Remote Sensing Application and Spatial Database Design For Sustainable Management of Coral Reefs in Banda Island, South Maluku, Indonesia

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Remote Sensing Application and Spatial Database Design for

Sustainable Management of Coral Reefs in

Banda Island, South Maluku, Indonesia

Mr. Jose Mari Balines Gonzales

P36500004/MIT

Graduate Program

Bogor Agricultural University

Indonesia

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ABSTRACT

Spatial databases are essential tools for preserving potential marine genetic resources. Banda Island, the study area for this project, is rich with marine biodiversity that can be easily exploited. A spatial database was designed for Banda Island in order to locate existing selected marine species among its rich coral reefs.

Two LANDSAT-7 ETM satellite images of the study area were processed to apply the Bottom Feature Index and perform ISOclass unsupe~ised classification. The images were then mosaicked to create a classified image showing the entire archipelago of Banda Island. The result was a raster image with classified features deviating relatively less from actual measurements of area in Banda Island.

A vector data of the study area was created from a topographic map and was used to create a geographic information system (GIs). The GIs was capable of helping users locate existing coral, algae and seagrass species on Banda Island's coral reefs and specifying area measurements. Using a software extension, the Banda ~slands GIs was made available through local network. A Web site was also created containing pertinent information on the marine ecosystem, socio-economic, climatic conditions and geography of Banda Island.

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DECLARATION LETTER

I, Mr. Jose Mari Balines Gonzales, hereby declare that the thesis title:

Remote Sensing Application and Spatial Database Design for Sustainable Management of Coral Reefs in

Banda Island, South Maluku, Indonesia

contains correct results from my own work, and that it have not been published ever before. All data sources and information used factual and clear methods in this project, and has been examined for its factualness.

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Remote Sensing Application and Spatial Database Design for

Sustainable Management of Coral Reefs in

Banda Island, South Maluku, Indonesia

B y :

Mr. Jose Mari Balines Gonzales

P36500004MT

A Thesis Submitted to the

Graduate School of Bogor Agricultural University, Indonesia In fulfillment of the requirements for the degree of

Master of Science in Information Technology for Natural Resources Management

Graduate Program

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Thesis Title Remote Sensing Application and Spatial Database Design For Sustainable Management of Coral Reefs in Banda Island, South Maluku, Indonesia

Student Name Mr. Jose Mari Bdines Gonzales

Student ID P36500004

Study Program Master of Science in Information Technology for Natural Resources Management

This thesis proposal is approved by the Advisory Board

Dr. Ir. Vincentius P. Siregar Supervisor

Dr. Ir. ~uda'ng B. Seminar Co-supervisor

Head of the Study Program

q&..-

Dr. Ir. Handoko, M.Sc

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AUTOBIOGRAPHY

The author, Mr. Jose Mari Balines Gonzales, was born on June 7, 1970 in

Sampaloc, Metro Manila, Philippines. He is the first of four children of Mr. Alfredo A.

Gonzales (deceased, February 2000) and Mrs. Vilma Balines Fountain (currently married to Mr. Quentain Dale Fountain).

His early five years of childhood were spent in Guam, USA- an American island

in the Polynesia. It would be the marine environment in Guam that would spark his

interest in Biology and the beaches. However, his basic education and college degree

were taken and earned hack in Manila. He was an active participant in public speaking

and drawing competitions during elementary, earning him his first set of awards,

including the school's institutional award Mananalzimpati ng Taon (Public Speaker of the Year) in 1982 at Julian Felipe Elementary School, Cavite City, Cavite.

In highschool, San Sebastian College-Recolletos (an exclusive school for boys),

he ranked among the class' top ten until in second year he was permanently disqualified

for voluntarily taking the responsibility for a supposed misconduct that another member

of the class did. His action not only saved the entire class from a gross penalty, but also

gained their respect. At this time, he was a good friend and an avid reader and viewer of

science-oriented books and TV programs. It would be through this exposure that he

would decide to be a Filipino Geneticist.

He took up and earned a degree of Bachelor of Science in Biology at De La Salle

University - Dasmariiias, Dasmariiias, Cavite. He was an active managing editor, later,

science editor, of the university's newspaper, Heruldo Filipino. It was during his first year when he founded, together with close friends, the science organization FEDISFRON

in the university and became its first elected president. Liiter, he was also elected as

president for the entire graduating class of the university. The school awarded him the

institutional award for science, Science Awardee, for 1990.

At the age of 20, he was invited to be a full-time faculty in the Department of

Natural Sciences in his ulma matter until 1993. He then resigned, and devoted three years of his life as a full time minister of Jehovah's Witnesses- a voluntary work helping

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De La Salle University-Manila, and taught Genetics, Ecology and General Biology until

2000. Eventually, he qualified for a SEAMEO-BIOTROP scholarship for the MSc in IT

for Natural Resources Management programme hosted by the Institut Pertanian Bogor

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This project would not have been possible if not through the kind assistance and technical support of several individuals and organizations. I would, therefore, like to take this opportunity to extend my sincerest appreciation to the following:

Foremost, I would like to thank the Sovereign God, Jehovah, through whom I have dedicated my life to, for constantly guiding me through the opportunities that opens to me. I can never repay the underserved-kindness He had shown me throughout my stay here in Indonesia, and will never be capable of doing so. However, I can only show my extreme gratitude by living up to my dedication to Him.

