Turbocharging rice photosynthesis – the vision and legacy of John Sheehy, a brilliant scientist

Yesterday, I received the sad news that my dear friend and former colleague at the International Rice Research Institute (IRRI), John  Sheehy, had passed away on 7 June after battling Parkinson’s Disease and Multiple System Atrophy (MSA) for several years. He was just 76.

I first met John in 1995, when he applied for the position of Systems Modeller at IRRI. I was Chair of the Search Committee. John came to IRRI after a successful career at the Grassland Research Institute (GRI) in Hurley, Berkshire, until it closed in 1992. His groundbreaking (and award-winning) work at GRI on nodulation, gaseous diffusion, and nitrogen fixation in grassland legumes, and other aspects of crop physiology focused on yield potential.

I knew the first time I spoke with John he was someone who would bring a very different scientific perspective to IRRI’s research. And that’s just what he did. He wasn’t some fresh-faced graduate or postdoc expected to toe the line in terms of rice science orthodoxy, so to speak. Always polite, he often challenged the perspectives and approaches of some IRRI old timers who couldn’t (or wouldn’t) appreciate John’s breadth of quantitative expertise. He had graduated with a BSc degree in Physics, completed an MSc in Electronics, and then studied for his PhD in ecophysiology under Professor John Cooper, CBE FRS at the Welsh Plant Breeding Station in Aberystwyth.

In coming to IRRI, he led research on and supported breeding the so-called New Plant Type (NPT) that was expected to push the yield barrier in rice.

Setting up the Applied Photosynthesis and Systems Modeling Laboratory, John came to the conclusion that a completely new approach was needed if rice yields were to be increased significantly. That’s because photosynthesis in rice (known as C3 photosynthesis) is inefficient compared to the system (C4) in other cereals like maize. John began to develop ideas to turbocharge photosynthesis by introducing ‘C4’ traits into rice, thereby aiming to increase photosynthetic efficiency by 50%, as well as improve nitrogen use efficiency, and double water use efficiency.

Rather than me trying to explain the rationale for this vision, why not listen to John explaining the need for a C4 rice.

John appreciated that IRRI could not realize this dream of a C4 rice alone. So he set about persuading, and bringing together, a group of many of the best scientists worldwide in a C4 Rice Project, that is partly funded by the Bill & Melinda Gates Foundation. The continuing Project is an important part of John’s scientific legacy.

It is now coordinated by Professor Jane Langdale, CBE FRS at the University of Oxford.

At the time of his death, and after 20 years of research, C4 rice is not yet a reality, but significant progress has been made.


John’s scientific output was prodigious, and his many publications appeared in some of the best rated journals in his field, like Field Crops Research for example, a reflection of his research stature at IRRI (and before he joined IRRI). You can check his publications on Google Scholar.

He also waded enthusiastically into the controversy over the System of Rice Intensification or SRI, questioning—based on solid quantitative analysis of yield potential in rice—the yield claims of SRI adherents.


John retired in 2009 and returned to the UK. Before leaving IRRI, he met with Gene Hettel (former Head of IRRI’s Communication and Publications Services, and ‘IRRI Historian’) to record his thoughts on rice science and the challenges that IRRI would face.


In 2012, John was recognized in the New Year Honours (see page N.24) with an OBE for services to agricultural research and development, which was conferred during an investiture at Buckingham Palace on 14 February.

John receiving his OBE from HRH The Prince of Wales (L), and after the ceremony with wife Gaynor (L), and daughters Isabel (L) and Rhiannon (R).

In July 2014, John was honoured as a Fellow of his alma mater, Aberystwyth University.


In 2011, Steph and I joined John and Gaynor’s many friends and relatives to celebrate their 40th wedding anniversary.

L-R: Rhiannon, Gaynor, John, and Isabel

While at IRRI, John had taken enthusiastically to golf, and could be seen almost every weekend out on the golf course south of Los Baños where he had become a member. On his retirement to the UK, he was unfortunately unable to continue with this passion, due to bouts of poor health.

After I retired in 2010 back to the UK, John and I kept in touch regularly by email, on the phone, or SMS, when either Wales or Ireland were doing well at rugby, especially in the Six Nations championship. He had divided loyalties, born in Wales of Irish ancestry.

The last time I saw John was in July 2017, when Steph and I spent the weekend with him and Gaynor in Marlow, and met up with other IRRI friends, Graham and Sue McLaren (who now reside in Canada),

L-R: Gaynor, Graham, Sue, Steph, John, and me.

It was also an opportunity for John and me to swap OBE investiture reminiscences. I had also been made an OBE in the same New Year Honours as John, but attended an investiture two weeks later on 29 February.


John was a far better scientist than I could ever aspire to be. I always sought his advice on science issues. In return, he asked my advice about how to manoeuvre through institute politics and management to influence his research agenda, especially after I had moved upstairs, so to speak, to join IRRI’s senior management team.

But what I remember most about John was his cracking, but rather dry, sense of humor. His generosity of spirit. He was an excellent host. Many’s the dinner or BBQ Steph and I enjoyed with John, at his house or ours.

Christmas Day 2006 Chez Sheehy. L-R: John, Sue McLaren, Steph, Catherine McLaren, me, Gaynor, Alex McLaren, and Graham McLaren.

John, you will be sadly missed. Rest in Peace!


This obituary (written by Gene Hettel) has just been published on the IRRI website.

And this obituary (written by me) appeared in The Guardian on 5 July 2019.

Everyone’s a taxonomist

I’ve just discovered (via Twitter) that 19 March was Taxonomist Appreciation Day. This was, as far as I can make out, a celebration of the important—fundamental even—contribution that biologists known as taxonomists make to our understanding of the living world. Taxonomists bring order to the biodiversity that’s all around us. Indeed, without this order and understanding, it would be more difficult to know for example which plants and animals are endangered, and to prioritize what to conserve, and where.

