Connect with us

CivicSciTimes - Stories in Science

Discovering Zoology Through My Passion for Birdwatching II: Is There a Final Word in Research?

Abdul Jamil Urfi: “I still have some years left before I retire. But the clock has started ticking and I can hear it loud and clear.”

CSM Lab

Published

on

Abdul Jamil Urfi

[su_boxbox title=”About”]Dr. Abdul Jamil Urfi has been involved in studying the Painted Stork, a tall elegant bird found in India for over thirty years. He has written extensively on the bird, including a species monograph The Painted Stork Ecology and Conservation and a cover story for Natural History Magazine, โ€˜A monsoon delivers storks.โ€™ Based on his lifelong experiences of studying the Painted Stork and other birds, he is now planning to write a book about his experiences as a field ecologist. Click here for more details about his work. Cover image by Arbin Thakur. [/su_boxbox]

[su_boxnote note_color=”#c8c8c8″]Story Key Points:

  • Think Locally: As a wildlife biologist, one can do a lot by simply looking for interesting problems locally. I was lucky to have a wild population of an endangered species of bird which had a nesting colony in my own city.ย 
  • Discovering the Unknown: While adding to the existing knowledge on your research topic, you end up knowing more about what you donโ€™t know.
  • Final Word: There is no final word on anything.[/su_boxnote]

[dropcap]B[/dropcap]eing always interested in birds (read part 1 of my story in science), I wanted to do a PhD in ecology, ornithology etc and pursue a career in academics. But in the 1980โ€™s, there seemed to be few avenues available for this in India. Since my MSc Zoology specialization was in fisheries, a fellowship offer to study fish muscle histophysiology at the University of Delhiโ€™s Zoology department landed in my lap and I happily accepted.

Prof. Abdul Jamil Urfi

Fish move in a dense medium, bedeviled by drag forces, and so their body muscles (what we eat, actually) or the myotomal musculature is uniquely adapted (click here for details). For instance, their arrangement of slow and fast contracting muscle fibers is very different from those of terrestrial vertebrates. My PhD project was to study how these fibers differentiate and develop from the time when the fish is an embryo to the point when it becomes an adult. To cut a long story short, while the theme was definitely interesting work, the histochemical and biochemical work wasn’t that appealing to me.

A view of the Painted Stork colonies at the Delhi zoo with the ramparts of the Old fort in the background. (Photo A J Urfi)

I was inside the lab most of the time working on tissue sections using a cryostat, staining them for enzymes or doing enzyme assays and gel electrophoresis. As time passed, I became cocksure that I wanted to be a field worker and not a laboratory scientist.

Meanwhile, as the outdoors and the world of birds continued to beckon me, I decided to revive my interest in birds, which had taken a backseat. I started revisiting my favorite birdwatching haunts, one of which was the Delhi zoo in which an absolutely free ranging population of Painted Stork has been regularly nesting for a very long time.

[su_boxspoiler title=”A Zoo Story: How the Delhi Zoo Accidentally Became a Water Bird Sanctuary ” style=”fancy”]The Painted Stork is a large, eye-catching, interesting looking, colonially nesting bird belonging to the stork family, listed as near threatened by international conservation agencies. It is found across large parts of India, Sri Lanka and in patches in South East Asia. However, right in the middle of a busy, crowded cityโ€”New Delhi, Indiaโ€™s capital, these birds can be found nesting in the local zoo.

Each year, come September, these tall, elegant birds start congregating in the zoo where they build their nests on mesquite trees planted on islands in the middle of ponds. During the period of their residence, they raise their young, oversee preliminary rites of passage and as soon as summer approaches, they are all gone, widely dispersed in the surrounding countryside, where they will live singly or in loose scattered parties seeking food and shelter for the rest of the year.

How the Delhi zoo became a bird sanctuary is a fascinating story, the origins of which can be traced to the initial decades after Indiaโ€™s independence. In a sense, the zoo is a reminder of a time in history when a young country, after a long period of struggle against foreign rule had come of its own and become independent.