I am indebted to my supervisor, Dr. Ir. Vincentius P. Siregar, and co-supervisor, Dr. IT. Kudang B. Seminar, for sharing their valuable expertise and scrupulous guidance to complete this project. Time had truly been a constraint on this work, yet through their supervision this project had turned out to be more than satisfactory. They have shown me remarkable patience and understanding worthy of mentors!

This project is an offshoot from a major project currently being worked on by the Coastal Regions and Small Islands Unit under the Regional Office for Science and Technology for Southeast Asia of UNESCO. It is through the initiative and support of Dr. Stefano Fazi, former head of the unit (2001), and guidance of Ms. Ina Punvadi that I was able to gather and process the data essential to the completion of the Banda Island spatial database. Thank you very much, Dr. Fazi and Ina.

The opportunity to pursue and complete this MSc. in Information Technology for Natural Resource Management (MIT) program was opened to me by Dr. Florencia Claveria (Biology Department, De La Salle University-Manila). I am very grateful for her underserved-kindness and assistance, and for setting a very remarkable example of what a true La Sallian scientist and teacher should be- always in pursuit of excellence!

I am also grateful to SEAMEO-BIOTROP for the financial assistance that has been extended to me throughout the course of my study here in Indonesia, and for the accommodations and facilities.

Heartfelt appreciation is also extended to Dr. Ir. Handoko, Director of the MIT program, for accepting me in this program and for providing technical and academic assistance through Mrs. Wahyu Sri Harini, program secretary, and Ms. Dedek Fanny Siregar, assistant to the program secretary.

My sincerest thanks to all my professors and lecturers, especially, Mr. Muhammad Helmi and Mr. Eddi Nugroho who both never failed to extend a helping hand to all the technical help and guidance I needed in satellite image processing.

I would also like to thank H. Iding Bahrudin (Alm.) and Hj. Djuarsih for bringing into this world the greatest Indonesian brother I could ever have, Mas Erlan Suherlan. I can never express my sincerest gratitude to Erlan for showing me how great the food, music, culture and the people of Indonesia are- the Sundanese way! I am now 10% Sundanese. I truly appreciate the time he had given me to relieve me of homesickness, and for his family who took me in as its eleventh child. I will always cherish the PAD1 rock band, even though the Sundanese song

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I would not only l i k e to thank my mom, Mrs. Vilma Balines Fountain, for her uncompromising love, sacrifice and support she had given me throughout my thirty-two years of life and stay here Indonesia, but would like to dedicate this accomplishment to her, too. Thank you for keeping the Vil~na Balines Foundation open to me. The same goes to my brother, James, and sisters, Jannete and Diane, who all kept the family barfire ablaze.

Lastly, I would like to thank my classmates, Mr. I. Hashim (Malaysia), Mr. P. Doydee (Thailand) and Ms. M. Aung (Myanmar), for the two years of companionship and friendly "quarrels" we had; to my former seniors who helped me out with my first year in the program, Dewi, Agung, Halili, Palm, Tint Khaing and Nani; and the MIT program personnel for the hilarious company, security and technical assistance, Pak Harry, Pak Iwan, Pak Arman, Pak Hasan, Pak Zein, Mas Andri, Mas Mulyadi and Pak Zaenudin.

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List of Figures

Page 2.1 Integration of GIs with a database management system

...

15

3.1 The Study Area, Banda Island

...

20

3.2 The Study Area, six major islands

...

21

3.3 The approach of creating the spatial database system

...

24

3.4 Summarized Flow-chart of Procedures

...

25

3.5 Conceptual Design, relational model

...

30

3.6 ERD for Logical Design

...

31

4.1 Output images from RGB processing

...

40

4.2 Cropped images

...

41

4.3 Histogram adjustments

...

42

4.4 Setting of 35 GCPs

...

44

4.5 Two classes of data in the spatial database

...

45

4.6 The fourth hypothetical "normalized" table

...

47

...

4.7 Product design from preconceived database design 49

4.8 Potential uses of the spatial database

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50

4.9 Two composite images for Bandal08

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53

. .

...

4.10 Lyzenga applied images 53

...

4.1 1 Final output for unsupervised classification of Bandal07 55

...

4.12 Re-classification of Bandal07 image 56

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4.13 Re-classification of Bandal08 image 57

...

4.14 Map lay-out of the Mosaicked Banda Island satellite images 58

4.15 Vector data

...

60

4.16 The GIs set-up for Banda Island

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61

4.17 The Classified Banda island view ... 62

...

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List of

Tables

3.1 Conceptual Design

...

29

3.2 Logical Design

...

31

3.3 Physical Design

...