The most celebrated taxonomist of all was surely the eighteenth century Swedish botanist Carl von Linné (whose Latinized name, Linnaeus, identifies him as the taxonomic authority, L., for many plants and animals).

So what do taxonomists do? One of their important roles is to describe and catalogue all plants and animals and, in the case of plants, publish this information in compendia known as Floras as an aid to identification, like those written about the plants of the British Isles and Europe that have been studied for hundreds of years.

Other Floras are still being written. Take the Flora Zambesiaca, for example, a project started in 1960 as the taxonomic study of native and naturalised plants of the Zambezi River basin, covering the territories of Botswana, Malawi, Mozambique, Zambia, Zimbabwe and the Caprivi Strip. This is a work in progress, and there are many other parts of the world where the diversity of plants is only now being discovered and documented, particularly in the Tropics.

But taxonomists also look at the variation within species, and assess the dynamics of species distribution and evolution.


Mr Les Watson

I had my first taste of taxonomy at the University of Southampton where, as first year students or freshmen in 1967/68, we studied the diversity of flowering plants under the tuition of taxonomist Les Watson. He and another colleague Alan Myers took us to the west coast of Ireland for a field course in July 1968 where we studied the vegetation of the Burren in Co Clare.

Professor Vernon Heywood

In my final or senior year in 1970, I sat in on a plant taxonomy course given by eminent taxonomist Professor Vernon Heywood from the University of Reading (Les Watson had moved to Australia in 1968/69, and had not been replaced in the Department of Botany). I met up with Professor Heywood in 1991 at a conference in Rome where we had an opportunity to reminisce about that course.

I never expected that, one day, I would engage in taxonomic research. However, I never participated in describing or naming plant species, nor undertaking the enormous task of contributing to Floras that is sometimes considered the be-all and end-all of taxonomists’ work. I take my hat off to those taxonomists who write Floras, often relying on dried herbarium specimens of plants collected in nature. Nevertheless, in my own work, I have used herbaria on occasion, and twice spent time looking at specimens of lentil (Lens culinaris Medik.) and grasspea (Lathyrus sativus L.) among the millions of herbarium sheets curated in the Herbarium at the Royal Botanic Gardens at Kew. My interest was in the relationships of these cultivated plants and their wild relatives.

Comparing notes in the field in the Andes of central Peru with potato taxonomist Professor Jack Hawkes (who supervised my PhD dissertation).

In 1973 I joined the International Potato Center in Peru as an Associate Taxonomist, studying the evolution of cultivated potatoes. Biosystematics, a sub-discipline of plant taxonomy, was my field, and I investigated species relationships through field experiments to understand patterns of morphological variation, through breeding experiments, and cytogenetic analysis of chromosome pairing in hybrids, among other several different approaches.

When I returned to Birmingham in 1981 as Lecturer in Plant Biology, I continued research on wild potatoes, and also several legume species. I also contributed about half the lectures to a second year module on flowering plant taxonomy.

On moving to the International Rice Research Institute (IRRI) in the Philippines in July 1991, my colleagues and I delved into the taxonomy and species relationships of the two cultivated species of rice, Oryza sativa L. and O. glaberrima Steud., and the 20 or so wild species in the genus Oryza. We published quite extensively, and you you can peruse a list of rice publications (many with PDF files) here.


Just last week I met up for lunch with six retired former colleagues from the School of Biological Sciences at the University of Birmingham: three plant scientists (including me), three geneticists, and a zoologist. Inevitably we began to discuss not only the administrative and organization changes that had occurred at the university (I taught there between 1981 and 1991), but how the teaching of biology had also changed, and the topics that now form a core biology curriculum.

Back in the day, whole organism biology still formed an important component of an undergraduate degree in biological sciences at Birmingham. Nowadays, and for obvious reasons, there’s much more focus on molecular biology, and recent hirings in what is now the School of Biosciences (Biological Sciences and Biochemistry merged some years back) reflect that change of emphasis.

Alas, it’s no longer possible to study at Birmingham for a biology degree with a plant sciences focus. But that’s not just a Birmingham issue; it’s nationwide. And taxonomy is perhaps the discipline that has suffered more than most. Taxonomists are just not coming through the system. Just at the time when one can argue there should be more demand for taxonomists than ever before, given the environmental changes that threaten the world’s vegetation. In some regions we may be losing species even before they have been identified. Harvard biologist EO Wilson wrote this in 2017: Our incomplete taxonomic knowledge impedes our attempts to protect biodiversity. A renaissance in the classification of species and their interactions is needed to guide conservation prioritization [1].


Now, I started this piece stating that everyone is a taxonomist. Is that a fair assumption?I think so.

Appa Rao collecting upland rice varieties from a farmer in the Lao PDR.

Taxonomy (and classification) is a fundamental human characteristic, something we do every day. We sort the complex world around us into meaningful categories, and we give them names. In many societies, farmers and their husbands use so-called ‘folk taxonomies’ to manage the various crops grown, and often the diversity of different varieties within a crop. I have myself talked to potato farmers in the Andes of southern Peru about their cultivation of different varieties, and why these are grown in different ways. In the Lao PDR, with my colleague Dr Appa Rao, we looked at how farmers name all their rice varieties.

Even before talking to my second year students about flowering plant taxonomy as such (and the different approaches used to study variation), I asked them to practice some simple taxonomies on themselves: males vs. females, blondes vs. brunettes, spectacle users vs. non-users, for example. These are discrete characteristics, binary, one or the other. Then we’d look at the complexity of coping with characters that vary quantitatively, such as height, length, etc.

