmaceuticals, sustainable chemical production, improved agriculture production, diagnostics and biodetection. We are also developing new technologies to address large scale data storage. For more information, please visit www.twistbioscience.com. Twist Bioscience is on Twitter. Sign up to follow our Twitter feed @TwistBioscience at https://twitter.com/TwistBioscience.

If you hadn’t read the EPFL press release first, it might have taken a minute to figure out why EPFL is being mentioned in the Twist Bioscience news release. Presumably someone was rushing to make a deadline. Ah well, I’ve seen and written worse.

I haven’t been able to find any video or audio recordings of the DNA-preserved performances but there is an informational video (originally published July 7, 2016) from Microsoft and the University of Washington describing the DNA-based technology,

I also found this description of listening to the DNA-preserved music in an Oct. 6, 2017 blog posting for the Canadian Broadcasting Corporation’s (CBC) Day 6 radio programme,

To listen to them, one must first suspend the DNA holding the songs in a solution. Next, one can use a DNA sequencer to read the letters of the bases forming the molecules. Then, algorithms can determine the digital code those letters form. From that code, comes the music.

It’s complicated but Ceze says his team performed this process without error.

You can find out more about UNESCO’s Memory of the World and its register here , more about the EPFL+ECAL Lab here, and more about Twist Bioscience here.

Science denial is not limited to the political right

These days, climate is the most likely topic to bring up charges of having anti-science views and/or ‘right wing’ thinking but according to a Sept. 19, 2017 news item on phys.org ‘left wing’ thinkers can also reject science,

In the wake of Hurricanes Harvey and Irma, many claims have been made that science denial, particularly as it relates to climate change, is primarily a problem of the political right.

But what happens when scientific conclusions challenge liberals’ attitudes on public policy issues, such as gun control, nuclear power or immigration?

A new study from social psychologists at the University of Illinois at Chicago [UIC] and published online in Social Psychological and Personality Science suggests people of all political backgrounds can be motivated to participate in science denial.

A Sept. 19, 2017 University of Illinois at Chicago news release (also on EurekAlert), which originated the news item, delves further,

UIC researchers Anthony Washburn, a graduate student in psychology, and Linda Skitka, professor of psychology, had participants indicate their political orientation, evaluate fabricated scientific results, and, based on the data, decide what the studies concluded.

Once they were informed of the correct interpretations of the data, participants were then asked to rate how much they agreed with, found knowledgeable, and trusted the researchers’ correct interpretation.

“Not only were both sides equally likely to seek out attitude confirming scientific conclusions, both were also willing to work harder and longer when doing so got them to a conclusion that fit with their existing attitudes,” says Washburn, the lead author of the study. “And when the correct interpretation of the results did not confirm participants’ attitudes, they were more likely to view the researchers involved with the study as less trustworthy, less knowledgeable, and disagreed with their conclusions more.”

These effects were constant no matter what issue was under consideration, which included six social issues — immigration, gun control, climate change, health care reform, nuclear power and same sex marriage — and one control issue — skin rash treatment.

Rather than strictly a conservative phenomenon, science denial may be a result of a more basic desire of people wanting to see the world in ways that fit with their personal preferences, political or otherwise, according to the researchers.

The results also shed light on science denial in public discourse, Skitka added.

“Before assuming that one group of people or another are anti-science because they disagree with one scientific conclusion, we should make an effort to consider different motivations that are likely at play, which might have nothing to do with science per se,” she said.

This research fits into a larger body of work where researchers are examining what we believe and how we use or dismiss science and fact to support our positions. Chris Mooney’s article “The Science of Why We Don’t Believe Science” for the May/June 2011 issue of Mother Jones examines the issue although it is strongly weighted with examples of research into intransigent opinion associated with right wing politics (climate change, etc.).

Getting back to more recent work, here’s link to and a citation for the paper,

Science Denial Across the Political Divide; Liberals and Conservatives Are Similarly Motivated to Deny Attitude-Inconsistent Science by Anthony N. Washburn, Linda J. Skitka. Social Psychological and Personality Science DOI: https://doi.org/10.1177/1948550617731500 First Published September 14, 2017

This paper is behind a paywall.