32

4.1 Three Tabular Forms

...

46

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List

of Appendices

App

.

A

.

Correcting the Information of the Images

...

71

App

.

B

.

Cropping the Images

...

72

App

.

C

.

The Scattergram Cut-off Atmospheric Correction Technique

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73

App

.

D

.

Geometric Correction on the Images

...

75

App

.

E

.

Procedure for Coral Reef Mapping Using ER Mapper 5.5

...

76

...

App

.

F

.

Ground Control Points and RMS Error Report 82

App

.

G

.

Collected Data from Banda Island

...

84

App

.

H

.

Data for Determining the kitkj Values

...

86

App

.

I

.

Vector Metadata of Coverages

...

88

...

App

.

J

.

Tables Supporting the Banda Island GIs 90

App

.

K

.

Available Data for Area

...

103

...

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1. Introduction

1.1 Background of the Problem

Indonesia is relatively rich with species that are widely distributed, and occupy a

range of different habitats that often involve adaptation to local conditions resulting to

genetic diversity between various populations. Genetic variation is important because it

provides the basic resource needed for the creation of new industrial natural products and

high-yielding agricultural varieties of crops in order to meet the ever growing demand of

a rapidly increasing human population. These resources, known as genetic resources, yield potentially valuable products, such as chemicals, enzymes, and genes; and include

terrestrial and marine microbes, plants insects, venomous animals and marine organisms

(Putterman, 2000). The small archipelago of Banda Island, located in the province of

South Maluku, is one of several places in Indonesia that is endowed with rich marine

organisms- namely, corals and algae- that have' potential value as genetic resources. If

these marine organisms are not identified and preserved by the Indonesian government

foreign biological companies involved in commerce could exploit them through illegal

bio-prospecting. Eventually, Indonesia may loose the right to utilize these genetic

resources through legal patenting.

Already, Indonesia had taken steps to conserve genetic diversity by

conceptualizing strategies to preserve its overall biodiversity (Indonesian Biodiversity

Country Study Standing Committee, 1992). To pursue a perpetual course towards

conservation of biodiversity richness, the government had established 376 protected areas

that include national parks, nature reserves, game reserves and marine reserves. In

addition, the Biodiversity Action Plan for Indonesia (BAPI) was formulated in 1991 that

sets out the strategy for action on both in situ and ex situ conservation (Indonesian Institute of Sciences, 1999). To meet problems concerning policies, technologies and

expenses, the government had collaborated with various international agencies, where the

governments of Japan and the United States of America had jointly aided in setting up the

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However, Indonesian biodiversity, which includes genetic resources, are

continually threatened. Banda Island is not spared from this environmental problem

because of the presence of human communities.

In an action plan developed by the World Resources Institute (1991) for

Indonesia, the strategy suggested coastal and marine conservation. Together with three

other concerns [in situ conservation in terrestrial parks and protected areas, in situ conservation outside the protected area network @reduction forests, wetlands,

agricultural lands), and ex situ conservation], the plan involved "outlining immediate and attainable priorities for conservation action", suggesting the seriousness of the threats

imposed on the marine ecosystem and urgency to create strategies that will preserve

them. Endangering coastal ecosystems results to severe impacts on marine biodiversity.

For example, marine genetic resources in Indonesia would likely diminish without even

being documented if no proper strategies are made to manage them effectively, and

would mean loss of potential source of income and gradual degradation of the ecological

communities.

Sustainable management entails meeting the current needs without compromising

the ability of future generations to meet their own needs. In Programme Element 1,

Sustainable Management and Use of Natural Resources, .posted in the Internet by the United Nations Environmental Programme (UNEP) committee (1997), one suggested

strategy to care for coastal and marine environments is to "develop tools and guidelines

for sustainable management and use of freshwater and coastal resources." These tools

and guidelines should be able to help local decision-makers to effectively manage coastal

resources, including marine genetic resources that would lead to economic benefits to the

local stakeholders and conservation of the coastal environment.

A spatial database developed for a coastal environment, with or without human

communities, is a likely tool that can help local decision-makers in their assessment,

auditing, formulation of strategies and guidelines for the identification, conservation and

sustainable use of local marine genetic resources. Spatial databases contain georeferenced

data with significant biophysical information of a study area, such as confirmed species

present in the area. It is often interactive so that users may be able to retrieve pertinent

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If a spatial database specifying genetic resources were available to coastal managers, then

decision-making, or any kind of analysis involving georeferenced information, would be

relatively easier. The database approach allows data sharing to be more effective by

developing new applications that will facilitate data sharing with others using other

application systems.

It is then highly significant to consider developing spatial databases for

institutions or organizations (involved in the conservation biodiversity) that handle a

great deal of data that can be shared and are vital for various analyses. Such an approach

would reduce the length of time and effort needed for planning, decision-making, and reinforcement of policies. It also makes analyses and processing more efficient since the

system is computer-based.