Fortunately, there are many numerical techniques that allow us to cope with all sorts of measurements, and reduce complexity to a state that can be interpreted more easily.

The classification of different rice species based on the measurement and analysis of a range of morphological characters.

The use of different molecular markers now allows us to refine taxonomies built using morphological data. But, as I once read in a letter published in a scientific journal, a professor of taxonomy decried the lack of basic species knowledge among many students using molecular approaches. They could wax lyrical, he stated, about the value of different molecular techniques, but they had hardly looked at a living plant. That brings me back to my concern about the reduction in teaching whole organism biology.

As I say, we are all taxonomists, one way or another. Unfortunately I don’t see any scientific expansion (in the UK at least) in this particular discipline.

The situation may be different in North America. Plant sciences are still very strong in many US universities, and indeed there is a bill before Congress that promotes botanical research & sciences capacity, generates demand for native plant materials, & authorizes related federal activities.


[1] Wilson, EO (2017). Biodiversity research requires more boots on the ground. Nature Ecology & Evolution 1, 1590 –1591

Around the world in 40 years . . . Part 23: An Anglo-Italian connection

I’ve twice traveled by train, in 2004 and 2006, from my home in Bromsgrove in northeast Worcestershire to Rome in central Italy. And if I had my way, I’d travel everywhere by train, if that were possible.

When visiting government agencies that provided financial support to the International Rice Research Institute (IRRI) when I was Director for Program Planning & Communications (DPPC), I tried to combine as many visits into a single trip as possible, thus making the best use of my time on the road. In Europe, traveling by train was by far the most convenient (and comfortable) way of visiting several cities on the way, rather than hopping on and off planes for relatively short flights. Not to mention the inconvenience of additional waiting time at airports and the hassle of actually getting to and from them.

Train travel in many European countries is reliable and, compared to the UK, competitively priced. Purchasing a Eurail pass was by far the cheapest option, even for First Class tickets, and could be bought online from the Philippines.

This was my itinerary on both occasions:

  • Bromsgrove – Birmingham New Street – London Euston (into Birmingham on London Midland—now operated by West Midlands Trains—then Virgin Trains to London; around 2 hours or so; map)
  • London Waterloo (Eurostar now operates from London St Pancras) – Brussels Midi (on Eurostar; around 2 hours; map)
  • Brussels Midi – Cologne – Bonn Central (on the Thalys to Cologne, and Deutsche Bahn, DB; just over 2 hours; map)
  • Bonn Central – Basel – Bern (Deutsche Bahn to Basel, then Swiss Federal Railways, or SBB/CFF/FFS), along the Rhine Valley (around 5½ hours; map)
  • Bern – Milan Central (on Swiss Federal Railways; around 4½ hours; map)
  • Milan Central – Rome Termini (on Trenitalia; 3 hours; map)

On the second trip I traveled with IRRI Director General Bob Zeigler (and his wife Crissan) to visit donor agencies in Brussels (Directorate General for International Cooperation or DGCI of Belgium, and the European Union, EU), the Federal Ministry for Economic Cooperation and Development (BMZ) in Bonn, the Swiss Development Cooperation (SDC) in Bern (and a side trip to Basel where Bob gave a seminar at the Syngenta Foundation), and finally, the International Fund for Agricultural Development (IFAD, an agency of the United Nations) in Rome – all members of the Consultative Group on International Agricultural Research or CGIAR.

Crissan and Bob Zeigler


We met at London’s Waterloo station for the Eurostar service to Brussels, arriving there mid-afternoon. Since no meetings had been arranged that same day, we enjoyed the warm afternoon sunshine for a stroll around La Grand-Place (a UNESCO World Heritage Site), before enjoying our dinner at one of the many cafes close by.

Bob and Crissan feasted on one of the local delicacies: moules (mussels).

I like mussels, but in moderation, just a few added to a fish pie or a fish soup. Not a whole meal. In any case, our meal was accompanied, of course, by several glasses of excellent Belgian beer.


The day after our meetings, we caught the Thalys (the Belgian TGV) to Cologne, and then a regional service for the short hop to Bonn. We had just one day of meetings in Bonn, with the German aid ministry (BMZ), and then spent an excellent day touring the vineyards of the Ahr Valley just south of Bonn. Our main contact was my old friend Marlene Diekmann who I’d known for many years before she joined the BMZ when she was a plant pathologist at the International Plant Genetic Resources Institute (IPGRI, now Bioversity International) in Rome.

On previous visits to Bonn, in all weathers, Marlene and I had gone walking along the terraces of the Ahr Valley, as I described in this blog post. On this current trip with the Zeiglers, as in the past, we sampled some of the fruits of the vintner’s art. And very good it was.

Each time I have visited the Ahr Valley I have never failed to be impressed at the cultivation of the vines on such steep slopes. In the early evening we headed to Rheinbach (map) to join Dr Hans-Jochen de Haas, who was Germany’s representative to the CGIAR, and became a good friend.

I’d last seen him the previous year in Bonn and presented him with a book on rice culture.

A few years later (and before I retired in 2010) he sadly passed away after contracting Creutzfeldt-Jakob disease or CJD.

Bob and I (with Marlene) also made a one-day visit to Hannover (again by train) to visit the Volkwagen Foundation to try and tempt them to support a research project on rice and climate change involving a German scientist seconded to IRRI.

Commitments in Germany completed, Switzerland was our next stop, so we took the train along the River Rhine to Basel, and transferring to Swiss railways to Bern.


I first visited Switzerland in July 1984 when I attended the 9th Triennial Conference of the European Association for Potato Research (EAPR), that was held in Interlaken in the heart of the Bernese Oberland.