‘Nano-hashtags’ for Majorana particles?

The ‘nano-hashtags’ are in fact (assuming a minor leap of imagination) nanowires that resemble hashtags.

Scanning electron microscope image of the device wherein clearly a ‘hashtag’ is formed. Credit: Eindhoven University of Technology

An August 23, 2017 news item on ScienceDaily makes the announcement,

In Nature, an international team of researchers from Eindhoven University of Technology [Netherlands], Delft University of Technology [Netherlands] and the University of California — Santa Barbara presents an advanced quantum chip that will be able to provide definitive proof of the mysterious Majorana particles. These particles, first demonstrated in 2012, are their own antiparticle at one and the same time. The chip, which comprises ultrathin networks of nanowires in the shape of ‘hashtags’, has all the qualities to allow Majorana particles to exchange places. This feature is regarded as the smoking gun for proving their existence and is a crucial step towards their use as a building block for future quantum computers.

An August 23, 2017 Eindhoven University press release (also on EurekAlert), which originated the news item, provides some context and information about the work,

In 2012 it was big news: researchers from Delft University of Technology and Eindhoven University of Technology presented the first experimental signatures for the existence of the Majorana fermion. This particle had been predicted in 1937 by the Italian physicist Ettore Majorana and has the distinctive property of also being its own anti-particle. The Majorana particles emerge at the ends of a semiconductor wire, when in contact with a superconductor material.

Smoking gun

While the discovered particles may have properties typical to Majoranas, the most exciting proof could be obtained by allowing two Majorana particles to exchange places, or ‘braid’ as it is scientifically known. “That’s the smoking gun,” suggests Erik Bakkers, one of the researchers from Eindhoven University of Technology. “The behavior we then see could be the most conclusive evidence yet of Majoranas.”

Crossroads

In the Nature paper that is published today [August 23, 2017], Bakkers and his colleagues present a new device that should be able to show this exchanging of Majoranas. In the original experiment in 2012 two Majorana particles were found in a single wire but they were not able to pass each other without immediately destroying the other. Thus the researchers quite literally had to create space. In the presented experiment they formed intersections using the same kinds of nanowire so that four of these intersections form a ‘hashtag’, #, and thus create a closed circuit along which Majoranas are able to move.

Etch and grow

The researchers built their hashtag device starting from scratch. The nanowires are grown from a specially etched substrate such that they form exactly the desired network which they then expose to a stream of aluminium particles, creating layers of aluminium, a superconductor, on specific spots on the wires – the contacts where the Majorana particles emerge. Places that lie ‘in the shadow’ of other wires stay uncovered.

Leap in quality

The entire process happens in a vacuum and at ultra-cold temperature (around -273 degree Celsius). “This ensures very clean, pure contacts,” says Bakkers, “and enables us to make a considerable leap in the quality of this kind of quantum device.” The measurements demonstrate for a number of electronic and magnetic properties that all the ingredients are present for the Majoranas to braid.

Quantum computers

If the researchers succeed in enabling the Majorana particles to braid, they will at once have killed two birds with one stone. Given their robustness, Majoranas are regarded as the ideal building block for future quantum computers that will be able to perform many calculations simultaneously and thus many times faster than current computers. The braiding of two Majorana particles could form the basis for a qubit, the calculation unit of these computers.

Travel around the world

An interesting detail is that the samples have traveled around the world during the fabrication, combining unique and synergetic activities of each research institution. It started in Delft with patterning and etching the substrate, then to Eindhoven for nanowire growth and to Santa Barbara for aluminium contact formation. Finally back to Delft via Eindhoven for the measurements.

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

Epitaxy of advanced nanowire quantum devices by Sasa Gazibegovic, Diana Car, Hao Zhang, Stijn C. Balk, John A. Logan, Michiel W. A. de Moor, Maja C. Cassidy, Rudi Schmits, Di Xu, Guanzhong Wang, Peter Krogstrup, Roy L. M. Op het Veld, Kun Zuo, Yoram Vos, Jie Shen, Daniël Bouman, Borzoyeh Shojaei, Daniel Pennachio, Joon Sue Lee, Petrus J. van Veldhoven, Sebastian Koelling, Marcel A. Verheijen, Leo P. Kouwenhoven, Chris J. Palmstrøm, & Erik P. A. M. Bakkers. Nature 548, 434–438 (24 August 2017) doi:10.1038/nature23468 Published online 23 August 2017

This paper is behind a paywall.