When a new India was born in 1947, the first few decades after independence were emblematic of the countryโ€™s first Prime Minister, Jawaharlal Nehru, who with his emphasis on science and technology, wanted to take the new country in the direction of progress and modernity. As a new country strove to throw away the shackles of the past and develop as a modern nation state, new institutions were being formed. And there was a need for also constructing a new zoo.

Zoological parks, in some form or the other have always existed down the ages though their objectives and purposes have varied. Some of the earlier zoos were not meant for public display of animals in the same manner as modern zoos are. In earlier times, when kings and monarchs ruled, animal exhibits served the purpose of advertisement of the expanse of the rulerโ€™s kingdom and the wild animals found in his state. Royal menageries were built in which live birds and animals were displayed in ornate, though wholly inappropriate and most certainly, terribly uncomfortable enclosures.

Worldwide, zoos were evolving and it may be worthwhile to view this in the broader context of the age of exploration and discovery. During this period as European sailors and explorers travelled to hitherto unknown lands, Asia, Africa, Americas, Australia etc, they brought back with them specimens of flora and fauna from places they had visited or conquered. These specimens were displayed in their home countries, leading to the creation of the first public zoos. Prior to that the general public in European countries had little idea about the biodiversity wealth across the globe and when confronted with exotic and strange looking creatures exhibited in zoos they were fascinated and thrilled.

For displaying the animals from different corners of the British Empireโ€”on which the sun never set, the London zoo developed region specific sections such as Asia section, Africa section, America section etc.

But things were changing and soon, colonial settings began to be replaced by thematic settings as far as the exhibition of animals in zoos were concerned. Ecological relationships, say โ€˜predator-preyโ€™ was depicted with the tiger or lion kept in one enclosure and its food, deer housed in a neighboring cage.

With the passage of time, a new type of thinking came aboutโ€”exhibition for the enjoyment of the visitor as well as the comfort for the live animal exhibit. While in the zoos of yore display animals were cooped inside small cages, in times to come, they began to be housed in larger, open enclosures where they could move around and exercise their muscles. Doing away with cages, rods and mesh etc altogether and removing all obstructions between the exhibit and the visitor, moated enclosures became the norm. In these the animal exhibits did not look like they were held in captivity at all and could be seen to be roaming about freely, almost as if in the wild.

In newly independent India, its rulers wanted to be modern in every respect. In 1952, the Indian Board for Wildlife created a committee for creating a zoo in New Delhi which would be the countryโ€™s national zoo (hence the formal name, National Zoological Park). The zoo would be built along modern lines with open moated enclosures, plenty of open spaces and gardens.

Because of his love for wildlife and animals, Nehru took a personal interest in the Delhi zoo project. As a zoo publication informs us, the exact site where the zoo is located was selected by himโ€”a nice spot on the western bank of the river Yamuna, located between the two historical monuments, the Old Fort and Humanyunโ€™s Tomb.

Carl Hagenbeck of the Zoological Garden of Hamburg was the creator of the open moated enclosures concept and the Hagenbeck model was the inspiration when drawing the plan of the Delhi zoo. One of the unique features about the new Zoo layout was that its exhibition areas or enclosures so to speak were to be located around a network of interconnected ponds and canals, which would be constricted and dilated in their shape at different points to accommodate various outdoor exhibits.

On a couple of such ponds, especially the ones facing the Old Fort ruins, an outdoor exhibit to showcase the waterbirds of India was planned. Here, some mesquite trees were planted on islands and a few pinioned storks, cranes and some other birds were released. The park was officially opened on 1stย  November 1959 but sometime in the same year, possibly in the month of September, it so happened that a small groupย  of wild Painted Storks happened to fly around the zoo. Possibly they were scouting for a safe place to nest. According to available records, about 59 birds descended upon the trees growing on an island in the pond facing the Old Fort. While in that year the birds did not build any nests, the next year after the monsoon rains, a large contingent consisting of about 400 Painted Stork landed in the zoo premises. This time they started building nests in the zoo and from that year till nowโ€”a period of almost six decades, Painted Storkโ€™s have been regularly nesting here.