A group of us from the UK flew from London Gatwick to Bern (Switzerland’s capital city) on a Swissair BAe 146, and then taken the train for the 1 hour rail journey to Interlaken. There are no flights to Bern nowadays; Switzerland is served by two major international airports in Geneva (in the west) and Zurich (in the north central part of the country). And, in any case, rail services across the country are frequent, convenient, and comfortable.

In 1984, I’d taken a trip up to Wengen (1274 m) from Interlaken, with the last leg on the funicular railway from Lauterbrunnen. The Zeiglers and I repeated this trip. And after lunch in Wengen, we took the cable car up to Männlichen (2343 m), before dropping to Grindelwald (1034 m) on Europe’s longest gondola cableway (and third longest in the world).

At Männlichen there are fabulous views of the Eiger, Jungfrau and other mountains.

Watch this video that I found on YouTube of the cable car ride to Männlichen and the gondola cableway down to Grindelwald.

All too soon, our Swiss visit was over, and we took the train to Milan, an impressive journey through the Alps and the Italian lakes.

In Milan, we transferred to the high speed train to Rome. That was an interesting journey. In 2006, the 18th FIFA World Cup was hosted by Germany. Although Mexico had been eliminated from the competition by then, our train was full of supporters from Mexico on their way to Rome to enjoy the sights. Bob, Crissan and I all spoke Spanish. Bob and Crissan had actually lived in Mexico for a few years before returning to IRRI in 2005. So we had a great time with the Mexicans, and our fast train journey to Rome (a city I have visited numerous times) passed even faster it seemed.


 

Around the world in 40 years . . . Part 22: Iberian capitals

As Director for Program Planning and Communications (DPPC, from 2001 until my retirement in 2010) at the International Rice Research Institute (IRRI), I managed the institute’s portfolio of research projects, reporting back to donor agencies on progress and outcomes, such as the UK’s DFID, USAID in the USA, or the SDC in Switzerland, to mention just three. And working with them to ensure continued financial support to the institute each year.

On a rolling basis, I tried to meet officials from these agencies on their home turf, so to speak, and would coordinate several meetings in a single trip. I often scheduled meetings with European donor agencies when I was back on leave in the UK each year. And this was the case in early July 2003 when I visited Portugal (Lisbon) and Spain (Madrid).


At that time, one of my IRRI colleagues, Dr Swapan Datta, had a joint research project with Professor M. Margarida Oliveira of the Instituto de Tecnologia Química e Biológica António Xavier (ITQB), a scientific research and advanced training institute of the Universidade NOVA de Lisboa in Portugal. One of her students, Marta Vasconcelos, worked on rice biofortification with ferritin in Datta’s lab. Another, Sónia Negrão, worked with IRRI’s plant breeders for part of her PhD study, and held a post-doctoral fellowship at IRRI as well.

On the beach at Oeiras close to ITQB, with Margarida, Marta, and Sonia (in the left image) and Sonia and Marta (right).

Prof. Oliveira and I visited the Portuguese overseas aid agency to seek funding for joint rice projects. Portugal, at that time, provided only a small amount of funding (if any—I don’t remember the details) to IRRI. I also got to see some rice growing at the ITQB experiment station.

During the visit to ITQB, I gave a seminar about the genetic resources of rice and, with the donor visit, most of my second day in Lisbon was quite full. But, as was often the case in visits to donor capitals, there also was an opportunity for some sight-seeing.

I had arrived to Lisbon the day before, in the early afternoon. After settling into the Hotel Lutécia in the Areeiro district (map), north of the city center, I decided to see what Lisbon had to offer and took the metro to the city center, about a 20 minute ride from the Roma-Areeiro station to the Baixa-Chiado station.

Lisbon is a lovely maze of narrow streets, and large open plazas. One thing that immediately struck me, especially from the heights of the Castelo de S. Jorge, were the orange tile roofs of all the houses spread over the surrounding hills, and the views over the Tagus River, and west to the expanses of the Atlantic Ocean.

Anyway, I made my way from the metro, south along Rua Agustina (mostly traffic free) full of designer shops and cafes and restaurants towards the Praça de Comércio.

And although I’d intended to carry on walking around the city, I did something I’d never done before. Seeing a line of double-decker open top buses to one side of the plaza, I decided to take a city tour. Having only a short time in Lisbon I realized this would be the best way of seeing much of the city.

The tour lasted about two hours, and I certainly saw many of the important sites, some of which I went back to explore on foot afterwards.

The tour took in: Praça da Figueira; Praça D. Pedro IV; Praça da Restauradores; Av. da Liberdade; Praça do Marquês de Pombal; the view down to the coast from the Alameda Cardeal Cerejeira; west to the Torre de Belém; and back to the city center via the Praça do Império and the magnificent Mosteiro dos Jerónimos, passing under the impressive  Ponte 25 de Abril over the Tagus.

Although it was getting on in the afternoon, I decided to walk up to the Castelo de S. Jorge and enjoy the views over the city.

Castelo de S. Jorge from Praça da Figueira (L) and the plaza from the castle (R).

Then, it was back down to enjoy a beer or three and a dish of bacalhau (a typical dish of cod), before heading back to my hotel.

On the second evening I decided to stay near my hotel, write up my notes, and get ready for a mid-morning departure to Madrid the following day.


I had just a couple of nights in Madrid. I’d been through the city’s airport in 1981 on my way to the Canary Islands. That was in June, and I remember stepping outside the airport terminal building to experience the heat. It was over 40ºC. Now, I’d lived in the tropics for over eight years up till then, but I’d never experienced heat like that.