Among the challenges facing Indonesia concerning coastal environmental

management are: (1) to create a national cross-sectoral coordinating agency; (2) develop

provincial management capabilities; and (3) to foster community and private sector

participation (Meltzer Research and Consulting, 1993). Therefore, an effective and

accessible spatial database would highly contribute in meeting some of these challenges.

1.2 Problem Conclusion

In order to conserve Banda's marine genetic diversity, conservation must begin at

the species level. To cover in situ and ex situ methods of conservation, a wide range of technologies would be needed. Technologies can be classified into: (a) 'soft' technologies

(training, management, behavioural patterns, etc.); (b) 'hard' technologies (aerial survey,

laboratory equipment, gene banks, etc.); and (c) 'high' technologies (DNA hybridization,

allozyme analysis, etc.) (Indonesian Biodiversity Country Study Standing Committee,

1993). Although the hard technologies for conservation are generally widely available,

Indonesia faces the issue of technology transfer and development.

To achieve successful technology transfer, there must be an availability of skilled

staff, clear responsibility for activities and the establishment of information systems. Indonesia had already established the Centre for Training on Conservation Management,

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in Indonesia. Through this action, human resource development was expected to occur.

However, because of the large areas of conservation to be covered and the lack of focus

in efforts, the results have yet to be seen. This focus is closely linked with the need to

have an effective information system.

The Indonesian Biodiversity Country Study Standing Committee, in their 1993

report, added that in the field of biodiversity information management, there was an

existing set of proposal by the Ministry of State for Population and Environment (KLH)

and the Indonesian Institute of Sciences (LIPI) in association with The Nature

Conservancy (TNC) and several donor agencies to establish a database on environmental

resources to accommodate several of the needs mentioned above. That database required

georeferenced and map information. Therefore, the database needed to interface

effectively with the national Geographic Information System (GIs) component at the

National Coordinating Body for Survey and Mapping (BAKOSURTANAL).

1.3 Framework for Solving the Problem

If Indonesia wants to manage marine genetic resources sustainably, especially in

Banda Island, effective tools and guidelines must be developed and formulated at the

species level. This will help coastal managers and decision-makers to audit existing

marine species in the coastal area, evaluate their conditions, and formulate a strategy to

utilize them without overexploiting these resources. Developing a spatial database that

stores the name of the species- bearers of the genetic resources- and their distribution

within the coastal area, will aid in whatever task a coastal manager or any decision-maker

may be faced with.

In order to arrive at an effective plan to conserve and manage these potential

genetic resources in Banda Island, a spatial database needs to be developed to help locate

the diverse species of the small archipelago and map significant geographical features

that are seen to have direct or indirect effects to the intended management sites.

Spatial analysis is essential in planning methods of coastal conservation and

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neighboring tributaries that have effect on the condition of the coastline there is difficulty

in estimating the degree of effectiveness of management over the coastal area.

Planners and decision-makers are also in need of available data coming from a

single source because the element of time is a major constraint in planning. This is where

a database will come as a solution to such problem. With significant information on the

coastal resources of Banda Island stored in a database, less time and effort is spent on

gathering and synthesizing data. A precursor database also prevents storing digital

information, collected by other researchers, in different formats that often prevent others

from integrating such formats with their data.

1.4 Objectives of the Study and Benefits

1.4.1 Objectives

The study aims to show the potential of Banda Island to protect and sustainably

manage the marine genetic resources it has. In so doing, the study involves:

1. Preparation of the spatial data by processing two LANDSAT TM7 satellite

images of Banda Island, and performing unsupervised classification on the

images.

2. Developing a spatial database for Banda Island that will show the location of all

coral, seagrass and algal species distributed among the islands of the small Banda

archipelago.

3. Creation of a digital map of the study area from an existing topographic map.

1.4.2 Benefits

Marine genetic resources are of value because of the various significant uses they

have in research and development (R&D). And since a wide range of commercial

industry have applied numerous biological technology as a means to produce and market

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organisms as potential genetic resources- sources of diverse chemicals, enzymes and

genes.

Although conservation and management of coastal resources have been reinforced

because of debates over issues of ecological balance and consideration of the

stakeholders' welfare, this newly identified economic and R&D role of marine organisms

further strengthens the cause of coastal zone conservation and management. The

development of marine genetic resources into new commercial products can be a

powerful tool for conservation and economic development, and as such, marine genetic

resources ought to be incorporated into integrated coastal zone management (ICZM)

planning (Putterman, 2000).

Solid understanding of the environmental conditions of the coastal resources

within a set management site and factors that affect the state of these resources are

essential elements vital in protecting coastal resources, or improving them if degraded.

Therefore, there is a need to identify the geographical features of the coastal management

site and its surrounding attributes in order to specify the location of the marine resources,

and its distribution, and to map significant georeferenced attributes that are potential

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2.

