Japan’s rising research stars: Yasuka Toda

Japanese literature is replete with references to nature, and reaches back over a thousand years to The Tale of Genji, written in the Heian Period by Murasaki Shikibu, a novelist, poet, and lady-in-waiting of the Imperial Court. Seasonal metaphors are used throughout. One particularly moving example evokes the pain of lost love: “The world know it not; but you, Autumn, I confess it: your wind at night-fall stabs deep into my heart.”

The Tale also references the Japanese gift for gardening in great and small places. The ancient interior courtyard garden continues today bringing nature literally into the home. Japanese contemporary architects such as Kengo Kuma, Toyo Ito, Shigeru Ban, Tadao Ando and Sou Fujimoto are well known for integrating nature into their practice.

Japan is often surrounded by the myth of featuring a unique “love for nature”, and its traditional culture and lifestyle as having been “in harmony with nature” before it was corrupted by modernization and Westernization. In this paper, I employ three examples to delineate images of nature in different times of Japanese history and point out the discrepancy between discourse on nature and physical engagement with nature. I argue that the environmental destruction that peaked in the Meiji period (1868–1912) is not primarily derived from a new, dualistic Euro-American understanding of nature. Rather, I demonstrate that environmental harm was already inherent in premodern Japan and was reconcilable with the respective concepts of nature. Therefore, industrialization and the adoption of Western technology solely released the potential for large-scale environmental impact.
Keywords: Japan; nature; culture; history of ideas; environment; pollution

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Recently a few Japanese geographers became aware that the concept of nature in modern geography differs from that of traditional Japanese thought. As modern geography in Japan was formed by the influence of European geography, most academic geographers in Japan have followed the occidental view that proposed an opposition between cultural and natural landscapes and that, due to the belief in man's power, sees the former as superior to the latter. From an economic view point, in fact, the European concept of nature which is opposed to culture has contributed to land exploitation that caused the destruction of Japan's natural landscape.

The time has come to consider the traditional Japanese idea of nature as Kami (gods) in comparison with the binary opposition of nature/culture which derives from modern rationalism. Kami who represent elements of nature belonged to a Pantheon in ancient Japan. Some examples of the Kami's names and their English explanations are as follows: Amaterasuomikami (godess of sun), Oyamatsumi-no-kami (god of the mountain's spirit), Nozuchi-no-kami (god of the field's spirit). In ancient Japan people believed that natural landscapes were created and inhabited by these Kami, and that the will of these Kami controlled the cultural domain. However, people provided shrines for Kami to placate their reckless domination. In this context, culture is in the hands of nature. This idea of nature's superiority to culture can explain the Japanese geographical concept of landscape.

There remain challenges that demand more complex solutions than cash injections. Robotics research, for example, was an area in which Japan enjoyed an edge as an enthusiastic and early adopter. But although the country’s engineers continue to excel in robotics hardware, Japanese science is lagging behind other major global players in the emerging field of artificial intelligence (AI). Without finding a way to incorporate this AI revolution, it could be difficult for Japan to stay relevant in the field. This is indicative of where Japanese science finds itself today more generally. It is still making impressive gains, but these achievements are fragile and need continual nurturing if they are to endure.

Japanese research seems to be performing better; its adjusted Share in the field fell by 7.7% from 2017 to 2021, a drop in Share that was lower than other subjects covered by the Nature Index. Kobe University’s Share in life sciences, meanwhile, has been rising consistently since 2019.

These potential green shoots in Japan’s research performance could be down to work that life-sciences researchers such as Nishida have been pursuing.