Dexter Johnson has some additional insight (interview with one of the researchers) in an Aug. 29, 2017 posting on his Nanoclast blog (on the IEEE [institute of Electrical and Electronics Engineers] website).

Cosmopolitanism and the Local in Science and Nature (a three year Canadian project nearing its end date)

Working on a grant from Canada’s Social Sciences and Humanities Research Council (SSHRC), the  Cosmopolitanism and the Local in Science and Nature project has been establishing a ‘cosmopolitanism’ research network that critiques the eurocentric approach so beloved of Canadian academics and has set up nodes across Canada and in India and Southeast Asia.

I first wrote about the project in a Dec. 12, 2014 posting which also featured a job listing. It seems I was there for the beginning and now for the end. For one of the project’s blog postings in its final months, they’re profiling one of their researchers (Dr. Letitia Meynell, Sept. 6, 2017 posting),

1. What is your current place of research?

I am an associate professor in philosophy at Dalhousie University, cross appointed with gender and women studies.

2. Could you give us some details about your education background?

My 1st degree was in Theater, which I did at York University. I did, however, minor in Philosophy and I have always had a particular interest in philosophy of science. So, my minor was perhaps a little anomalous, comprising courses on philosophy of physics, philosophy of nature, and the philosophy of Karl Popper along with courses on aesthetics and existentialism. After taking a few more courses in philosophy at the University of Calgary, I enrolled there for a Master’s degree, writing a thesis on conceptualization, with a view to its role in aesthetics and epistemology. From there I moved to the University of Western Ontario where I brought these three interests together, writing a thesis on the epistemology of pictures in science. Throughout these studies I maintained a keen interest in feminist philosophy, especially the politics of knowledge, and I have always seen my work on pictures in science as fitting into broader feminist commitments.

3. What projects are you currently working on and what are some projects you’ve worked on in the past?

4. What’s one thing you particularly enjoy about working in your field?

5. How do you relate your work to the broader topic of ‘cosmopolitanism and the local’?

As feminist philosophers have long realized, having perspectives on a topic that are quite different to your own is incredibly powerful for critically assessing both your own views and those of others. So, for instance, if you want to address the exploitation of nonhuman animals in our society it is incredibly powerful to consider how people from, say, South Asian traditions have thought about the differences, similarities, and relationships between humans and other animals. Keeping non-western perspectives in mind, even as one works in a western philosophical tradition, helps one to be both more rigorous in one’s analyses and less dogmatic. Rigor and critical openness are, in my opinion, central virtues of philosophy and, indeed, science.

Dr. Maynell will be speaking at the ‘Bridging the Gap: Scientific Imagination Meets Aesthetic Imagination‘ conference Oct. 5-6, 2017 at the London School of Economics,

On 5–6 October, this 2-day conference aims to connect work on artistic and scientific imagination, and to advance our understanding of the epistemic and heuristic roles that imagination can play.

Why, how, and when do scientists imagine, and what epistemological roles does the imagination play in scientific progress? Over the past few years, many philosophical accounts have emerged that are relevant to these questions. Roman Frigg, Arnon Levy, and Adam Toon have developed theories of scientific models that place imagination at the heart of modelling practice. And James R. Brown, Tamar Gendler, James McAllister, Letitia Meynell, and Nancy Nersessian have developed theories that recognize the indispensable role of the imagination in the performance of thought experiments. On the other hand, philosophers like Michael Weisberg dismiss imagination-based views of scientific modelling as mere “folk ontology”, and John D. Norton seems to claim that thought experiments are arguments whose imaginary components are epistemologically irrelevant.