Review

of

Related Literature

2.1 Introduction

Biodiversity is a popular way of describing the diversity of life on earth: it

includes all life forms and the ecosystems of which they are a part. It forms the

foundation for sustainable development, constitutes the basis for the health of our planet,

and is the source of economic and ecological security for future generations. In the

developing world, biodiversity provides the assurance of food, many raw materials such

as fiber for clothing, materials for shelter, fertilizer, fuel and medicines, as well as a

source of work energy in the form of animal traction. The rural poor depend upon

biological resources for an estimated 90% of their needs. In the industrialized world,

access to diverse biological resources is necessary to support a vast variety of industrial

products. In the continuing drive to develop efficient and sustainable agriculture for many

different conditions, these resources provide raw material for plant and animal breeding

as well as the new biotechnologies. In addition, biodiversity maintains the ecological

balance necessary for planetary and human survival (Kumar, 1999).

2.2 Genetic Diversity

Although there is no one "correct" level at which to measure and analyze

biodiversity, because different scientific issues and practical problems find their focus at

different levels, the various levels of biodiversity can be understood in a hierarchical

fashion- genetic diversity, species diversity, and ecosystem and biome diversity (Meffe et

al, 1997). Each of these levels characterizes the main units of variation, namely genes

(genetic diversity), species (species diversity) and ecosystems (ecosystem and biome

diversity) (United Nations Environment Programme, 1995). However, genetic vari&ility

is considered to be the ultimate source of biodiversity at all levels.

Recent advances in molecular biology have provided tools needed to measure the

amount of genetic variation present in organisms. Measurements of variability within

local populations are important for testing theories about the nature and forces acting on

genetic variation that are responsible for evolutionary change. Such knowledge has

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rare species so as to reduce deleterious effects of inbreeding, or determine the best

sources of individuals for reestablishing populations in areas from which they have been

exterminated. Measurements of the amount of genetic difference among species are

important for estimating rates of evolution and for establishing phylogenetic relationships

among organisms. These are significant concerns for biological consewation (Meffe et al,

1997).

2.2.1 Marine Genetic Resources

Biodiversity that is of interest to industry for its potential to provide diverse

chemicals, enzymes and genes is known as genetic resources (Putterman, 2000). These

may come from terrestrial and marine microbes, plants, insects, venomous animals and

marine organisms.

Because of rapid technological changes, the economic value of genetic resources

as a whole had increased. Moreover, as the potential use of material has expanded

considerably, e.g., increased salinity andlor cold tolerance of freshwater species through

selective breedinglselection it brings about an extension on the use of and geographic

distribution of the species. Not only are genetic resources highly significant to agriculture

and livestock, these are also important contributors to the pharmaceutical and health

industries.

In agriculture and livestock, genetic resources are used for selecting certain

species or populations for domestication and cultivation. In addition, it is also used for

genetically improving economically important species. Pharmaceutical companies are

becoming increasingly interested in the potential biochemical properties of tropical

species and varieties for developing new drugs.

In effect, biotechnology have not only found ways and means to relieve the

growing demands of the human population forecasted to double in size by the need of

this new century, it had also generated a significant amount of income. The aggregate

direct use value of biological resources and genetic material as "raw materials" in

agriculture is approximated by the potential returns on investments in research and

development of biotechnologies that may generate animal and crop breeds of potential

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amounted to $100 million, and earned an estimated return of $190 million (UNEP, 1995).

Pharmaceutical prospecting of biological resources from Costa Rica is around $4.8

million per new drug developed.

Marine genetic resources have similar economic value in terms of its biochemical

properties for nutritional, pharmaceutical and industrial purposes. This potential is as

great as that of genetic resources from terrestrial plants and animals. However, unlike

terrestrial plants and animals, only a few marine species have been domesticated and the

major portion of production comes from wild organisms. The marine microalgae, for

example, represents a potentially new and largely untapped natural resource. They are

rich sources of natural products such as pigments, enzymes, fats, proteins, amino acids

and vitamins, and at present there is a great demand for microalgae as health foods for

human consumption. Microalgae are also widely used as biofertilizers and as feed

supplements due to their high content of fats and oils, the chemical composition of which

is very similar to vegetable oil. In fact, there is the potential application of these algal fats

and oils as substitutes of commercial vegetables in the future. Microalgae have also

become a target of research for bioactive compounds with neurotoxic, antitumor, or

antibiotic activity. Although other marine species have potential uses for a variety of

purposes, most are not yet known andor tapped. Therefore, there is a need to preserve

these marine species until their significant use for a rapidly growing human population is

discovered.

2.2.2 Conserving Marine Genetic Resources

The need to preserve marine genetic resources comes from our awareness that

biological products from the coding genes of various species are essential in ecological

interactions (between species, between populations of different species, between species

and its environment). It is an element, in the molecular level, that is important and vital

for maintaining a healthy and efficiently functioning environment. Moreover, preserving

genetic diversity allows for more possible combinations of traits essential in the process

of evolution.

At a human standpoint, the need to preserve marine genetic resources comes from

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medicine, and industry. However, not all of it are hlly known and/or tapped. One of

several reasons is because of its degradation and eventual loss.