After he returned to Japan, Nishida set to work on devising a way in which the country could play an important role in the emerging industry of gene editing. Nishida hoped to address some of the limitations of CRISPR–Cas9, which, as he describes it, didn’t always slice genes at the precise target location. He was lucky enough to get both funding and freedom from another chemist, Akihiko Kondo, his mentor at Kobe University.

burst of visible light from the accretion disc of V404 Cygni, a black hole more than 2,450 parsecs (8,000 light years) away. V404 Cygni has the mass of about nine Suns and is intermittently growing by consuming a companion star. The burst of light provided insights into the flow of mass from the star to the black hole, but they also underscored the potential to find and track black holes with optical telescopes. Kimura says that even amateur astronomers with higher-end telescopes could see the light signal from V404 Cygni if they knew where to look.

Amateur astronomers have much to contribute to space science, Kimura says. The first hints that something unusual was happening at SS Cygni came from a network of amateurs and professionals who watch for anomalies in the night sky and upload their findings to a database. Once alerted, Kimura was able to guide the 3.8-metre SEIMEI telescope at the Okayama Astrophysical Observatory to focus in on the target.

Kimura and her co-author proposed a possible explanation for the abnormal light patterns from SS Cygni in a 2023 paper2. They suspect that an overflow of gas escaping from one of the stars in the binary system to the other distorted the view. Kimura says she’s inspired by the ways that observed light can illuminate the physics of distant objects. “Prior to this work, astronomers had not considered that overflow occurs in this system,” she says.

The popular Asian condiment contains large amounts of glutamic acid, which gives umami its unique flavour profile. “We wanted to identify how human umami taste receptors can detect glutamate,” explains Toda, who spent ten years as a researcher at Kikkoman.

During that time, the firm sponsored her PhD studies in agriculture at the University of Tokyo. Toda and her university colleagues developed a method for measuring the response of taste receptors1 and described the molecular mechanisms involved in humans and mice2. The technique for measuring receptor response was a luminescence-based assay comprising jellyfish-derived photoproteins that emit varying quantities of blue light when the receptor is activated. Toda describes the array as her proudest accomplishment so far, and it proved crucial to her later studies. “We revealed many phenomena using the new assay,” she says.

It allowed Toda to unravel the evolutionary story of how humans came to be capable of sensing glutamate. Palaeontological studies indicate that our primate ancestors were small. They ate mainly insects, which are rich in both amino acids such as glutamate and nucleotides. “Their umami taste receptors had a high sensitivity to nucleotides, which made insects seem tasty,” she says.

As primates became bigger over time, their diets diversified to include leaves — a puzzling transition because leaves contain plenty of bitter compounds and glutamates, but no nucleotides, so they were “probably not delicious”, says Toda.

But when she and her collaborators analysed the responses of taste receptors in primates from various lineages including gorillas, orangutans and howler monkeys, they discovered that larger primates were more sensitive to glutamate compared with their smaller counterparts3.

This indicates their umami taste receptors gradually evolved to detect glutamate in leaves, allowing larger primates to overcome the bitterness and transition to a diet that included plants, she explains.

Mountains and volcanoes
Japan has a mountainous interior which is mostly made up of volcanoes. These heights provide plenty of hiking opportunities and scenic viewpoints from which to see the surrounding areas.


Yamanashi and Shizuoka prefectures
Mount Fuji
Mount Fuji, the highest mountain in the country, is a beautifully symmetrical volcano and the symbol of Japan. Climbing Mount Fuji is popular during summer with people ascending via four different trails. The Fuji Five Lakes region at the northern foot of Mount Fuji and Hakone are popular resort destinations with views of the mountain.

Tokyo
Takaosan
Mount Takao is one of the closest natural recreation areas to central Tokyo offering beautiful scenery, an interesting temple and attractive hiking opportunities. Visitors can choose to hike all the way up to the top of the mountain or take the cablecar or chair lift halfway up.

Aso
Mount Aso
Mount Aso lies in the center of Kyushu and is part of the Aso-Kuju National Park. Its caldera is one of the largest in the world with a diameter of about 25 kilometers and a circumference of over 100 kilometers. Nakadake Crater at the center of the caldera is easily visited but not always accessible due to volcanic activities.
Capes, coasts and beaches
Japan's coastline is one of the world's longest, and many sections of it are quite impressive. Not only are there rugged cliffs, geological formations and hiking trails, but there are also plenty of beaches offering swimming and snorkeling opportunities.