Sixty years down the line from that momentous year, the Painted Stork continue to visit the zoo each year for nesting. But even though all looks fine problems may be looming on the horizon. The river Yamuna which is a favorite foraging ground for these birds is severely polluted and extensive areas of the riparian zone have been encroached upon. Many areas of the floodplains were lost during subsequent constructions, particularly housing complexes, bridges and flyways. For more about the Delhi zooโ€™s wild Painted stork population and the work done on it, and its relevance for urbanization and climate change studies, click here.ย 

Explore Next:  From Poverty to Science: Becoming a Scientist Amidst Financial Adversity

[/su_boxspoiler]

Running away from the lab every other day, I was in the zoo watching the storks as they went about doing their daily chores. Not being a trained ecologist or behavioral scientist, I tried my best to make sense of the things they were doing. Word got around that someone was hanging around the Painted Stork nesting colonies quite often. One day, an officer there during the course of a conversation asked whether I had discovered any new knowledge about the Painted Stork from my studies. I said nothing, so far. Then, rather haughtily he said, “โ€ฆand you will discover nothing new. All the work on it has already been done.”

A Painted Stork foraging in the marshes (Photo Arbin Thakur)

In a way, he was right because a person by the name of Dr. J.H. Desai, an ex-director of the zoo, had done his PhD on the Painted Stork of the Delhi zoo. That had been in the 1960โ€™s, about two decades earlier when species specific studies on wildlife, usually involving documenting facts about a particular species were becoming fashionable. Say, if it was a bird, then its clutch size, weight of the nest, duration of incubation period, what items were in its diet etc.

Desaiโ€™s research was an impressive tome of work no doubt but when I began studying it in detail, I discovered that there were some shortcomings which was typical of those times. For instance, no aspect of population biology had been assessed. Among some methodological issues, important parameters such as โ€˜nest successโ€™ had been estimated in an old fashioned way as percentages. (A chap called Mayfield had come along later and proposed an entirely new way to estimate nest success. However, the Mayfield method took its own time to become commonly used by ornithologists. Now, in the age of computers, this parameter is modeled, using specialized software (Program Mark) as daily nest survival rate (DSR) along with a host of parameters (covariates) which can influence nest survival).

But at a time when I was trying to look at the Painted Stork afresh with unblinkered eyes, essentially what my zoo officer friend was telling me was the following: “Since Dr Desai has said the final word on this subject, donโ€™t waste your time. Go home and sit quietly.”

Is there such a thing as a final word on any subject and how exactly does knowledge advance? An insight into this came from a fairly erudite person – also an impressive speaker, Prof Moonis Raza – who was then the Vice-Chancellor of the Delhi University. During a speech about advancement in knowledge at a function organized in our department, Prof. Raza alluded to a lighted candle placed in a dark room by way of illustration.

I still have some years left before I retire. But the clock has started ticking and I can hear it loud and clear.

He said, its illuminated zone represents, in terms of drawing an analogy to knowledge, the answers to certain questions. But surrounding the flame is a thin translucent zone, which is a bit diffuse and you can only partly see things through it. This, according to the Professor, was the zone signifying โ€˜you know what you donโ€™t knowโ€™. And all around the candle, beyond a point, is an area of darkness, where the light emanating from the small candle does not reach; where nothing is known!

Now, if you increase the size of the candle then you increase the core illuminated region. You now have answers to many more questions, but the size of the translucent zone has also increased because more questions have arisen based on earlier research. So now you also know more about what you donโ€™t know.

All this sounded very impressive back then when we were young students. But it said a thing or two about the final word which my friend in the zoo had flagged. No one knew for sure if this was Prof Razaโ€™s original formulation or he had heard or read it from somewhere. I have since tried to Google for quotations on candle light to find out if anybody had said something similar but no luck so far. For curiosities sake, I have also placed a lighted candle in a room to see what the translucent zone actually looks like.

