Category Archives: science

Online art/science exhibit on stem cells and Canadians, Dr. Jim Till and Dr. Ernest McCulloch

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Before getting to the exhibit, here’s some background information from Stacey Johnson’s July 22, 2016 posting on the Signals blog (Note: Links have been removed),

You would be hard-pressed to find a Canadian stem cell scientist who doesn’t know that Drs. Jim Till and Ernest McCulloch advanced medical research across the globe with their discovery, in 1961, of blood stem cells at Toronto’s Princess Margaret Hospital, today the Princess Margaret Cancer Centre.

Recently, a group of artists, doctors, scientists and educators launched an art exhibit based on Till and McCulloch. The group, NASCENT Art Science Collective, created portraits of the two men, produced drawings and designed banners to honour these pioneers and their ground-breaking work.

You can find the show, The Protean SELF here. Before clicking on the link I encourage you to read Johnson’s piece in its entirety. Whether you choose to read it further or not, I highly (!) recommend that you scroll down the exhibit page or click on Interpretive Guide for Museum of Health Care before when viewing the images and text otherwise it will seem a hodgepodge. The guide was for the real life exhibit, which is over.

The guide won’t answer all your questions but will help greatly to contextualize the images and the text. For example,

Hanging in the main windows are two banners by Elizabeth Greisman. Elizabeth has been extending her work on stem cells, their discovery by Dr. James Till and the importance of “ah hah’ moments to the field of dance. Elizabeth has worked with the National Ballet – cross fertilization through this work has expanded her understanding of the two defining features of stem cells – the ability to regenerate and the ability to differentiate.

That description applies to this image (I believe),

Artist: Elizabeth Greisman

Artist: Elizabeth Greisman

It’s also very helpful for understanding why there’s a fair chunk text devoted to open access,

On entering the museum, you will find a banner with an original written piece by Dr. James Till, produced for this show. Dr. Till has become a tireless advocate for Open Access. His words speak for themselves.

Artist: Dr. James Till. Formatted by Wendy Wobeser

Artist: Dr. James Till. Formatted by Wendy Wobeser

Enjoy!

arXiv which helped kickoff the open access movement contemplates its future

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arXiv is hosted by Cornell University and lodges over a million scientific papers that are open to access by anyone. Here’s more from a July 22, 2016 news item on phys.org,

As the arXiv repository of scientific papers celebrates its 25th year as one of the scientific community’s most important means of communication, the site’s leadership is looking ahead to ensure it remains indispensable, robust and financially sustainable.

A July 21, 2016 Cornell University news release by Bill Steele, which originated the news item, provides more information about future plans and a brief history of the repository (Note: Links have been removed),

Changes and improvements are in store, many in response to suggestions received in a survey of nearly 37,000 users whose primary requests were for a more robust search engine and better facilities to share supplementary material, such as slides or code, that often accompanies scientific papers.

But even more important is to upgrade the underlying architecture of the system, much of it based on “old code,” said Oya Rieger, associate university librarian for digital scholarship and preservation services, who serves as arXiv’s program director. “We have to create a work plan to ensure that arXiv will serve for another 25 years,” she said. That will require recruiting additional programmers and finding additional sources of funding, she added.

The improvements will not change the site’s essential format or its core mission of free and open dissemination of the latest scientific research, Rieger said.

arXiv was created in 1991 by Paul Ginsparg, professor of physics and information science, when he was working at Los Alamos National Laboratory. It was then common practice for researchers to circulate “pre-prints” of their papers so that colleagues could have the advantage of knowing about their research in advance of publication in scientific journals. Ginsparg launched a service (originally running from a computer under his desk) to make the papers instantly available online.

Ginsparg brought the arXiv with him from Los Alamos when he joined the Cornell faculty in 2001. Since then, it has been managed by Cornell University Library, with Ginsparg as a member of its scientific advisory board.

In 2015, arXiv celebrated its millionth submission and saw 139 million downloads in that year alone.

Nearly 95 percent of respondents to the survey said they were satisfied with arXiv, many saying that rapid access to research results had made a difference in their careers, and applauding it as an advance in open access.

“We were amazed and heartened by the outpouring of responses representing users from a variety of countries, age groups and career stages. Their insight will help us as we refine a compelling and coherent vision for arXiv’s future,” Rieger said. “We’re continuing to explore current and emerging user needs and priorities. We hope to secure funding to revamp the service’s infrastructure and ensure that it will continue to serve as an important scientific venue for facilitating rapid dissemination of papers, which is arXiv’s core goal.”

Though some users suggested new or additional features, a majority of respondents emphasized that the clean, unencumbered nature of the site makes its use easy and efficient. “I sincerely wish academic journals could try to emulate the cleanness, convenience and user-friendly nature of the arXiv, and I hope the future of academic publishing looks more like what we’ve been able to enjoy in the arXiv,” one user wrote.

arXiv is supported by a global collective of nearly 200 libraries in 24 countries, and an ongoing grant from the Simons Foundation. In 2012, the site adopted a new funding model, in which it is collaboratively governed and supported by the research communities and institutions that benefit from it most directly.