Genetic resources are lost either through the extinction of a species or through the

extinction of individual populations of the species (genetic impoverishment) (Salm and

Clark, 1984). The first process is final and irreversible. The second is a matter of degree

and is to some extent reversible (FAOIUNEP, 1981). In the sea, where endemism (the

restricted distribution of a species to a relatively small geographic area) is low compared

to that of land, the problem is less one of species extinction than of genetic

impoverishment. For example, no significant or detectable increase in extinction rates of

fish species has been observed in the ocean, but populations have been extinguished by

overfishing, pollution, and habitat destruction. Organisms occupying disappearing

habitats will likely never again reach their present level of genetic diversity (Salm and

Clark, 1984).

It is also important to recognize the difference between biological diversity,

reflected by the number of species, and genetic diversity, reflected by the variation within

a species. Note, for example, that land has more species than the sea, and hence greater

biological diversity. Marine organisms, however, tend to exhibit more genetic variability

(Nevo, 1978); thus, they have greater genetic diversity. Both types of diversity are

important and of use to people.

Broadly speaking, there are three ways to preserve marine genetic resources

against human-caused losses. One is establishing gene banks, "storehouses" that maintain

genes for future use (more widely used for terrestrial genetic resources). A second means

is preventing the overexploitation of species by managing the harvest, or by

supplementing the harvest of wild stocks with cultivated products, or by prohibiting the

harvest and trade of depleted and endangered species. A third means is creating protected

areas for habitats, since a major threat to the survival of some populations of species is

the destruction of critical elements of their habitat. Such coastal and marine protected

areas function as in situ gene banks, preserving genetic material within an ecosystem rather than a special "storehouse" (Prescott-Allen and Prescott-Allen, 1984).

Coastal and marine protected areas can help maintain in situ gene banks in a

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or species known or likely to be of value as genetic resources (e.g., the wild relatives of farmed species or other wild species useful to people) Local extinctions and depletions of

stocks have resulted in part from habitat destruction and in part from the high demand of

such species, for example, whales, turtles, dugongs, and certain mollusks and corals

(Salm and Clark, 1984).

2.2:3 Sustainable Management of Marine Genetic Resources

Many people who live in coastal regions have small cash incomes and subsist on

local resources. The lives and destinies of these people are linked to the sustainability of

their resources. With or without conservation they will continue to turn to these

resources. Although many can manage for themselves, they still need help.

Conservation aims to satisfy short-term needs in a way that ensures the survival of

resources in long-terms. Protected areas help channel development to avoid sacrificing

one resource by harvesting another or by modifying habitats. The World Conservation

Strategy (1984) defined roles for living resource conservation for sustainable

development as its goals, which are:

1. To maintain essential ecological processes and life support systems, on which

human survival and development depend.

2. To preserve genetic diversity, on which depend the functioning of many processes

and life support systems; the breeding programmes necessary for the protection

and improvement of cultivated plants, domesticated animals, and microorganisms;

much scientific and medical advance and technical innovation; and the security of

many industries that use living resources.

3. To ensure the sustainable utilization of species and ecosystems, which support

millions of rural communities as well as major industries.

Sustainable exploitation implies that wise use (development) and careful

management (conservation) of individual species and communities together with the

habitats and ecosystems on which they depend, so that their current or potential

usefulness to people is not impaired directly or indirectly by these people. Resources

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jeopardized. Such management maintains biological potential and enhances the long-term

economic potential of renewable natural marine resources.

Conservation of biodiversity in Indonesia has been a concern since the Dutch

occupation, yet limited in terms of initiative. Although mandates and regulations exist,

these overlap between the central and regional governments, among sectors, and between

public and exclusive society in certain places. Moreover, the effort of the Indonesian

government to practice conservation has not been fully linked to its utilization.

Institutions have no comprehension on the benefits of conservation, especially on long-

term benefits, and certain strategies had been ineffective (Indonesian State Ministry of

Environment, 1995).

In utilizing the Indonesian biodiversity, the government, general public and

private sectors are not always in agreement. There are conflicts of interests among sectors

in conservation areas, especially when important minerals are found (Indonesian State

Ministry of Environment, 1995). Direct harvesting of plants and animals from their

natural habitats has not been fully based on their reproductive capacity resulting to

decrease in population size and increase on limited distribution. Alteration of habitats had

caused species depletion without even documenting these species.

Information on Indonesian biodiversity, obtained from surveys and researches, is

scattered among various institutions in charge of the activities. Many have not even been

published, although a significant number had been presented as papers in national

scientific meetings. To retrieve such information, much time and energy are consumed.

Development of a database on biodiversity is an absolute need for scientific community

and planners.

Concept on sustainable utilization of the Indonesian biodiversity has not been

developed based on scientific basis. Researches on biodiversity cover a vast area but the

planning has not been integrated, so that the benefit is inadequate for making national

policy (Indonesian State Ministry of Environment, 1995).

2.2.4 Sustainable Management Strategies of Marine Genetic Resources

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environment and the local communities relying on these marine resources for social and

economic purposes.