In July 2003 it was pretty hot as well. I arrived mid-afternoon on my flight from Lisbon. I was booked into a boutique hotel near Real Madrid’s Santiago Bernabéu Stadium. By the time I was settled into my hotel, it was late afternoon, and fortunatley it was cooling down. So I took the metro to the Puerta del Sol plaza.

I wandered along the Calle Mayor, taking in the Plaza Mayor and Plaza de la Villa on my left, on on towards the Catedral de Santa María la Real de la Almudena and the Palacio Real.

Nearby there was a cafe where I could sit outside and enjoy a cold beer, before I headed back towards the Puerta del Sol plaza to choose a restaurant for my evening meal. Then it was back on the metro to my hotel.

I had meetings the next day, all day at the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA) in the Moncloa-Aravaca district, northwest of the city center.

In the evening I chose a small restaurant close to the hotel. Excellent food!

Then, early the next day, it was off to the Madrid-Barajas Adolfo Suárez Airport, and an Iberia flight to Switzerland (Zurich), where I had a meeting in Bern at the SDC.

Before heading back to BHX, I visited old friends in The Hague, Gordon and Joan MacNeil. Gordon had been IRRI’s Deputy Director General for Finance, and left the institute in 2002.

All in all, an enjoyable trip, but not very fruitful donor-wise, unfortunately.

In 2012, Steph and I had a short holiday in Portugal, visiting my eldest brother Martin and his wife Pauline who live about 100 km north of Lisbon.


 

Around the world in 40 years . . . Part 21: Taking in Tokyo (and Tsukuba)

I recently wrote about a trip to Bali in 2005 when the IRRI Board of Trustees (BoT) held one of its biannual meetings there.

Four years later, in September 2009,  Steph joined me when I attended the BoT meeting in Japan that was held in Tsukuba, the science city just over 60 km or so northeast of Tokyo, followed by a couple of days in Tokyo itself. Since  the meeting was held in the week before Steph’s 60th birthday, we decided to stay on an extra couple of nights and see something of Tokyo. I had been in Tokyo just once before¹, around 1994; Steph had never visited. However, we’d both passed through Tokyo’s Narita airport many times while flying to the USA.

In the good old days, before Northwest Airlines merged with and was taken over by Delta. Narita was a major hub for NW flights to and from the USA, as is the case now with Delta.

Leaving Manila for Tokyo on the early morning flight (a very early start from Los Baños to check-in three hours ahead of the flight) was not without its challenges, and we weren’t entirely certain we’d be able to fly. The Philippines had been hit the day before by Typhoon Ketsana (known in the Philippines as Ondoy), the first of two typhoons to hit the country within one week. There was extensive flooding in parts of Manila (which we saw as the Delta 747 climbed out of the city). At Manila’s Ninoy Aquino International Airport or NAIA there was chaos at the check-in and in the departure areas. Many flights had failed to leave the previous day, and with so many passengers with nowhere else to go, the airport was heaving with people hoping to get a flight out.

Since Steph was traveling with me, I used air miles to upgrade our booking to Business Class as a special treat. The flight to Narita takes four hours. On arrival at Narita, we had a short wait for the bus to Tsukuba, around an hour northwest from the airport. We stayed at the Okura Frontier Hotel (the square building on the right) in the center of the city.

The Board and IRRI Management (and scientists as needed) met for three and a half days at the Tsukuba International Conference Center (just over a five minute walk south from the hotel).

The entrance to the Tsukuba International Conference Center.

Meanwhile, Steph joined the other spouses for several excursions in the surrounding region, as well as into Tokyo, to visit markets, see local handicrafts, take part in traditional Japanese flower arranging, a tea ceremony, and the like.

Then, after four days in Tsuskuba, we all decamped to central Tokyo, to the the Sheraton Miyako Hotel where, close-by, several events were organized by IRRI’s Japanese partner organization, the Japan International Research Center for Agricultural Sciences or JIRCAS.

The Sheraton Miyako Hotel (on the left) in the Minato district of Tokyo.

As I mentioned earlier, Steph and I stayed on for an extra couple of nights, so we could explore parts of Tokyo at the weekend, on Saturday 3 October, departing for Manila on the Sunday evening flight.

I’ve marked the places we visited on the map below.

We took full advantage of the extensive Tokyo subway system. We were able to purchase day tickets that gave access to the whole of the Tokyo subway system, over both the Toei Line and the Tokyo Metro Line. However, our first challenge was to purchase two tickets using the ticket machines. Eventually a very kind Japanese gentleman saw we were having a little difficulty, and helped us successfully navigate the menu.

The entrance to Shirokanedai subway station.

Starting at Shirokanedai Station (station I02, center bottom left on the map) on the Mita Line (Toei Line system), we traveled to the commercial district of Akihabara (I08), well known for its many electronics outlets. From there we visited Hibiyakōen (via Hibiya station, I08/H07), a park (near the Imperial Palace) where an agricultural exhibition was being held, that also featured a booth for the Consultative Group on International Agricultural Research (including IRRI). Then it was on to the Shinjuku Gyoen National Garden (via Shinjuku-Gyoemmae station, M10), and back to the hotel.

One thing struck us quite forcefully during this day excursion: how quickly one could get away from the hustle and bustle of Tokyo at the Shinjuku Gyoen National Garden. It was a haven of peace and tranquility. Early October was perhaps not the best time of the year to see the garden. But it was lovely, nevertheless, and being enjoyed by locals with their families, although not at all busy.

Here is a 17 minute video that I made of the day.

One day is surely not enough to explore a city the size of Tokyo, but we did get to visit three areas that we had chosen. Getting around Tokyo was much easier than I anticipated, and more so than I remembered from my visit in the 1990s.

Of course there are many other places in Japan that we never had the opportunity and maybe one day we will return. The only other city I have seen—from the airport constructed on an artificial island—is Osaka.