Having a bee in my bonnet about overproduced websites (MIT [Massachusetts Institute of Technology], I’m looking at you), I can’t help but applaud this user and, of course, arXiv, “I sincerely wish academic journals could try to emulate the cleanness, convenience and user-friendly nature of the arXiv, and I hope the future of academic publishing looks more like what we’ve been able to enjoy in the arXiv, …”

For anyone interested in arXiv plans, there’s the arXiv Review Strategy here on Cornell University’s Confluence website.

Prometheus (a tiny rain frog) emerges from Ecuadorian forest

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Caption: Adult female Prometeo Rain Frog in its natural habitat. Credit: Dan Cog?lniceanu [sic]

Caption: Adult female Prometeo Rain Frog in its natural habitat. Credit: Dan Cog?lniceanu [sic]

I’m not sure why Prometheus was considered an appropriate inspiration for the Promoteo program but more about the Greek mythological character and the program later. First, in honour of this blog’s name, here’s the announcement of a ‘new’ frog in a July 21, 2016 news item on phys.org (Note: Links have been removed),

Prometheus, the mythological Greek heroic deity, has been given a namesake in a new species of tiny rain frog, discovered in southwestern Ecuador. The name was chosen by the international team of scientists, led by Dr Paul Szekely, Ovidius University, Constanta, Romania, in acknowledgement of the Prometeo program, funded by the Ecuadorian government.

The description of this new species (Pristimantis prometeii) is the result of the cooperation between three Romanian Prometeo investigators affiliated with the Universidad Tecnica Particular de Loja and Universidad Nacional de Loja, and two Ecuadorian specialists from Pontificia Universidad Catolica del Ecuador. …

A July 21, 2016 Pensoft Publishers news release on EurekAlert, which originated the news item, provides more information about this ‘promethean’ frog,

During the day, frogs of the new species were found hiding in flowering plants, while at night — perching on leaves at low heights in well preserved cloud forests. They grow to 2-3 cm with the females being larger than the males.

The newly described species is part of a group of frogs called Terrarana (meaning ‘Land or terrestrial frogs’). This is a lineage of frogs that has evolved directly developing eggs, which are deposited in terrestrial habitats. Unlike other frogs, these ones do not have an aquatic tadpole stage and the embryos develop directly into froglets on land.

The newly described species is only known from Reserva Biologica Buenaventura, southwestern Ecuador, at elevations between 878 and 1082 m. This reserve is privately owned by the Jocotoco Conservation Foundation. The reserve has at least another four endemic species of amphibians, reptiles, and birds.

With more than 470 species, the directly developing rain frogs of the genus Pristimantis continue to surprise everyone.

“While new species are described every year, there are over a hundred discovered over the last decade only,” remind the authors.

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

A new species of Pristimantis from southern Ecuador  (Anura, Craugastoridae) by Paul Székely, Dan Cogălniceanu, Diana Székely, Nadia Paez, Santiago Ron.  ZooKeys 606: 77-97 (21 Jul 2016) DOI: 10.3897/zookeys.606.9121

This article is open access.

Finally getting to Prometheus, here’s a description from the mythological figure’s Wikipedia entry (Note: Links have been removed),

Prometheus (/prəˈmiːθiːəs/ prə-MEE-thee-əs; Greek: Προμηθεύς [promɛːtʰeús], meaning “forethought”)[1] is a Titan in Greek mythology, best known as the deity in Greek mythology who was the creator of mankind and its greatest benefactor, who stole fire from Mount Olympus and gave it to mankind.

That’s a lot to hang on a tiny frog, eh? Also, you can find the Prometeo program here but you will need your Spanish language skills.

New Wave and its non-shrimp shrimp

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I received a news release from a start-up company, New Wave Foods, which specializes in creating plant-based seafood. The concept looks very interesting and sci fi (Lois McMaster Bujold, and I’m sure others, has featured vat-grown meat and fish in her novels). Apparently, Google has already started using some of the New Wave product in its employee cafeteria. Here’s more from the July 19, 2016 New Wave Foods news release,

New Wave Foods announced today that it has successfully opened a seed round aimed at developing seafood that is healthier for humans and the planet. Efficient Capacity kicked off the round and New Crop Capital provided additional funding.

New Wave Foods uses plant-based ingredients, such as red algae, to engineer new edible materials that replicate the taste and texture of fish and shellfish while improving their nutritional profiles. Its first product, which has already been served in Google’s cafeterias, will be a truly sustainable shrimp. Shrimp is the nation’s most popular seafood, currently representing more than a quarter of the four billion pounds of fish and shellfish consumed by Americans annually. For each pound of shrimp caught, up to 15 pounds of other animals, including endangered dolphins, turtles, and sharks, die.

The market for meat analogs is expected to surpass $5 billion by 2020, and savvy investors are increasingly taking notice. In recent years, millions in venture capital has flowed into plant-based alternatives to animal foods from large food processors and investors like Bill Gates and Li Ka-shing, Asia’s richest businessman.

“The astounding scale of our consumption of sea animals is decimating ocean ecosystems through overfishing, massive death through bycatch, water pollution, carbon emissions, derelict fishing gear, mangrove deforestation, and more,” said New Wave Foods co-founder and CEO Dominique Barnes. “Shrimping is also fraught with human rights abuses and slave labor, so we’re pleased to introduce a product that is better for people, the planet, and animals.”