Sanriku Coast
Kitayamazaki Coast
The Kitayamazaki Coast is an eight kilometer long stretch of coastline in northern Iwate Prefecture featuring sheer, 150-200 meter high cliffs. The coast is best seen from the Kitayamazaki Observatory, a park at the northern end of the coastline.

Izu Peninsula
Jogasaki Coast
The Jogasaki Coast is a beautiful section of coastline along the Izu Peninsula's eastern shore. There is an attractive hiking trail that follows the coast for almost ten kilometers, offering beautiful views of the jagged cliffs and stone formations along the edge.

Shimokita Peninsula
Cape Oma
Cape Oma is the northernmost point of the Shimokita Peninsula and of the entire Honshu Island, Japan's main island. The cape looks across over the Tsugaru Kaikyo Strait to southern Hokkaido where the city of Hakodate is visible on clear days. The area is most famous for the large tuna caught in its waters.
Gorges
Many gorges with beautiful views of cliffs, forests and waterfalls can be found in Japan. Many of the gorges can be hiked, while others can be enjoyed from boat tours or sightseeing trains.


Takachiho
Takachiho Gorge
The Takachiho Gorge in Miyazaki Prefecture is a narrow gorge lined with sheer cliffs and a 17 meter high waterfall along the way. Visitors can rent row boats to paddle down the river through the gorge or walk along paved paths that run along its edges.

Toyama Prefecture
Kurobe Gorge
The Kurobe Gorge is a beautiful, forested ravine in the rugged mountains of the Northern Japanese Alps. It is one of the deepest gorges in Japan with steep, nearly vertical cliffs, untouched virgin forests and outdoor hot springs. The main attraction is the sightseeing train that operates twenty kilometers into the gorge.

Near Hiraizumi
Geibikei Gorge
The Geibikei Gorge is a spectacular natural site outside Hiraizumi in the interior of Iwate Prefecture. The best way to view the tall cliffs and rock formations in the gorge is to take a 90-minute ride on a flat-bottomed boat that leads about one kilometer in.
Caves
Large limestone caves can be found across Japan and offer natural formations like limestone pools, underground waterfalls and streams that were formed millions of years ago. Visitors can explore a portion of these caves via walking courses and marvel at their natural beauty.


Yamaguchi Prefecture
Akiyoshido
Akiyoshido Cave in Yamaguchi Prefecture is Japan's largest and longest limestone cave. One kilometer of the nine kilometer long cave is open to the public, and various natural formations like limestone pools, underground waterfalls and streams, can be seen.

Fukushima Prefecture
Abukumado
Abukumado Cave is a 3000 meter limestone cave network in eastern Fukushima Prefecture that was formed over 80 million years ago. About 600 meters of the caverns are opened to the public, and it takes about an hour to explore the main walking course.

Sanriku Coast
Ryusendo Cave
Regarded as one of Japan's three great limestone caves, Ryusendo extends nearly 5000 meters into the mountains of Iwaizumi Town in Iwate Prefecture. About 700 meters of the cave are open to the public, and visitors can walk along the underground river and view three of the cave's four underground lakes.
Marshlands
Marshlands are popular hiking destinations found both up in the mountains and in lower elevations. Many marshlands are particularly beautiful during the autumn color season.


Gunma Prefecture
Oze National Park
Oze National Park is an excellent hiking destination that is popular during the skunk cabbages blooming season in late spring and early summer and during the fall colors if autumn. There are numerous trailheads to access the well maintained trails that lead around the marshlands and park.

Nikko
Senjogahara Marsh
The Senjogahara Marshland covers the plateau between Lake Chuzenji and Yumoto Onsen. It offers some of the best hiking in Nikko National Park and is particularly beautiful during the autumn leaf season in October.