¹ During that trip, when I was hosted by a former member of IRRI’s Board of Trustees, and another who was currently serving on the Board, I visited both Tsukuba and Tokyo. In  Tokyo I met officials at the Ministry of Agriculture, Forestry, and Fisheries (MAFF), and there I came across one of my former students, Yoshi Nishikawa, who attended the University of Birmingham plant genetic resources MSc course in 1987-88.

Around the world in 40 years . . . Part 20: Volcanoes, temples, and rice in Bali

During the 19 years I worked at the International Rice Research Institute (IRRI) in the Philippines, I traveled to most of the countries in Asia, some repeatedly (Laos, for example) and others (such as Sri Lanka) just the once.

I must have visited Indonesia half a dozen times, mostly to Jakarta (on the island of Java) and to Bogor, about 64 km south of the capital, where one of IRRI’s sister centers, the forestry institute CIFOR, has its headquarters.

My first visit to Asia, in 1982, was to Indonesia. I stayed in Bogor for a couple of nights at the famous botanical garden there before returning to Jakarta to attend a genetic resources conference. However, it wasn’t until 2005 that I experienced the beauty of Bali for the first and only time.

Bali’s landscapes are dominated by three volcanoes in the north and northeast, the highest of which is Mt Agung, active since 2017.

These landscapes have been molded by generations of rice farmers who built and still maintain terraces to grow their precious crops. The soils, volcanic in origin, are fertile, and appear very productive.

IRRI’s Board of Trustees (BoT) meets twice a year. One meeting, in April, is always held at the institute’s headquarters in Los Baños, some 70 km south of Manila. The other meeting is often co-hosted by one of the institute’s national program partners with which IRRI collaborates to develop better rice technologies. Such joint meetings are often the opportunity for Board members (who come from a wide range of backgrounds, not necessarily agricultural) to better understand national rice production issues, and to see first hand how technologies are being tested, and disseminated to and adopted by farmers to increase agricultural productivity.

Rice varieties on display (above) and technologies (below) at a field day for IRRI’s Board of Trustees.

In 2005, the September BoT meeting was held at the Pan Pacific Nirwana Bali Resort 27 km west of Bali’s capital Denpasar. Steph joined me on this trip for only the second time (she did join me on a trip to Laos in 1997, then to Japan in 2009). We flew from Manila via Singapore on Singapore Airlines.

The BoT meeting lasted three days, and while we were locked away in presentations and discussions, the group of IRRI wives who had come along for the trip took various excursions around the island. Fortunately, we scientists and management also got to see something of Bali, the fertile volcanic landscapes, and rice agriculture on the picturesque and iconic rice terraces typical of the island.

Bali has a thriving tourist industry, but at the Nirwana resort we saw very little of the multitudes that flock to Bali each year. In any case most tourists stick close to Denpasar and its nightlife, in resorts located to the east and south of the capital. The coast west of Denpasar still remains unspoiled and uncrowded, however, according to an article that appeared in The Guardian today.

The hotel was very comfortable, and we enjoyed a large room with a balcony overlooking the restless Indian Ocean (next stop south: Antarctica!). The resort lies in the middle of an 18 hole golf course, interspersed with rice fields and lotus ponds, so there were ample opportunities for long walks at sunset. Several bars and restaurants are dotted around the complex, most with views over the golf course or the ocean. There were several pools to relax in.

Lotus ponds

Once the IRRI Board meeting was done and dusted, Steph and I decided to extend our stay over a long weekend.Just a short distance along the coast from the resort stands the famous and revered 16th century Hindu temple at Tanah Lot with access along the beach.

Unlike much of Indonesia (which is the world’s largest Muslim nation), Bali is primarily Hindu, and that is reflected in its culture, dances, and customs, some of which we experienced at a reception one evening.

In just over a week, we just sampled the flavor of Bali, but it would take an extended stay to become immersed in its vibrant culture. While I would like to return, one day, there are so many other places that I just have to explore first, given the opportunity.

 

 

 

 

Discovering Vavilov, and building a career in plant genetic resources: (3) Becoming a genebanker in the 1990s, and beyond

My decision to leave a tenured position at the University of Birmingham in June 1991 was not made lightly. I was about to be promoted to Senior Lecturer, and I’d found my ‘home’ in the Plant Genetics Research Group following the reorganization of the School of Biological Sciences a couple of years earlier.

But I wasn’t particularly happy. Towards the end of the 1980s, Margaret Thatcher’s Conservative Government had become hostile to the university sector, demanding significant changes in the way they operated before acceding to any improvements in pay and conditions. Some of the changes then forced on the university system still bedevil it to this day.

I felt as though I was treading water, trying to keep my head above the surface. I had a significant teaching load, research was ticking along, PhD and MSc students were moving through the system, but still the university demanded more. So when an announcement of a new position as Head of the Genetic Resources Center (GRC) at the International Rice Research Institute (IRRI) in the Philippines landed on my desk in September 1990, it certainly caught my interest. I discussed such a potential momentous change with Steph, and with a couple of colleagues at the university.

Nothing venture, nothing gained, I formally submitted an application to IRRI and, as they say, the rest is history. However, I never expected to spend the next 19 years in the Philippines.


Since 1971, I’d worked almost full time in various aspects of conservation and use of plant genetic resources. I’d collected potato germplasm in Peru and the Canary Islands while at Birmingham, learned the basics of potato agronomy and production, worked alongside farmers, helped train the next generation of genetic conservation specialists, and was familiar with the network of international agricultural research centers supported through the Consultative Group on International Agricultural Research or CGIAR.