Efficient Capacity is an investment fund that advises and invests in companies worldwide. Efficient Capacity partners have founded or co-founded more than ten companies and served as advisors or directors to dozens of others.

New Crop Capital is a specialized private venture capital fund that provides early-stage investments to companies that develop “clean,” (i.e., cultured) and plant-based meat, dairy, and egg products or facilitate the promotion and sale of such products.

The current round of investments follows investments from SOS Ventures via IndieBio, an accelerator group funding and building biotech startups. IndieBio companies use technology to solve our culture’s most challenging problems, such as feeding a growing population sustainably. Along with investment, IndieBio offers its startups resources such as lab space and mentorship to help take an idea to a product.

Along with its funding round, New Wave Foods announced the appointment of John Wiest as COO. Wiest brings more than 15 years of senior management experience in food and consumer products, including animal-based seafood companies, to the company. As an executive and consultant, Wiest has helped dozens of food ventures develop new products, expand distribution channels, and create strategic partnerships.

New Wave Foods, founded in 2015, is a leader in plant-based seafood that is healthier and better for the environment. New Wave products are high in clean nutrients and deliver a culinary experience consumers expect without the devastating environmental impact of commercial fishing. Co-founder and CEO Dominique Barnes holds a master’s in marine biodiversity and conservation from Scripps Institution of Oceanography, and co-founder and CTO Michelle Wolf holds a bachelor’s in materials science and engineering and a master’s in biomedical engineering. New Wave Foods’ first products will reach consumers as early as Q4 2016.

I found a February 5, 2016 review article about the plant-based shrimp written by Ariel Schwartz for Tech Insider (Note: A link has been removed),

… after trying a lab-made “shrimp” made of plant proteins and algae, I’d consider giving it up the real thing. Maybe others will too.

The shrimp I ate came from New Wave Foods, a startup that just graduated from biotech startup accelerator IndieBio. When I first met New Wave’s founders in the fall of 2015, they had been working for eight weeks at IndieBio’s San Francisco lab. …

…

Barnes and Wolf [marine conservationist Dominique Barnes and materials scientist Michelle Wolf ] ultimately figured out a way to use plant proteins, along with the same algae that shrimp eat — the stuff that helps give the crustaceans their color and flavor — to come up with a substitute that has a similar texture, taste, color, and nutritional value.

The fact that New Wave’s product has the same high protein, low fat content as real shrimp is a big source of differentiation from other shrimp substitutes, according to Barnes.

In early February, I finally tried a breaded version of New Wave’s shrimp. Here’s what it looked like:

New Wave Foods Ariel Schwartz/Tech Insider

It was a little hard to judge the taste because of the breading, but the texture was almost perfect. The lab-made shrimp had that springiness and mixture of crunch and chew that you’d expect from the real thing. I could see myself replacing real shrimp with this in some situations.

Whether it could replace shrimp all the time depends on how the product tastes without the breading. “Our ultimate goal is to get to the cocktail shrimp level,” says Barnes.

I’m glad to have stumbled across Ariel Schwartz again as I’ve always enjoyed her writing and it has been a few years.

For the curious, you can check out more of Ariel Schwartz’s work here and find out more about Efficient Capacity in a listing on CrunchBase, New Crop Capital here, SOS Ventures here, IndieBio here. and, of course,  New Wave Foods here.

One final comment, I am not endorsing this company or its products. This is presented as interesting information and, hopefully, I will be hearing more about the company and its products in the future.

More about the Antikythera (an ancient computer)

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Since 2004, an international consortium has been attempting to decode the mechanism known as an Antikythera. Discovered at the beginning of the 20th century, it has puzzled and intrigued scientists ever since. Last mentioned here in an Oct. 2, 2012 posting, this update is based on a July 20, 2016 essay by Mike Edmunds for The Conversation website. First, here’s a brief overview (Note: A link has been removed),

When we talk of the history of computers, most of us will refer to the evolution of the modern digital desktop PC, charting the decades-long developments by the likes of Apple and Microsoft. What many don’t consider, however, is that computers have been around much longer. In fact, they date back millennia, to a time when they were analogue creations.

Today, the world’s oldest known “computer” is the Antikythera mechanism, a severely corroded bronze artefact which was found at the beginning of the 20th Century, in the remains of a shipwreck near the Mediterranean island of Antikythera. It wasn’t until the 1970s that the importance of the Antikythera mechanism was discovered, when radiography revealed that the device is in fact a complex mechanism of at least 30 gear wheels.

The mechanism has since been established as the first known astronomical calendar, a complex system which can track and predict the cycles of the solar system. Technically, it is a sophisticated mechanical “calculator” rather than a true “computer”, since it cannot be reprogrammed, but nonetheless an impressive artefact.

Edmunds is an emeritus professor at the University of Cardiff (Wales) and the lead academic on the Antikythera Mechanism Research Project.

He describes the mechanism as it is presently understood and includes the latest findings (Note: Links have been removed),

When first made, the mechanism was about the size of a shoe box, with dials on both its front and back faces. A handle or knob on the side of the box enabled the user to turn the trains of gears inside –- originally there were considerably more gears than the 30 that still survive. On the front, pointers showed where the sun and moon were in the sky, and there was a display of the phase of the moon. On the rear, dials displayed a 19-year cycle of lunar months, the 18.2 year Saros cycle of lunar and solar eclipses, and even a four-year cycle of athletic competitions including the Olympic games.