After my PhD, I decided to switch over to birds completely. Though I was largely self taught, I spent a couple of years with Dr J D Goss-Custard at ITE Furzebrook, as a European Commission Fellow. My project was studying the foraging ecology of the Oystercatcherโ€”a small wading bird which eats mussels among other things, over wintering on the Exe estuary in South England. John G-C had been a pioneer in foraging ecology, having published one of the earliest studies testing Optimal Foraging Theory (OFT) diet models on a wader (Redshank) by using observational methods in the field way back in the 1970โ€™s.

My years with G-C, discussions with colleagues and learning how to collect data on bird behavior and analyze it using statistical software (which was a new emerging tool in those days) I learnt a lot which gave me confidence about how to study bird behavior in the field and how to frame questions in behavioral ecology. I returned home with some good papers which undoubtedly helped me professionally.

One of things which appealed to me about the Oystercatcher study at the Exe was that my English colleagues had developed a system for field studies on a long term basis and were studying its different dimensions. A lot of things were known but each successive study posed new questions which the field researcherโ€™s team addressed. After years of field work and collection of empirical data they had come to a stage where they were making individual based simulation models, based on Game theory, by which they could make predictions about many things.

Could I do something similar here in India? At least develop a system for field studies on which I could explore the basic aspects of population ecology of a bird on a long term basis.

Well, the primary thing was to have a job. In this respect, I was lucky. Here at the Delhi University where I have been for the past 20 years as a faculty, my salary and security are taken care of. I could say I feel good, except, true to human nature, there is also a tendency to feel dissatisfied at times. After-all, surviving in the academe in India is often an ordeal.

The position itself came after a long period of struggle but finally, when I did join as a lecturer in 2001 my choice was clearโ€”I wanted to develop the Delhi Zoo Painted Stork population as a system for conducting ecological studies on a long term basis.

For the service of science! Well letโ€™s not be totally absurd. Also for building a career. With a population of wild birds, amenable to study at close quarters, it would have been pointless to run off to faraway places or study exotic species.

All the years that I have been here at Delhi University, I have guided several PhDโ€™s on birds of which four have been on different aspects of Painted Stork ecology. I have published in international peer reviewed journals (and nowadays, they donโ€™t publish easily) so there must be something new in what I have done. Which also makes me wonder if the final word had been said!

There have been criticisms of my work. My most vociferous critics, some of them being my colleagues, say I am merely doing birdwatching, which is true to an extent. I still watch a bird but it is not exactly that sort of birdwatching which involves ticking on checklists, akin to stamp collecting, or chasing rarities. For my work, I go to the field with a carefully researched data recording protocol and once I have collected the data then research becomes a game of numbers and it is me and my computer doing data crunching. My field work is largely observational and non-invasiveย  (and I circumvent problems associated with catching and trapping live animals and permits for it).

My critics also say what they are doing is useful for humanity (for instance developing transgenics of food crops which they think is the answer to mankindโ€™s hunger problems). But my work has its uses too. (See the Zoo story above in the box).

Interestingly, among my critics are those who work in areas of biological research where they are able to ask for big sums of money in grants for instrumentation, chemicals etc. My work is comparatively low cost and I fear, in their eyes I score low; I have less power to hire and fire, less over heads etc.

In my book on the Painted Stork, acknowledging Desaiโ€™s work I quoted a line which is attributed to Sir Isaac Newton: โ€˜If I have seen further it is only by standing on the shoulders of giantsโ€™.

That may sound like a big thing coming from a small guy like me who is just an ordinary worker among the millions of professional biologists in the world.

I still have some years left before I retire but the clock has started ticking and I can hear it loud and clear. In the long run, while some of what we did will become incorporated in the corpus of ornithological literature, much of it will also become obsolete. But someone (I hope) will likely to come along and take a look at this wonderful opportunity for researchโ€”a large population of an endangered species of bird nesting in urban premises which is possible to study from close quarters. Just as I did, new questions will be asked using new techniques of analysis. Desaiโ€™s work will be used as a base to ask fresh questions or revisit old questions, either because they are still unresolved or because they appear to be interesting.