What I had never done was manage a genebank or headed a department with tens of staff at all professional levels. Because the position in at IRRI involved both of these. The head would be expected to provide strategic leadership for GRC and its three component units: the International Rice Germplasm Center (IRGC), the genebank; the International Network for the Genetic Evaluation of Rice (INGER); and the Seed Health Unit (SHU). However, only the genebank would be under the day-to-day management of the GRC head. Both INGER and the SHU would be managed by project leaders, while being amalgamated into a single organizational unit, the Genetic Resources Center.

I was unable to join IRRI before 1 July 1991 due to teaching and examination commitments at the university that I was obliged to fulfill. Nevertheless, in April I represented IRRI at an important genetic resources meeting at FAO in Rome, where I first met the incoming Director General of the International Board for Plant Genetic Resources (soon to become the International Plant Genetic Resources Institute or IPGRI), Dr Geoff Hawtin, with whom I’ve retained a friendship ever since.

On arrival at IRRI, I discovered that the SHU had been removed from GRC, a wise decision in my opinion, but not driven I eventually discerned by real ‘conflict of interest’ concerns, rather internal politics. However, given that the SHU was (and is) responsible, in coordination with the Philippines plant health authorities, to monitor all imports and exports of rice seeds at IRRI, it seemed prudential to me not to be seen as both ‘gamekeeper and poacher’, to coin a phrase. After all the daily business of the IRGC and INGER was movement of healthy seeds across borders.


Klaus Lampe

My focus was on the genebank, its management and role within an institute that itself was undergoing some significant changes, 30 years after it had been founded, under its fifth Director General, Dr Klaus Lampe, who had hired me. He made it clear that the head of GRC would not only be expected to bring IRGC and INGER effectively into a single organizational unit, but also complete a ‘root and branch’ overhaul of the genebank’s operations and procedures, long overdue.

Since INGER had its own leader, an experienced rice breeder Dr DV Seshu, somewhat older than myself, I could leave the running of that network in his hands, and only concern myself with INGER within the context of the new GRC structure and personnel policies. Life was not easy. My INGER colleagues dragged their feet, and had to be ‘encouraged’ to accept the new GRC reality that reduced the freewheeling autonomy they had become accustomed to over the previous 20 years or so, on a budget of about USD1 million a year provided by the United Nations Development Program or UNDP.

When interviewing for the GRC position I had also queried why no germplasm research component had been considered as part of the job description. I made it clear that if I was considered for the position, I would expect to develop a research program on rice genetic resources. That indeed became the situation.


Once in post at IRRI, I asked lots of questions. For at least six months until the end of 1991, I made no decisions about changes in direction for the genebank until I better understood how it operated and what constraints it faced. I also had to size up the caliber of staff, and develop a plan for further staff recruitment. I did persuade IRRI management to increase resource allocation to the genebank, and we were then able to hire technical staff to support many time critical areas.

But one easy decision I did make early on was to change the name of the genebank.  As I’ve already mentioned, its name was the ‘International Rice Germplasm Center’, but it didn’t seem logical to place one center within another, IRGC in GRC. So we changed its name to the ‘International Rice Genebank’, while retaining the acronym IRGC (which was used for all accessions in the germplasm collection) to refer to International Rice Genebank Collection.

In various blog posts over the past year or so, I have written extensively about the genebank at IRRI, so I shall not repeat those details here, but provide a summary only.

I realized very quickly that each staff member had to have specific responsibilities and accountability. We needed a team of mutually-supportive professionals. In a recent email from one of my staff, he mentioned that the genebank today was reaping the harvest of the ‘seeds I’d sown’ 25 years ago. But, as I replied, one has to have good seeds to begin with. And the GRC staff were (and are) in my opinion quite exceptional.

In terms of seed management, we beefed up the procedures to regenerate and dry seeds, developed protocols for routine seed viability testing, and eliminated duplicate samples of genebank accessions that were stored in different locations, establishing an Active Collection (at +4ºC, or thereabouts) and a Base Collection (held at -18ºC). Pola de Guzman was made Genebank Manager, and Ato Reaño took responsibility for all field operations. Our aim was not only to improve the quality of seed being conserved in the genebank, but also to eliminate (in the shortest time possible) the large backlog of samples to be processed and added to the collection.

Dr Kameswara Rao (from IRRI’s sister center ICRISAT, based in Hyderabad, India) joined GRC to work on the relationship between seed quality and seed growing environment. He had received his PhD from the University of Reading, and this research had started as a collaboration with Professor Richard Ellis there. Rao’s work led to some significant changes to our seed production protocols.

Since I retired, I have been impressed to see how research on seed physiology and conservation, led by Dr Fiona Hay (now at Aarhus University in Denmark) has moved on yet again. Take a look at this story I posted in 2015.

Screen house space for the valuable wild species collection was doubled, and Soccie Almazan appointed as  wild species curator.

One of the most critical issues I had to address was data management, which was in quite a chaotic state, with data on the Asian rice samples (known as Oryza sativa), the African rices (O. glaberrima), and the remaining 20+ wild species managed in separate databases that could not ‘talk’ to each another. We needed a unified data system, handling all aspects of genebank management, germplasm regeneration, characterization and evaluation, and germplasm exchange. We spent about three years building that system, the International Rice Genebank Collection Information System (IRGCIS). It was complicated because data had been coded differently for the two cultivated and wild species, that I have written about here. That’s a genebank lesson that needs to be better appreciated in the genebank community. My colleagues Adel Alcantara, Vanji Guevarra, and Myrna Oliva did a splendid job, which was methodical and thorough.

In 1995 we released the first edition of a genebank operations manual for the International Rice Genebank, something that other genebanks have only recently got round to.