Hokkaido
Kushiro Marshlands
The Kushiro Marshland in eastern Hokkaido is a national park supporting the only known population of endangered Japanese cranes in the country. The park offers bird watching, nature viewing and walking trails.
Waterfalls
There are hundreds of waterfalls across Japan, and some of them, like the Nachi Waterfall, have been religious sites with long histories. Some waterfalls can only be accessed by hiking along nature trails, while others can be conveniently viewed from observation decks.


Kumano
Nachi Waterfall
At 133 meters tall, Nachi Waterfall (Nachi no Taki) is the tallest single-tiered waterfall in Japan and is ranked as one of Japan's three most beautiful falls. Nachi no Taki was the original religious site in the Kumano Region and was venerated by the earliest Japanese people.

Okinawa Honto
Hiji Waterfall
Hiji Waterfall is a 26 meter tall waterfall located in the northern Yambaru area of Okinawa Honto. The waterfall is at the end of a nature trail through the forest and is a good spot for a rest before making the return trip back.

Nikko
Kegon Waterfall
The almost 100 meter tall Kegon Waterfall is the most famous of Nikko's many beautiful waterfalls, and ranked as one of Japan's three most beautiful falls. The waterfall is also a popular autumn color spot around mid to late October.
Rivers
There are many rivers in Japan, and some of them can be explored by river cruises. Other rivers are lined by hiking trails allowing visitors to enjoy the scenery at their own pace.


Yaeyama Islands
Iriomote Island
Most of Iriomote Island's interior is covered in dense jungle accessible by rivers that head inland from the sea. Kayak tours are offered on several of the rivers, while jungle boat cruises are organized on the island's two longest rivers.
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Towada
Oirase Stream
The Oirase Stream is a picturesque mountain stream in Aomori Prefecture that is one of Japan's most famous and popular autumn colors destinations. Visitors can choose to hike, drive or take a bus to enjoy the views along the stream.

Kyoto
Hozugawa Cruise
The Hozugawa River allows visitors to see the natural scenery of the largely undeveloped ravine from Kameoka to Arashiyama by joining a sightseeing cruise on traditional, flat-bottomed boats piloted by boatmen using oars and bamboo poles. The cruise is popularly combined with a ride on the Sagano Scenic Railway.
Lakes
There are a variety of lakes in Japan including caldera lakes, subterranean lakes and lagoons. Often surrounded by beautiful scenery, many lakes are popular hiking destinations, and some of them also offer sightseeing cruises.


Towada
Lake Towada
Lake Towada is the largest caldera lake on Honshu, Japan's main island, and is characterized by its two peninsulas. The best way to see the lake is by sightseeing cruises which offer close up views of the peninsulas, while the shores of the lake and the nearby Oirase Stream offer beautiful autumn colors around late October.

Akan National Park
Lake Mashu
Lake Mashu is a caldera lake in the Akan National Park. It is widely considered to be Japan's most beautiful lake, and also vies for the position of being the clearest lake in the world. Visitors are not allowed to go down to the water, but can view it from two observation decks stationed along the rim of the caldera.

Shiretoko Peninsula
Shiretoko Five Lakes
The Shiretoko Five Lakes are a set of five small lakes that offer beautiful views of the surrounding mountains and wilderness in Shiretoko. Visitors can walk along an elevated boardwalk to enjoy views of the first lake, while nature trails lead around the others.
Bays
Bays have been admired for their scenic beauty for centuries, and even hold the three top spots on the famed list of Japan's three most scenic places.


Yaeyama Islands
Kabira Bay
Emerald blue Kabira Bay (Kabirawan) is considered Ishigaki Island's most scenic view. Swimming, snorkeling and diving in the bay are not allowed, but a touristy, 30-minute glass bottom boat ride lets you take a look at the bay's underwater world.