His efficiency lies, among others, on how much he knows the protected area and

the site management plan and its stated objectives, zones, and management decisions that

can readily recognize situations or activities that are not in accord with these. He must

also have sufficient knowledge of the area (both in and out of water) that he can relate the

management plan to actual field locations- identifying important animal and plant species

(Salm and Clark, 1984).

Among the resource management tools that one must have on hand are maps and

overlays to relate pertinent data with specific locations (Salm and Clark, 1984). These are

means by which biological resources become more recognizable. Conservation plans

need to be built upon our understanding of spatial distribution of biological resources,

which is generally inadequate. However, recent developments in the areas of Geographic

Information Systems (GIs) and Remote Sensing (RS) techniques have brought within

reach new ways to develop, analyze and monitor the spatial distribution patterns of

biological resources. These tools have greatly speeded up the efficiency with which the

biological resources can be mapped (Kumar, 1999).

2.3 Employing Remote Sensing and Geographic Information System (GIS)

Sustainable management of marine genetic resources is brought about by changes

in the environment caused by man and natural phenomena in the immediate surrounding.

To understand the significance of environmental changes one must view it in an

integrated perspective. Environmental problems rarely respect conventional subject

boundaries, and their solution requires both an understanding of the physical and

ecological aspects of environmental systems and the way in which they interact with

economic, social and political factors (Haines-Young, Green and Cousins, 1994).

In the 80s analytical tools for ecological studies, such as conservation of

biodiversity, did not match the scale of questions that faced ecologists and alike. At the

regional scale consistent data about the Earth's surface and its cover were difficult, time

consuming, and expensive to collect. There was difficulty in processing complex data

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data. With the availability of computer-based systems for handling geographical or

spatial data, now popularly known as "geographic information systems" (GIs), many of

these difficulties had been overcome (Haines-Young, Green and Cousins, 1994).

What makes a GIs significant to biodiversity conservation and natural resources

management is its capacity to handle many layers of map information relating to an area.

Each layer describes a different aspect of its geography. One layer might hold data on,

say, sea surface temperature, another on specific location of coral species. Others might

include other pertinent data, such as, socio-economic characteristics of the human

population, distribution of other species within the same site, etc. By combining'these

layers problems that cannot be answered by using only one layer can now be solved.

Moreover, as problems change, the data can be processed in different ways to address

different issues in a highly flexible way. A GIs can also hold non-spatial attribute

information that can be associated with the various map features in a database

management system of some kind. These data can also be used to access the map

information. Ln figure 2.1 a query about the location of sites of special scientific interest

(SSSI) might be made starting either from the location on one of the map layers or by

means of text data relating to management status of the site.

Using GIs to provide spatially explicit input to ecological simulation models and

to spatially analyze the output has been a powerful method to investigate ecological

problems (Coleman at al, 1994). It is with this objective, for example, that EcoVision was

developed. EcoVision is a graphical user interface (GUI) that automates the connection

between GIs data and ecological simulation models. Through a series of menus the user

is guided through the process of selecting GIs data, connecting these data to the

ecological simulation model, conducting model simulations and viewing the results. This

shows how GIs, together with ecological tools for analysis, can increase the rate and

breadth of ecological investigations. Applied with the conservation of marine genetic

resources the result would show the same potential efficiency that can be used by a

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QUERRY:

I. Do any SSSls occur in this region?

Coastal boundary, species disfributiort, socio-ecortonric status, ctc.

Site related database

Location Identifier

002002

QUERRY:

1. Tell me about SSSI 002W2

[image:164.576.51.447.17.832.2]

r _{2. Find all SSSls with Mlticular attributes}

Figure 2.1 A geographic information system can be integrated with a database management system that will further provide information about one location for ecological studies and investigations.

(Mod9edfrom Haines-Young, R., Green D.R. and

S.

Cousins, 1993)

Remote sensing further adds to the brevity of analysis a natural resource manager

can make on spatially related ecological studies. With most remote sensing imagery now

available in digital form, images can be enhanced to facilitate visual interpretation or

classified to produce a digital thematic map. Both remote sensing and GIs technology,

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data have heightened monitoring and management of natural resources, including marine

genetic resources.

However, although many view GIs as a panacea solving data volume and

management problems, more important problems still underlie GIs, including the lack of

adequate "database management systems" (DBMS) software to manage scientific data

effectively and the lack of sophisticated statistical software and other analytical tools

within the GIs environment (Stafford et al, 1994).

2.4 The Concept of Database Design

Database had been defined as an integrated collection of computer data that is

organized and stored in a way that facilitates easy retrieval for the intended user.

(McLeod Jr, 1998) In order to achieve this, there must be a direct access storage device.

In principle, the database concept observes two objectives, that is, to minimize (if not

eliminate) data redundancy and to achieve data independence. This means, a database

must have data that is not stored in multiple files and that when changes are made in the

data structure it would not affect the programs that process the data. Moreover, to achieve

data independence, data specifications are placed in tables and dictionaries that are

physically separate from the programs. The programs are the ones that reference the

tables in order to access the data. Following this principle, changes to data structure are

made only once, and that is in the tables.