The inscriptions are thought to have been a description for the user of what it was they were viewing as they operated the mechanism. However, the newly published texts add more to what we know of the mechanism: they establish that the positions of the five planets known in antiquity were also shown – Mercury, Venus, Mars, Jupiter and Saturn.

The planets were displayed on the machine in a way that took account of their rather irregular “wanderings” about the sky. Such a display had been suspected, and the confirmation reinforces that this was a very sophisticated and quite complicated device. The actual gear trains needed for the display of the planets are missing – presumably lost in the shipwreck – but we know from the very ingenious way that the sun and moon drives are designed and constructed that the makers of the mechanism certainly had the skills necessary to make the planetary drive.

The newly uncovered inscriptions include passages about what stars were just becoming visible –- or about to be lost in the glare of the sun – at different times of year. The style of these passages is very close to that of a well-known astronomical text by Greek astronomer and mathematician Geminos from the first Century BC. Not only does this tie in perfectly with the presumed date of the shipwreck (around 60BC), but also the latitude – which is implied by stellar data to be mid-Mediterranean – which would fit nicely with the mechanism originating on the island of Rhodes, from where there is a contemporary historic record from the writer Cicero of such devices.

Apparently divers have returned to the site this year to see if they can find more parts to the Antikythera and , hopefully unlock more of its secrets. (h/t July 20, 2016 phys.org news item),

First hologram of a single photon (light particle)

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Polish scientists have created a technique for something thought to be impossible. From a July 19, 2016 news item on Nanowerk,

Until quite recently, creating a hologram of a single photon was believed to be impossible due to fundamental laws of physics. However, scientists at the Faculty of Physics, University of Warsaw, have successfully applied concepts of classical holography to the world of quantum phenomena. A new measurement technique has enabled them to register the first ever hologram of a single light particle, thereby shedding new light on the foundations of quantum mechanics.

A July 18, 2016 University of Warsaw press release on EurekAlert, which originated the news item, describes the breakthrough in more detail,

Scientists at the Faculty of Physics, University of Warsaw, have created the first ever hologram of a single light particle. The spectacular experiment, reported in the prestigious journal Nature Photonics, was conducted by Dr. Radoslaw Chrapkiewicz and Michal Jachura under the supervision of Dr. Wojciech Wasilewski and Prof. Konrad Banaszek. Their successful registering of the hologram of a single photon heralds a new era in holography: quantum holography, which promises to offer a whole new perspective on quantum phenomena.

“We performed a relatively simple experiment to measure and view something incredibly difficult to observe: the shape of wavefronts of a single photon,” says Dr. Chrapkiewicz.

In standard photography, individual points of an image register light intensity only. In classical holography, the interference phenomenon also registers the phase of the light waves (it is the phase which carries information about the depth of the image). When a hologram is created, a well-described, undisturbed light wave (reference wave) is superimposed with another wave of the same wavelength but reflected from a three-dimensional object (the peaks and troughs of the two waves are shifted to varying degrees at different points of the image). This results in interference and the phase differences between the two waves create a complex pattern of lines. Such a hologram is then illuminated with a beam of reference light to recreate the spatial structure of wavefronts of the light reflected from the object, and as such its 3D shape.

One might think that a similar mechanism would be observed when the number of photons creating the two waves were reduced to a minimum, that is to a single reference photon and a single photon reflected by the object. And yet you’d be wrong! The phase of individual photons continues to fluctuate, which makes classical interference with other photons impossible. Since the Warsaw physicists were facing a seemingly impossible task, they attempted to tackle the issue differently: rather than using classical interference of electromagnetic waves, they tried to register quantum interference in which the wave functions of photons interact.

Wave function is a fundamental concept in quantum mechanics and the core of its most important equation: the Schrödinger equation. In the hands of a skilled physicist, the function could be compared to putty in the hands of a sculptor: when expertly shaped, it can be used to ‘mould’ a model of a quantum particle system. Physicists are always trying to learn about the wave function of a particle in a given system, since the square of its modulus represents the distribution of the probability of finding the particle in a particular state, which is highly useful.

“All this may sound rather complicated, but in practice our experiment is simple at its core: instead of looking at changing light intensity, we look at the changing probability of registering pairs of photons after the quantum interference,” explains doctoral student Jachura.

Why pairs of photons? A year ago, Chrapkiewicz and Jachura used an innovative camera built at the University of Warsaw to film the behaviour of pairs of distinguishable and non-distinguishable photons entering a beam splitter. When the photons are distinguishable, their behaviour at the beam splitter is random: one or both photons can be transmitted or reflected. Non-distinguishable photons exhibit quantum interference, which alters their behaviour: they join into pairs and are always transmitted or reflected together. This is known as two-photon interference or the Hong-Ou-Mandel effect.

“Following this experiment, we were inspired to ask whether two-photon quantum interference could be used similarly to classical interference in holography in order to use known-state photons to gain further information about unknown-state photons. Our analysis led us to a surprising conclusion: it turned out that when two photons exhibit quantum interference, the course of this interference depends on the shape of their wavefronts,” says Dr. Chrapkiewicz.