Metrics

Sessions

[analytify-stats metrics=”ga:sessions” analytics_for=”current” custom_page_id = “”permission_view=””]

Total number of Sessions. A session is the period time a user is actively engaged with the page.

Visitors

[analytify-stats metrics=”ga:visitors” analytics_for=”current” custom_page_id = “”permission_view=””]

Users that have had at least one session within the selected date range. Includes both new and returning users.

Page views

[analytify-stats metrics=”ga:pageviews” analytics_for=”current” custom_page_id = “”permission_view=””]

Pageviews is the total number of time the article was viewed. Repeated views are counted.

CivicSciTimes - Stories in Science

Unexpected Stories and Spindle Mistakes: Discovering that Wild-type Cells are Full of Surprises

CSM Lab

Published

on

By

Natalie Nannas

Natalie Nannas is an Associate Professor of Biology at Hamilton College in Clinton, NY. She teaches courses in genetics, molecular biology, and bioethics. Dr. Nannas graduated from Grinnell College with bachelor’s degrees in biological chemistry and French. She received her Masterโ€™s and PhD from Harvard University in molecular biology and genetics. Dr. Nannas conducted her postdoctoral research at the University of Georgia where she won a National Science Foundation Plant Genome Postdoctoral Fellowship. At Hamilton College, Dr. Nannas enjoys teaching and sharing her passion for microscopy with her undergraduate research students. When not glued to a microscope, she loves spending time with her husband and two daughters. The narrative below by Natalie Nannas captures the human stories behind the science from a 2022 paper titled โ€œFrequent spindle errors require structural rearrangement to complete meiosis in Zea maysโ€ which was published by her group in 2022 in the International Journal of Molecular Sciences.

Science never works out the way we plan. As scientists, we ask questions, hypothesize and outline our goals โ€ฆ then reality of science occurs. The reality of science is often full of failed controls, endless troubleshooting, and sometimes strange findings that lead us in new and unpredictable directions. Our publications give the impression that we planned these scientific journeys from the beginning and do not tell the human side of the process with all of its twists and turns, dead-ends and U-turns. I want to tell you the real story behind my first publication as a faculty member with my own lab. It did not go as planned due to the COVID-19 pandemic. My lab was shut down in the middle of our investigation, and my students and I were unable to generate new data. In the beginning, it seemed like we were stranded with only control data and no story to tell, but the time away from the lab allowed us to spend more time looking carefully at wild-type cells. What seemed like a dead-end suddenly became its own story when we found something unexpected hiding within microscopy movies. Our wild-type cells were making mistakes, attempting fixes and changing directions, just like we do as scientists.

My scientific journey began with flickering green lights and a microscope (you can read more about it here). As an undergraduate, I was mesmerized by the beauty of watching living cells shuffle fluorescently labeled proteins throughout their cytoplasm. I followed this passion for microscopy into my doctoral dissertation research at Harvard University where I investigated how yeast cells build the machinery needed to pull their chromosomes apart. This machinery is a dynamic collection of long protein tubes called microtubules and other organizing proteins that help move and shuffle microtubules. I loved watching the delicate dance of chromosomes interacting with microtubules of the spindle, and I wanted to continue studying this process in my postdoctoral studies.

During postdoctoral studies at the University of Georgia, I won a fellowship from the National Science Foundation to develop a new technique in microscopy. No one had ever watched plants building their spindles in meiosis, the specialized cell division that produces egg and sperm. Other scientists had performed beautiful microscopy studies observing how mitotic spindles function inside of plant cells, but due to the technical challenges, no one had ever observed live plant cells building spindles in meiosis. I was thrilled to take on this challenge by using version of maize that had fluorescently labeled tubulin, the protein that makes up microtubules of the spindle. With this line of maize, spindles would glow fluorescent green, allowing me to image if only I could extract the meiotic cells.

Dr. Natalie Nannas

We were so busy collecting data and prepping for our mutant studies that we never really took time to analyze the wild-type cells.