In this conference we turn to aesthetics for help in addressing issues concerning scientific imagination-use. Aesthetics is said to have begun in 1717 with an essay called “The Pleasures of the Imagination” by Joseph Addison, and ever since imagination has been what Michael Polyani called “the cornerstone of aesthetic theory”. In recent years Kendall Walton has fruitfully explored the fundamental relevance of imagination for understanding literary, visual and auditory fictions. And many others have been inspired to do the same, including Greg Currie, David Davies, Peter Lamarque, Stein Olsen, and Kathleen Stock.

This conference aims to connect work on artistic and scientific imagination, and to advance our understanding of the epistemic and heuristic roles that imagination can play. Specific topics may include:

  • What kinds of imagination are involved in science?
  • What is the relation between scientific imagination and aesthetic imagination?
  • What are the structure and limits of knowledge and understanding acquired through imagination?
  • From a methodological point of view, how can aesthetic considerations about imagination play a role in philosophical accounts of scientific reasoning?
  • What can considerations about scientific imagination contribute to our understanding of aesthetic imagination?

The conference will include eight invited talks and four contributed papers. Two of the four slots for contributed papers are being reserved for graduate students, each of whom will receive a travel bursary of £100.

Invited speakers

Margherita Arcangeli (Humboldt University, Berlin)

Andrej Bicanski (Institute of Cognitive Neuroscience, University College London)

Gregory Currie (University of York)

Jim Faeder (University of Pittsburgh School of Medicine)

Tim de Mey (Erasmus University of Rotterdam)

Laetitia Meynell (Dalhousie University, Canada)

Adam Toon (University of Exeter)

Margot Strohminger (Humboldt University, Berlin)

This event is organised by LSE’s Centre for Philosophy of Natural and Social Science and it is co-sponsored by the British Society of Aesthetics, the Mind Association, the Aristotelian Society and the Marie Skłodowska-Curie grant agreement No 654034.

I wonder if they’ll be rubbing shoulders with Angelina Jolie? She is slated to be teaching there in Fall 2017 according to a May 23, 2016 news item in the Guardian (Note: Links have been removed),

The Hollywood actor and director has been appointed a visiting professor at the London School of Economics, teaching a course on the impact of war on women.

From 2017, Jolie will join the former foreign secretary William Hague as a “professor in practice”, the university announced on Monday, as part of a new MSc course on women, peace and security, which LSE says is the first of its kind in the world.

The course, it says, is intended to “[develop] strategies to promote gender equality and enhance women’s economic, social and political participation and security”, with visiting professors playing an active part in giving lectures, participating in workshops and undertaking their own research.

Getting back to ‘Cosmopolitanism’, some of the principals organized a summer 2017 event (from a Sept. 6, 2017 posting titled: Summer Events – 25th International Congress of History of Science and Technology),

CosmoLocal partners Lesley Cormack (University of Alberta, Canada), Gordon McOuat (University of King’s College, Halifax, Canada), and Dhruv Raina (Jawaharlal Nehru University, India) organized a symposium “Cosmopolitanism and the Local in Science and Nature” as part of the 25th International Congress of History of Science and Technology.  The conference was held July 23-29, 2017, in Rio de Janeiro, Brazil.  The abstract of the CosmoLocal symposium is below, and a pdf version can be found here.

Science, and its associated technologies, is typically viewed as “universal”. At the same time we were also assured that science can trace its genealogy to Europe in a period of rising European intellectual and imperial global force, ‘going outwards’ towards the periphery. As such, it is strikingly parochial. In a kind of sad irony, the ‘subaltern’ was left to retell that tale as one of centre-universalism dominating a traditionalist periphery. Self-described ‘modernity’ and ‘the west’ (two intertwined concepts of recent and mutually self-supporting origin) have erased much of the local engagement and as such represent science as emerging sui generis, moving in one direction. This story is now being challenged within sociology, political theory and history.

… Significantly, scholars who study the history of science in Asia and India have been examining different trajectories for the origin and meaning of science. It is now time for a dialogue between these approaches. Grounding the dialogue is the notion of a “cosmopolitical” science. “Cosmopolitics” is a term borrowed from Kant’s notion of perpetual peace and modern civil society, imagining shared political, moral and economic spaces within which trade, politics and reason get conducted.  …

The abstract is a little ‘high falutin’ but I’m glad to see more efforts being made in  Canada to understand science and its history as a global affair.