Quantum interference can be observed by registering pairs of photons. The experiment needs to be repeated several times, always with two photons with identical properties. To meet these conditions, each experiment started with a pair of photons with flat wavefronts and perpendicular polarisations; this means that the electrical field of each photon vibrated in a single plane only, and these planes were perpendicular for the two photons. The different polarisation made it possible to separate the photons in a crystal and make one of them ‘unknown’ by curving their wavefronts using a cylindrical lens. Once the photons were reflected by mirrors, they were directed towards the beam splitter (a calcite crystal). The splitter didn’t change the direction of vertically-polarised photons, but it did diverge diplace horizontally-polarised photons. In order to make each direction equally probable and to make sure the crystal acted as a beam splitter, the planes of photon polarisation were bent by 45 degrees before the photons entered the splitter. The photons were registered using the state-of-the-art camera designed for the previous experiments. By repeating the measurements several times, the researchers obtained an interference image corresponding to the hologram of the unknown photon viewed from a single point in space. The image was used to fully reconstruct the amplitude and phase of the wave function of the unknown photon.

The experiment conducted by the Warsaw physicists is a major step towards improving our understanding of the fundamental principles of quantum mechanics. Until now, there has not been a simple experimental method of gaining information about the phase of a photon’s wave function. Although quantum mechanics has many applications, and it has been verified many times with a great degree of accuracy over the last century, we are still unable to explain what wave functions actually are: are they simply a handy mathematical tool, or are they something real?

“Our experiment is one of the first allowing us to directly observe one of the fundamental parameters of photon’s wave function – its phase – bringing us a step closer to understanding what the wave function really is,” explains Jachura.

The Warsaw physicists used quantum holography to reconstruct wave function of an individual photon. Researchers hope that in the future they will be able to use a similar method to recreate wave functions of more complex quantum objects, such as certain atoms. Will quantum holography find applications beyond the lab to a similar extent as classical holography, which is routinely used in security (holograms are difficult to counterfeit), entertainment, transport (in scanners measuring the dimensions of cargo), microscopic imaging and optical data storing and processing technologies?

“It’s difficult to answer this question today. All of us – I mean physicists – must first get our heads around this new tool. It’s likely that real applications of quantum holography won’t appear for a few decades yet, but if there’s one thing we can be sure of it’s that they will be surprising,” summarises Prof. Banaszek.

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

Hologram of a single photon by Radosław Chrapkiewicz, Michał Jachura, Konrad Banaszek, & Wojciech Wasilewski.  Nature Photonics (2016) doi:10.1038/nphoton.2016.129 Published online 18 July 2016

This paper is behind a paywall.

Beatrix Potter and her science on her 150th birthday

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July 28, 2016 was the 150th anniversary of Beatrix Potter‘s birthday. Known by many through her children’s books, she has left an indelible mark on many of us. Hop-skip-jump.com has a description of an extraordinary woman, from their Beatrix Potter 150 years page,

An artist, storyteller, botanist, environmentalist, farmer and impeccable businesswoman, Potter was a visionary and a trailblazer. Single-mindedly determined and ambitious she overcame professional rejection, academic humiliation, and personal heartbreak, going on to earn her fortune and a formidable reputation.

A July 27, 2016 posting by Alex Jackson on the Guardian science blogs provides more information about Potter’s science (Note: Links have been removed),

Influenced by family holidays in Scotland, Potter was fascinated by the natural world from a young age. Encouraged to follow her interests, she explored the outdoors with sketchbook and camera, honing her skills as an artist, by drawing and sketching her school room pets: mice, rabbits and hedgehogs. Led first by her imagination, she developed a broad interest in the natural sciences: particularly archaeology, entomology and mycology, producing accurate watercolour drawings of unusual fossils, fungi, and archaeological artefacts.

Potter’s uncle, Sir Henry Enfield Roscoe FRS, an eminent nineteenth-century chemist, recognised her artistic talent and encouraged her scientific interests. By the 1890s, Potter’s skills in mycology drew Roscoe’s attention when he learned she had successfully germinated spores of a class of fungi, and had ideas on how they reproduced. He used his scientific connections with botanists at Kew’s Royal Botanic Gardens to gain a student card for his niece and to introduce her to Kew botanists interested in mycology.

Although Potter had good reason to think that her success might break some new ground, the botanists at Kew were sceptical. One Kew scientist, George Massee, however, was sufficiently interested in Potter’s drawings, encouraging her to continue experimenting. Although the director of Kew, William Thistleton-Dyer refused to give Potter’s theories or her drawings much attention both because she was an amateur and a female, Roscoe encouraged his niece to write up her investigations and offer her drawings in a paper to the Linnean Society.

In 1897, Potter put forward her paper, which Massee presented to the Linnean Society, since women could not be members or attend a meeting. Her paper, On the Germination of the Spores of the Agaricineae, was not given much notice and she quickly withdrew it, recognising that her samples were likely contaminated. Sadly, her paper has since been lost, so we can only speculate on what Potter actually concluded.