After almost a year spent dissecting maize plants, I finally managed to develop a method to isolate these tiny cells and keep them alive in a growth media long enough to image them. This new method of live imaging was going to serve as the foundation of my new lab at Hamilton College, a primarily undergraduate institution. With my students, I planned to investigate the pathways governed spindle assembly. Most animal mitotic cells have a structure called a centrosome that dictates how spindles are formed; however, female animal meiotic cells lack these structures and must use other pathways to direct spindle assembly. Plants also lack centrosomes, and I wanted to inhibit these known animal pathways in our plant live imaging system.

Explore Next:  The Journey Continues: Finding My Questions in Science

As I set up my lab, my students and I collected live movies of wild-type maize cells building their spindles. I told my students and myself that these movies were not the main event, they were just the control cells so we would have a baseline comparison for our experimental conditions. We were so busy collecting data and prepping for our mutant studies that we never really took the time to analyze the wild-type cells. At the surface level, they built spindles and segregated chromosomes in a generally expected amount of time, so we focused on preparing for our upcoming experimentsโ€ฆ. then March 2020 occurred.

The pandemic forced us to slow down and look more carefully at our wild-type data, and I am grateful for the detour.

My students headed home for spring break with a warning that there may be a delay in coming back to campus due to the spread of COVID-19. None of us were prepared for the shutdown that followed. Like many colleges and universities, our campus was closed for the remainder of the spring 2020 semester and the summer of 2020. My students and I began meeting on Zoom, trying to make a new plan for our research. The only data we had to work with were the microscopy of wild-type maize cells, so we decided to spend time digging more deeply into these movies. Originally, we had only measured the total time it took to build a spindle as it would be a baseline for comparison to our mutants. We had not looked carefully at any of the intermediate time points in the assembly process. When my students looked more closely at our movies, they discovered that wild-type cells built an incorrectly shaped spindle over 60% of the time!

We found that maize meiotic cells often built spindles with three poles instead of two, and they had to actively rearrange their spindle structure to correct this mistake. We also found that in these cells, there was a delay in meiosis as cells refused to progress until this correction had been made. This is an exciting discovery as it showed that plants are error-prone in their spindle assembly, much like human female meiotic cells. Our findings also suggested that meiotic cells were monitoring their spindle shape when determining if they should move forward in meiosis. Previous work has shown that cells monitor the attachment of chromosomes to the spindle to make this decision, but our work adds a new dimension, showing that they also monitor spindle shape. As we continued to analyze our videos, we also learned that cells corrected their spindle morphology in a predictable way. They always collapsed the two poles that were closest together, creating a single pole and resulting in a correct bipolar spindle.

The image shows the first page of the paper which can be accessed here.

My students and I had begun our scientific journey planning to breeze over wild-type cells, moving on to what we envisioned would be a more exciting story of spindle mutants. The pandemic forced us to slow down and look more carefully at our wild-type data, and I am grateful for the detour. I rediscovered my love of closely watching flickering green fluorescent lights, the dance of microtubules sliding into place or making missteps and shuffling into new arrangements. Watching life attempt a complicated process, make mistakes, and try again, is a lesson that never grows old. It reminds me that our scientific journeys are just the same, they start in one direction but are fluid and constantly changing, and hopefully, they end with a functional spindle!

Read the Published Paper

Weiss, J.D., McVey, S.L., Stinebaugh, S.E., Sullivan, C.F., Dawe, R.K., and N.J. Nannas. 2022. Frequent spindle errors require structural rearrangement to complete meiosis in Zea maysInternational Journal of Molecular Sciences, 23 (8):4293โ€“4312.

โ€”

ABOUT: Stories in Science is a special series on the Civic Science Times. The main aim is to document the first-hand accounts of the human stories behind the science being published by scientists around the world. Such stories are an important element behind the civic nature of science.

SUBMISSION: Click here to access the story guidelines and submission portal. Please note that not all stories are accepted for publication. After submission, we will let you know whether we have selected the story for the review process.

Continue Reading

Upcoming Events

Trending