Our germplasm research focused on four areas:

  • seed conservation (with Richard Ellis at the University of Reading, among others);
  • the use of molecular markers to better manage and use the rice collection (with colleagues at the University of Birmingham and the John Innes Centre in Norwich);
  • biosystematics of rice, concentrating on the closest wild relative species (led by Dr Bao-Rong Lu and supported by Yvette Naredo and the late Amy Juliano);
  • on farm conservation – a project led by French geneticist Dr Jean-Louis Pham and social anthropologists Dr Mauricio Bellon and Steve Morin.

At the beginning of the 1990s there were no genome data to support the molecular characterization of rice. Our work with molecular markers was among use these to study a germplasm collection. The research we published on association analysis is probably the first paper that showed this relationship between markers and morphological characteristics or traits.

In 1994, I developed a 5-year project proposal for almost USD3.3 million that we submitted for support to the Swiss Development Cooperation. The three project components included:

  • germplasm exploration (165 collecting missions in 22 countries), with about half of the germplasm collected in Laos; most of the collected germplasm was duplicated at that time in the International Rice Genebank;
  • training: 48 courses or on-the-job opportunities between 1995 and 1999 in 14 countries or at IRRI in Los Baños, for more than 670 national program staff;
  • on farm conservation to:
    • to increase knowledge on farmers’ management of rice diversity, the factors that
      influence it, and its genetic implications;
    • to identify strategies to involve farmers’ managed systems in the overall conservation of
      rice genetic resources.

I was ably assisted in the day-to-day management of the project by my colleague Eves Loresto, a long-time employee at IRRI who sadly passed away a few years back.

When I joined IRRI in 1991 there were just under 79,000 rice samples in the genebank. Through the Swiss-funded project we increased the collection by more than 30%. Since I left the genebank in 2001 that number has increased to over 136,000 making it the largest collection of rice germplasm in the world.

We conducted training courses in many countries in Asia and Africa. The on-farm research was based in the Philippines, Vietnam, and eastern India. It was one of the first projects to bring together a population geneticist and a social anthropologist working side-by-side to understand how, why, and when farmers grew different rice varieties, and what incentives (if any) would induce them to continue to grow them.

The final report of this 5-year project can be read here. We released the report in 2000 on an interactive CD-ROM, including almost 1000 images taken at many of the project sites, training courses, or during germplasm exploration. However, the links in the report are not active on this blog.

During my 10 year tenure of GRC, I authored/coauthored 33 research papers on various aspects of rice genetic resources, 1 co-edited book, 14 book chapters, and 23 papers in the so-called ‘grey’ literature, as well as making 33 conference presentations. Check out all the details in this longer list, and there are links to PDF files for many of the publications.


In 1993 I was elected chair of the Inter-Center Working Group on Genetic Resources, and worked closely with Geoff Hawtin at IPGRI, and his deputy Masa Iwanaga (an old colleague from CIP), to develop the CGIAR’s System-wide Genetic Resources Program or SGRP. Under the auspices of the SGRP I organized a workshop in 1999 on the application of comparative genetics to genebank collections.

Professor John Barton

With the late John Barton, Professor of Law at Stanford University, we developed IRRI’s first policy on intellectual property rights focusing on the management, exchange and use of rice genetic resources. This was later expanded into a policy document covering all aspects of IRRI’s research.

The 1990s were a busy decade, germplasm-wise, at IRRI and in the wider genetic resources community. The Convention on Biological Diversity had come into force in 1993, and many countries were enacting their own legislation (such as Executive Order 247 in the Philippines in 1995) governing access to and use sovereign genetic resources. It’s remarkable therefore that we were able to accomplish so much collecting between 1995 and 2000, and that national programs had trust in the IRG to safely conserve duplicate samples from national collections.

Ron Cantrell

All good things come to an end, and in January 2001 I was asked by then Director General Ron Cantrell to leave GRC and become the institute’s Director for Program Planning and Coordination (that became Communications two years later as I took on line management responsibility for Communication and Publications Services, IT, and the library). On 30 April, I said ‘goodbye’ to my GRC colleagues to move to my new office across the IRRI campus, although I kept a watching brief over GRC for the next year until my successor, Dr Ruaraidh Sackville Hamilton, arrived in Los Baños.

Listen to Ruaraidh and his staff talking about the genebank.


So, after a decade with GRC I moved into IRRI’s senior management team and set about bringing a modicum of rationale to the institute’s resource mobilization initiatives, and management of its overall research project portfolio. I described here how it all started. The staff I was able to recruit were outstanding. Running DPPC was a bit like running a genebank: there were many individual processes and procedures to manage the various research projects, report back to donors, submit grant proposals and the like. Research projects were like ‘genebank accessions’ – all tied together by an efficient data management system that we built in an initiative led by Eric Clutario (seen standing on the left below next to me).

From my DPPC vantage point, it was interesting to watch Ruaraidh take GRC to the next level, adding a new cold storage room, and using bar-coding to label all seed packets, a great addition to the data management effort. With Ken McNally’s genomics research, IRRI has been at the forefront of studies to explore the diversity of genetic diversity in germplasm collections.

Last October, the International Rice Genebank was the first to receive in-perpetuity funding from the Crop Trust. I’d like to think that the significant changes we made in the 1990s to the genebank and management of rice germplasm kept IRRI ahead of the curve, and contributed to its selection for this funding.

I completed a few publications during this period, and finally retired from IRRI at the end of April 2010. Since retirement I have co-edited a second book on climate change and genetic resources, led a review of the CGIAR’s genebank program, and was honored by HM The Queen as an Officer of the British Empire (OBE) in 2012 for my work at IRRI.

So, as 2018 draws to a close, I can look back on almost 50 years involvement in the conservation and use of plant genetic resources for food and agriculture. What an interesting—and fulfilling—journey it has been.