Tag Archives: Waseda University

Climate measurements as music

Given that it was Earth Day yesterday (April 22, 2024), this seems like a good second act. From an April 18, 2024 news item on phys.org,

A geo-environmental scientist from Japan has composed a string quartet using sonified climate data. The 6-minute-long composition—titled “String Quartet No. 1 “Polar Energy Budget”—is based on over 30 years of satellite-collected climate data from the Arctic and Antarctic and aims to garner attention on how climate is driven by the input and output of energy at the poles.

This is a little longer video than I usually like to embed here at 6 mins. 29 secs. and it is one of the more aesthetically pleasing I’ve heard,

An April 18, 2024 Cell Press press release, which originated the news item, describes the data sonification work and its application to art/science projects, Note: A link has been removed,

“I strongly hope that this manuscript marks a significant turning point, transitioning from an era where only scientists handle data to one where artists can freely leverage data to craft their works,” writes author and composer Hiroto Nagai, a geo-environmental scientist at Rissho University.

Scientist-composer Hiroto Nagai asserts that music, as opposed to sound, evokes an emotional response and posits that “musification” (as opposed to sonification) of data requires some intervention by the composer to build tension and add dynamics. For this reason, Nagai was more liberal in adding a “human touch” compared to previous data-based musical compositions, aiming to meld sonification with traditional music composition.

“As a fundamental principle in music composition, it is necessary to combine temporal sequences from tension-building to resolution in various scales, from harmonic progressions to entire movements,” Nagai writes. “So far, there haven’t been published attempts and open discussion on sonification-based music composition, nor attempts to demonstrate the methodology required to intentionally affect the audience’s emotions with an artistic piece.”

To do this, he first used a program to sonify environmental data by assigning sounds to different data values. The publicly available data was collected from four polar locations between 1982 and 2022: an ice-core drilling site in the Greenland ice sheet, a satellite station in Norway’s Svalbard archipelago, and two Japanese-owned research stations in the Antarctic (Showa Station and Dome Fuji Station). For each of the sites, Nagai used data on monthly measurements of short- and longwave radiation, precipitation, surface temperature, and cloud thickness.

In the next step, he transformed this collection of sounds into a musical composition to be played by two violins, a viola, and a cello. This process involved many steps, including manipulating the pitch of different datapoints and assigning sections of data to the different instruments, overlaying passages created from different data, and introducing musical playing techniques such as pizzicato and staccato. Nagai also intervened in more artistic ways by introducing rhythm, deliberately removing certain sounds, and introducing handwritten (non-data derived) parts into the composition.

The quartet’s premiere live performance was shared at Waseda University in Tokyo in March 2023 followed by a panel discussion. A filmed performance of the piece by PRT Quartet, a Japanese professional string quartet, was also released on YouTube in March 2023.

“Upon listening, my initial reaction was like, ‘What is this?’ It felt like a typical contemporary piece,” said Haruka Sakuma, the professional violinist who performed 2nd violin. “The flow of the music was a bit hard to memorize quickly, and it was quite challenging at first.”

Nagai says that, in contrast to graphical representations of data, music elicits emotion before intellectual curiosity and suggests that using graphical and music representations of data in conjunction might be even more powerful.

“It grabs the audiences’ attention forcefully, while graphical representations require active and conscious recognition instead,” Nagai writes. “This reveals the potential for outreach in the Earth sciences through music.”

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

String Quartet No. 1 “Polar Energy Budget” – Music composition using Earth observation data of polar regions by Hiroto Nagai. iScience DOI: https://doi.org/10.1016/j.isci.2024.109622 Published: April 18, 2024 Copyright © 2024 The Author(s). Published by Elsevier Inc. User license Creative Commons Attribution (CC BY 4.0)

As you may have guessed on seeing the Creative Commons licence, this is an open access paper,

Watching motor proteins at work

Researchers in the UK and in Japan have described these motor proteins as ‘swinging on monkey bars’,

A Sept. 14, 2015 news item on Nanowerk provides more information about the motor protein observations,

These proteins are vital to complex life, forming the transport infrastructure that allows different parts of cells to specialise in particular functions. Until now, the way they move has never been directly observed.

Researchers at the University of Leeds and in Japan used electron microscopes to capture images of the largest type of motor protein, called dynein, during the act of stepping along its molecular track.