…

Until quite recently, Potter’s accomplishments and her experiments in natural science went unrecognised. Upon her death in 1943, Potter left hundreds of her mycological drawings and paintings to the Armitt Museum and Library in Ambleside, where she and her husband had been active members. Today, they are valued not only for their beauty and precision, but also for the assistance they provide modern mycologists in identifying a variety of fungi.

In 1997, the Linnean Society issued a posthumous apology to Potter, noting the sexism displayed in the handling of her research and its policy toward the contributions of women.

A rarely seen very early Beatrix Potter drawing, A Dream of Toasted Cheese was drawn to celebrate the publication of Henry Roscoe’s chemistry textbook in 1899. Illustration: Beatrix Potter/reproduced courtesy of the Lord Clwyd collection (image by way of The Guardian newspaper)

A rarely seen very early Beatrix Potter drawing, A Dream of Toasted Cheese was drawn to celebrate the publication of Henry Roscoe’s chemistry textbook in 1899. Illustration: Beatrix Potter/reproduced courtesy of the Lord Clwyd collection (image by way of The Guardian newspaper)

I’m sure you recognized the bunsen burner. From the James posting (Note: A link has been removed),

London-born, Henry Roscoe, whose family roots were in Liverpool, studied at University College London, before moving to Heidelberg, Germany, where he worked under Robert Bunsen, inventor of the new-fangled apparatus that inspired Potter’s drawing. Together, using magnesium as a light source, Roscoe and Bunsen reputedly carried out the first flashlight photography in 1864. Their research laid the foundations of comparative photochemistry.

These excerpts do not give full justice to James’ piece which I encourage you to read in its entirety.

Should you be going to the UK and inclined to follow up further, there’s a listing of 2016 events being held to honour Potter on the UK National Trust’s Celebrating Beatrix Potter’s anniversary in the Lake District webpage.

A couple of Frankenstein dares from The Frankenstein Bicentennial project

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Drat! I’ve gotten the information about the first Frankenstein dare (a short story challenge) a little late in the game since the deadline is 11:59 pm PDT on July 31, 2016. In any event, here’s more about the two dares,

And for those who like their information in written form, here are the details from the Arizona State University’s (ASU) Frankenstein Bicentennial Dare (on The Franklin Bicentennial Project website),

Two centuries ago, on a dare to tell the best scary story, 19-year-old Mary Shelley imagined an idea that became the basis for Frankenstein. Mary’s original concept became the novel that arguably kick-started the genres of science fiction and Gothic horror, but also provided an enduring myth that shapes how we grapple with creativity, science, technology, and their consequences.
Two hundred years later, inspired by that classic dare, we’re challenging you to create new myths for the 21st century along with our partners National Novel Writing Month (NaNoWriMo), Chabot Space and Science Center, and Creative Nonfiction magazine.

FRANKENSTEIN 200

Presented by NaNoWriMo and the Chabot Space and Science Center

Frankenstein is a classic of Gothic literature – a gripping, tragic story about Victor Frankenstein’s failure to accept responsibility for the consequences of bringing new life into the world. In this dare, we’re challenging you to write a scary story that explores the relationship between creators and the “monsters” they create.

Almost anything that we create can become monstrous: a misinterpreted piece of architecture; a song whose meaning has been misappropriated; a big, but misunderstood idea; or, of course, an actual creature. And in Frankenstein, Shelley teaches us that monstrous does not always mean evil – in fact, creators can prove to be more destructive and inhuman than the things they bring into being

Tell us your story in 1,000 – 1,800 words on Medium.com and use the hashtag #Frankenstein200. Read other #Frankenstein200 stories, and use the recommend button at the bottom of each post for the stories you like. Winners in the short fiction contest will receive personal feedback from Hugo and Sturgeon Award-winning science fiction and fantasy author Elizabeth Bear, as well as a curated selection of classic and contemporary science fiction books and  Frankenstein goodies, courtesy of the NaNoWriMo team.

Rules and Mechanics

  • There are no restrictions on content. Entry is limited to one submission per author. Submissions must be in English and between 1,000 to 1,800 words. You must follow all Medium Terms of Service, including the Rules.
  • All entries submitted and tagged as #Frankenstein200 and in compliance with the rules outlined here will be considered.
  • The deadline for submissions is 11:59 PM on July 31, 2016.
  • Three winners will be selected at random on August 1, 2016.
  • Each winner receives the following prize package including:
  • Additionally, one of the three winners, chosen at random, will receive written coaching/feedback from Elizabeth Bear on his or her entry.
  • Select stories will be featured on Frankenscape, a public geo-storytelling project hosted by ASU’s Frankenstein Bicentennial Project. Stories may also be featured in National Novel Writing Month communications and social media platforms.
  • U.S. residents only [emphasis mine]; void where prohibited by law. No purchase is necessary to enter or win.

Dangerous Creations: Real-life Frankenstein Stories

Presented by Creative Nonfiction magazine

Creative Nonfiction magazine is daring writers to write original and true stories that explore humans’ efforts to control and redirect nature, the evolving relationships between humanity and science/technology, and contemporary interpretations of monstrosity.

Essays must be vivid and dramatic; they should combine a strong and compelling narrative with an informative or reflective element and reach beyond a strictly personal experience for some universal or deeper meaning. We’re open to a broad range of interpretations of the “Frankenstein” theme, with the understanding that all works submitted must tell true stories and be factually accurate. Above all, we’re looking for well-written prose, rich with detail and a distinctive voice.