Simon Fraser University (Vancouver, Canada) and its president’s (Andrew Petter) dream colloquium: women in technology

I’m a little late with this event news (sadly,. I only received the information yesterday, Sept. 20, 2017) but even with two event dates already past (happily, videos for the two events have been posted), there are still several “Women in Technology” events to attend or view live according to the Simon Fraser University (SFU) President’s Dream Colloquium: Women in Technology; Attaining, Retaining, and Promoting Diverse Talent’s webpage text by Wan Yee Lok,

Women in Technology: Attracting, Retaining and Promoting Diverse Talent is a seven-part public [emphasis mine] lecture series beginning on Sept. 13. Key experts from around the world will identify challenges to gender equity and discover solutions for improving recruitment, retention and leadership options for women.

Diversity and inclusion are critical to high-tech corporate success. Yet statistics reveal that less than 25 per cent of those working in the science, technology, engineering and math sectors (STEM) are women, and that they earn seven-and-a-half per cent less than men.

“There is a crucial need to achieve gender equality in the tech sector, especially at a time when it is growing faster than ever,” says colloquium organizer Lesley Shannon, an SFU engineering science professor. She holds the Natural Sciences and Engineering Research Council (NSERC) Chair for Women in Science and Engineering for the B.C. and Yukon region.

“We hope the colloquium will help people engage in a multidisciplinary dialogue about the value of creating more space in technology for women and other under-represented groups.”

Six of the lectures are free, except for Cathy O’Neil’s lecture on Oct. 26.

The President’s Dream Colloquium schedule is as follows:

Sept. 13: SFU KEY presents: We the Data
Juliette Powell, founder, Turing AI and WeTheData.org, author of 33 Million People in the Room

Sept. 14: Diversity 101: The Case for Diversity in Technology
Maria Klawe, president, Harvey Mudd College

Sept. 21: Women in Media and Advertising
Shari Graydon, catalyst, Informed Opinions

Oct. 12: Social Psychological Phenomena
Steven Spencer, the Robert K. and Dale J. Weary Chair in Social Psychology, Ohio State University

Oct. 26: Gender and Bias in Algorithmic Design
Cathy O’Neil, author, Weapons of Math Destruction [tickets are $5 for students; $15 for the rest of us; go here to buy tickets, click on green button in the upper right, below the banner; the event will be held at SFU’s Harbour Centre Vancouver location]

Nov 9: Gendered Language
Danielle Gaucher, associate professor, Department of Psychology, University of Winnipeg

Nov. 23: Women as Leaders and Innovators
Jo Miller, founder, Be Leaderly

Lectures will be webcast live and available on the President’s Dream Colloquium website, www.sfu.ca/womenintech.

SFU engineering science professor Lesley Shannon is the colloquium organizer as well as the Natural Sciences and Engineering Research Council (NSERC) Chair for Women in Science and Engineering for the B.C. and Yukon region.

 

As a part of the colloquium, students can enroll in a graduate course covering a broad range of topics related to diversity in the technology sector. Shannon says the course will focus on women and their role in technology as well as issues that affect other under‐represented groups.

“I hope the course will establish a foundation for future managers, supervisors, sponsors, mentors and others wanting to pursue leadership roles to work towards creating a level playing field in technology and other industries,” says Shannon.

The colloquium course (SAR 897) is still accepting students. Visit go.sfu.ca to enroll.

A reminder after the last few paragraphs of the event text, you don’t actually have to be a student to attend the lectures although for anyone who doesn’t want to make the trek up the hill (SFU is located on a hill in Burnaby, BC) for the majority of the events, there is the livestream video. For those who can’t make the scheduled times, given that both the Sept. 13 and Sept. 14, 2017 event videos have been posted, they are being pretty quick about uploading the videos afterwards.

I have mentioned Cathy O’Neil here a couple of times, more substantively in a Feb. 28, 2017 posting about a major’ big data’ collaboration between the province of BC and the state of Washington (for Cathy O’Neil, scroll down to the subsection titled: Algorithms and big data) and briefly at the end in a May 24, 2017 posting that was chiefly concerned with bias in algorithms.