A Sept 14, 2015 Leeds University press release, (also on EurekAlert*) which originated the news item, expands on the theme with what amounts to a transcript of sorts for the video (Note: Links have been removed),

Dr Stan Burgess, at the University of Leeds’ School of Molecular and Cellular Biology, who led the research team, said: “Dynein has two identical motors tied together and it moves along a molecular track called a microtubule. It drives itself along the track by alternately grabbing hold of a binding site, executing a power stroke, then letting go, like a person swinging on monkey bars.

“Previously, dynein movement had only been tracked by attaching fluorescent molecules to the proteins and observing the fluorescence using very powerful light microscopes. It was a bit like tracking vehicles from space with GPS. It told us where they were, their speed and for how long they ran, stopped and so on, but we couldn’t see the molecules in action themselves. These are the first images of these vital processes.”

An understanding of motor proteins is important to medical research because of their fundamental role in complex cellular life. Many viruses hijack motor proteins to hitch a ride to the nucleus for replication. Cell division is driven by motor proteins and so insights into their mechanics could be relevant to cancer research. Some motor neurone diseases are also associated with disruption of motor protein traffic.

The team at Leeds, working within the world-leading Astbury Centre for Structural Molecular Biology, combined purified microtubules with purified dynein motors and added the chemical fuel ATP (adenosine triphosphate) to power the motor.

Dr Hiroshi Imai, now Assistant Professor in the Department of Biological Sciences at Chuo University, Japan, carried out the experiments while working at the University of Leeds.

He explained: “We set the dyneins running along their tracks and then we froze them in ‘mid-stride’ by cooling them at about a million degrees a second, fast enough to prevent the water from forming ice crystals as it solidified. Then using a cryo-electron microscope we took many thousands of images of the motors caught during the act of stepping. By combining many images of individual motors, we were able to sharpen up our picture of the dynein and build up a dynamic idea of how it moved. It is a bit like figuring out how to swing along monkey bars by studying photographs of many people swinging on them.”

Dr Burgess said: “Our most striking discovery was the existence of a hinge between the long, thin stalk and the ‘grappling hook’, like the wrist between a human arm and hand. This allows a lot of variation in the angle of attachment of the motor to its track.

“Each of the two arms of a dynein motor protein is about 25 nanometres (0.000025 millimetre) long, while the binding sites it attaches to are only 8 nanometres apart. That means dynein can reach not only the next rung but the one after that and the one after that and appears to give it flexibility in how it moves along the ‘track’.”

Dynein is not only the biggest but also the most versatile of the motor proteins in living cells and, like all motor proteins, is vital to life. Motor proteins transport cargoes and hold many cellular components in position within the cell. For instance, dynein is responsible for carrying messages from the tips of active nerve cells back to the nucleus and these messages keep the nerve cells alive.

Co-author Peter Knight, Professor of Molecular Contractility in the University of Leeds’ School of Molecular and Cellular Biology, said: “If a cell is like a city, these are like the truckers on its road and rail networks. If you didn’t have a transport system, you couldn’t have specialised regions. Every part of the cell would be doing the same thing and that would mean you could not have complex life.”

“Dynein is the multi-purpose vehicle of cellular transport. Other motor proteins, called kinesins and myosins, are much smaller and have specific functions, but dynein can turn its hand to a lot of different of functions,” Professor Knight said.

For instance, in the motor neurone connecting the central nervous system to the big toe—which is a single cell a metre long— dynein provides the transport from the toe back to the nucleus. Another vital role is in the movement of cells.

Dr Burgess said: “During brain development, neurones must crawl into their correct position and dynein molecules in this instance grab hold of the nucleus and pull it along with the moving mass of the cell. If they didn’t, the nucleus would be left behind and the cytoplasm would crawl away.”

The study involved researchers from the University of Leeds and Japan’s Waseda and Osaka universities, as well as the Quantitative Biology Center at Japan’s Riken research institute and the Japan Science and Technology Agency (JST). The research was funded by the Human Frontiers Science Program and the Biotechnology and Biological Sciences Research Council (BBSRC).

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

Direct observation shows superposition and large scale flexibility within cytoplasmic dynein motors moving along microtubules by Hiroshi Imai, Tomohiro Shima, Kazuo Sutoh, Matthew L. Walker, Peter J. Knight, Takahide Kon, & Stan A. Burgess. Nature Communications 6, Article number: 8179  doi:10.1038/ncomms9179 Published 14 September 2015

This paper is open access.

*The EurekAlert link added Sept. 15, 2015 at 1200 hours PST.