Creative Nonfiction editors and a judge (to be announced) will award $10,000 and publication for Best Essay and two $2,500 prizes and publication for runners-up. All essays submitted will be considered for publication in the winter 2018 issue of the magazine.

Deadline for submissions: March 20, 2017.
For complete guidelines: www.creativenonfiction.org/submissions

[Note: There is a submission fee for the nonfiction dare and no indication as to whether or not there are residency requirements.]

A July 27, 2016 email received from The Frankenstein Bicentennial Project (which is how I learned about the dares somewhat belatedly) has this about the first dare,

Planetary Design, Transhumanism, and Pork Products
Our #Frankenstein200 Contest Took Us in Some Unexpected Directions

Last month [June 2016], we partnered with National Novel Writing Month (NaNoWriMo) and The Chabot Space and Science Center to dare the world to create stories in the spirit of Mary Shelley’s Frankenstein, to celebrate the 200th anniversary of the novel’s conception.

We received a bevy of intriguing and sometimes frightening submissions that explore the complex relationships between creators and their “monsters.” Here are a few tales that caught our eye:

The Man Who Harnessed the Sun
By Sandra Knisely
Eliza has to choose between protecting the scientist who once gave her the world and punishing him for letting it all slip away. Read the story…

The Mortality Complex
By Brandon Miller
When the boogeyman of medical students reflects on life. Read the story…

Bacon Man
By Corey Pressman
A Frankenstein story in celebration of ASU’s Frankenstein Bicentennial Project. And bacon. Read the story… 

You can find the stories that have been submitted to date for the creative short story dare at Medium.com.

Good luck! And, don’t forget to tag your short story with #Frankenstein200 and submit it by July 31, 2016 (if you are a US resident). There’s still lots of time to enter a submission for a creative nonfiction piece.

Connecting chaos and entanglement

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Researchers seem to have stumbled across a link between classical and quantum physics. A July 12, 2016 University of California at Santa Barbara (UCSB) news release (also on EurekAlert) by Sonia Fernandez provides a description of both classical and quantum physics, as well as, the research that connects the two,

Using a small quantum system consisting of three superconducting qubits, researchers at UC Santa Barbara and Google have uncovered a link between aspects of classical and quantum physics thought to be unrelated: classical chaos and quantum entanglement. Their findings suggest that it would be possible to use controllable quantum systems to investigate certain fundamental aspects of nature.

“It’s kind of surprising because chaos is this totally classical concept — there’s no idea of chaos in a quantum system,” Charles Neill, a researcher in the UCSB Department of Physics and lead author of a paper that appears in Nature Physics. “Similarly, there’s no concept of entanglement within classical systems. And yet it turns out that chaos and entanglement are really very strongly and clearly related.”

Initiated in the 15th century, classical physics generally examines and describes systems larger than atoms and molecules. It consists of hundreds of years’ worth of study including Newton’s laws of motion, electrodynamics, relativity, thermodynamics as well as chaos theory — the field that studies the behavior of highly sensitive and unpredictable systems. One classic example of chaos theory is the weather, in which a relatively small change in one part of the system is enough to foil predictions — and vacation plans — anywhere on the globe.

At smaller size and length scales in nature, however, such as those involving atoms and photons and their behaviors, classical physics falls short. In the early 20th century quantum physics emerged, with its seemingly counterintuitive and sometimes controversial science, including the notions of superposition (the theory that a particle can be located in several places at once) and entanglement (particles that are deeply linked behave as such despite physical distance from one another).

And so began the continuing search for connections between the two fields.

All systems are fundamentally quantum systems, according [to] Neill, but the means of describing in a quantum sense the chaotic behavior of, say, air molecules in an evacuated room, remains limited.

Imagine taking a balloon full of air molecules, somehow tagging them so you could see them and then releasing them into a room with no air molecules, noted co-author and UCSB/Google researcher Pedram Roushan. One possible outcome is that the air molecules remain clumped together in a little cloud following the same trajectory around the room. And yet, he continued, as we can probably intuit, the molecules will more likely take off in a variety of velocities and directions, bouncing off walls and interacting with each other, resting after the room is sufficiently saturated with them.

“The underlying physics is chaos, essentially,” he said. The molecules coming to rest — at least on the macroscopic level — is the result of thermalization, or of reaching equilibrium after they have achieved uniform saturation within the system. But in the infinitesimal world of quantum physics, there is still little to describe that behavior. The mathematics of quantum mechanics, Roushan said, do not allow for the chaos described by Newtonian laws of motion.

To investigate, the researchers devised an experiment using three quantum bits, the basic computational units of the quantum computer. Unlike classical computer bits, which utilize a binary system of two possible states (e.g., zero/one), a qubit can also use a superposition of both states (zero and one) as a single state. Additionally, multiple qubits can entangle, or link so closely that their measurements will automatically correlate. By manipulating these qubits with electronic pulses, Neill caused them to interact, rotate and evolve in the quantum analog of a highly sensitive classical system.

The result is a map of entanglement entropy of a qubit that, over time, comes to strongly resemble that of classical dynamics — the regions of entanglement in the quantum map resemble the regions of chaos on the classical map. The islands of low entanglement in the quantum map are located in the places of low chaos on the classical map.

“There’s a very clear connection between entanglement and chaos in these two pictures,” said Neill. “And, it turns out that thermalization is the thing that connects chaos and entanglement. It turns out that they are actually the driving forces behind thermalization.

“What we realize is that in almost any quantum system, including on quantum computers, if you just let it evolve and you start to study what happens as a function of time, it’s going to thermalize,” added Neill, referring to the quantum-level equilibration. “And this really ties together the intuition between classical thermalization and chaos and how it occurs in quantum systems that entangle.”

The study’s findings have fundamental implications for quantum computing. At the level of three qubits, the computation is relatively simple, said Roushan, but as researchers push to build increasingly sophisticated and powerful quantum computers that incorporate more qubits to study highly complex problems that are beyond the ability of classical computing — such as those in the realms of machine learning, artificial intelligence, fluid dynamics or chemistry — a quantum processor optimized for such calculations will be a very powerful tool.

“It means we can study things that are completely impossible to study right now, once we get to bigger systems,” said Neill.

Experimental link between quantum entanglement (left) and classical chaos (right) found using a small quantum computer. Photo Credit: Courtesy Image (Courtesy: UCSB)

Experimental link between quantum entanglement (left) and classical chaos (right) found using a small quantum computer. Photo Credit: Courtesy Image (Courtesy: UCSB)

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

Ergodic dynamics and thermalization in an isolated quantum system by C. Neill, P. Roushan, M. Fang, Y. Chen, M. Kolodrubetz, Z. Chen, A. Megrant, R. Barends, B. Campbell, B. Chiaro, A. Dunsworth, E. Jeffrey, J. Kelly, J. Mutus, P. J. J. O’Malley, C. Quintana, D. Sank, A. Vainsencher, J. Wenner, T. C. White, A. Polkovnikov, & J. M. Martinis. Nature Physics (2016)  doi:10.1038/nphys3830 Published online 11 July 2016

This paper is behind a paywall.

A selection of science songs for summer

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Canada’s Perimeter Institute for Theoretical Physics (PI) has compiled a list of science songs and it includes a few Canadian surprises. Here’s more from the July 21, 2016 PI notice received via email.

Ah, summer.

School’s out, the outdoors beckon, and with every passing second a 4.5-billion-year-old nuclear fireball fuses 620 million tons of hydrogen so brightly you’ve gotta wear shades.

Who says you have to stop learning science over the summer?

All you need is the right soundtrack to your next road trip, backyard barbeque, or day at the beach.

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Did we miss your favourite science song? Tweet us @Perimeter with the hashtag #SciencePlaylist.

You can find the list and accompanying videos on The Ultimate Science Playlist webpage on the PI website. Here are a few samples,

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“History of Everything” – Barenaked Ladies (The Big Bang Theory theme)

You probably know this one as the theme song of The Big Bang Theory. But here’s something you might not know. The tune began as an improvised ditty Barenaked Ladies’ singer Ed Robertson performed one night in Los Angeles after reading Simon Singh’s book Big Bang: The Most Important Scientific Discovery of All Time and Why You Need to Know About It. Lo and behold, in the audience that night were Chuck Lorre and Bill Prady, creators of The Big Bang Theory. The rest is history (of everything).

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“Bohemian Gravity” – A Capella Science (Tim Blais)

Tim Blais, the one-man choir behind A Capella Science, is a master at conveying complex science in fun musical parodies. “Bohemian Gravity” is his most famous, but be sure to also check out our collaboration with him about gravitational waves, “LIGO: Feel That Space.”

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“NaCl” – Kate and Anna McGarrigle

“NaCl” is a romantic tale of the courtship of a chlorine atom and a sodium atom, who marry and become sodium chloride. “Think of the love you eat,” sings Kate McGarrigle, “when you salt your meat.”

This is just a sampling. At this point, there are 15 science songs on the webpage. Surprisingly, rap is not represented. One other note, you’ll notice all of my samples are Canadian. (Sadly, I had other videos as well but every time I saved a draft I lost at least half or more. It seems the maximum allowed to me is three.).

Here are the others I wanted to include:

“Mandelbrot Set” – Jonathan Coulton

Singer-songwriter Jonathan Coulton (JoCo, to fans) is arguably the patron saint of geek-pop, having penned the uber-catchy credits songs of the Portal games, as well as this loving tribute to a particular set of complex numbers that has a highly convoluted fractal boundary when plotted.

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“Higgs Boson Sonification” – Traq 

CERN physicist Piotr Traczyk (a.k.a. Traq) “sonified” data from the experiment that uncovered the Higgs boson, turning the discovery into a high-energy metal riff.

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“Why Does the Sun Shine?” – They Might Be Giants

Choosing just one song for this playlist by They Might Be Giants is a tricky task, since They Definitely Are Nerdy. But this one celebrates physics, chemistry, and astronomy while also being absurdly catchy, so it made the list. Honourable mention goes to their entire album for kids, Here Comes Science.

In any event, the PI list is a great introduction to science songs and The Ultimate Science Playlist includes embedded videos for all 15 of the songs selected so far. Happy Summer!