A database consist of tabulated data that is related to each other by data

specifications, such as a given code or ID on the item, or data element. It observes the

principle of normalization whereby the process identifies "stable" attribute groupings,

with high interdependency and affinity (Information Systems and Technology Hand-out,

2001). In the relational model, there are several standard forms of normalized tables.

These are: First Normal Form (1-NF), Second Normal Form (2-NF), Third Normal Form

(3-NF), Fourth Normal Form (4-NF), Fifth Normal Form (5-NF) and the BoyceICodd

Normal Form (BCNF). To simplify, each of these standard forms normalize tables

through specific requirements that reduce redundancy and undesirable update anomalies

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attribute groupings is to go through the entire existing table and decompose it to several

tables as prescribed by the standard forms.

2.5 Database Design

Database design provides a comprehensive framework for the database. With

such a working blueprint the database can be viewed in its entirety so that interaction

between elements can be evaluated. For example, potential problems and design

alternatives can be identified. Data can be further scrutinized; if found irrelevant it can be

removed from the database system. This working framework can also show whether data

have update potential or none.

Database design allows the designer to see all the involved components of the

database and set the appropriate representation to the entities involved. It also allows

through this that one sees which parts of the database cannot be integrated and cannot be

supported by an application. In terms of future revision that may be intended on the

database, the "comprehensive firnewor!? can give a relative estimate of costs that would

be needed.

It is also recognized that database design is the most crucial step in developing

any database application. (Ashenfelter, 1999) In order to help web database designers it

was suggested that databases be developed around metaphors. Some metaphors provide

better ways of modeling certain kinds of data; others are more efficient from a storage or

access point of view. Three common types of metaphors used for designing web

databases were identified: flat files, relational databases, and object-oriented databases.

(Ashenfelter, 1999)

2.6 Steps in Database Design

Three steps in database design are known: conceptual, logical and physical.

(SDBM Lecture, 2001)

3 Conceptual Design - in this phase all entities and spatial objects are described and defined. It tells how entities will be represented in the database. This phase

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represented. For example, when evaluating spatial objects, the designer might

choose among points, lines, areas or even raster cells to represent a feature. Of

course, the selection is based on the processing that will be done over these

objects. For instance, a building could either be represented as an area or a point.

The entities involved in this initial stage are both hardware and software

independent.

3 Logical Design - in this phase, the components involved are hardware independent but software specific. The logical design is usually determined by the

database management system, and gives the details about how entities are related

to each other. It is also at this phase where the type of database design, type of

data and width or range of the data is determined.

3 Pl~ysical Design - this phase is related to issues of file structure, memoly size and access requirements. The components involved in this stage are both

hardware and software specific.

Database design has nothing to do with using computers. It has everything to do

with research and planning. The design process should be completely independent of

sofhvare choices. The basic elements of the design process are: (Ashenfelter, 1999)

1. Defining the problem or objective.

2. Researching the current database.

3. Designing the data structures.

4. Constructing relationships.

5. Implementing rules and constraints.

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3. Materials and Methodology

3.1 Study Area

The Banda Islands are at the heart of an area characterized by high marine

biodiversity and fascinating geological processes. They are important historical and

cultural sites (TERANGI, 2001). Lying isolated between the Sunda Shelf and Sahul

Shelf- east of the Wallacea region- the small archipelago of Banda and the Banda Sea is

approximately 140 km from the nearest landmass at the heart of the Indonesian through

flow.

The reefs around Banda Islands are considered to be among the most diverse in

the world. Its rich marine diversity is attributed to the small island's isolated condition,

complex geology and oceanography, and its unusual geographic position. Several coral

genera not reported from the Great Banier Reef have been found in Indonesian waters:

Oulastrea, Nemenzophyllia, Boninastrea, Zoopilus, Physophyllia and Indophyllia. However, the highest coral diversity in the world is still found in the waters of North

Sulawesi, Indonesia, with 80 genera.

Moreover, marine macro algae, or seaweed, and seagrasses, in very good

condition- as reported by Sutarna (1990) and by Yusron and Edward (1999) (cited in

TERANGI, 2001)- were found on reef flats. Three seagrass species were reported by

Yusron and Edward in 1999, while fifty species of macro algae were reported in 1993 by

the same researchers.

With such marine diversity of corals, seaweeds and seagrasses in Banda Islands, it

is essential that coastal managers designated on this site develop an appropriate strategy

to sustainably manage them while the entire eccjsystem remains unexploited by tourism,

commercial industry and growing local communities along the coastline. As already

recognized, these marine organisms are potentially valuable genetic resources that can be

preserved to allow natural means of variation to occur over time, and from which the

local communities may derive economic support later on when biological products from

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3.1.1 Time and Location

This project covered the period of January 2002 until July 2002. The chosen site

for developing a simple spatial database is the coastline of the Banda Islands in South

Maluku, Indonesia. (Fig.3.1) Pertinent information, though not complete, were collected

in the field from April 27 to May 5 by a team of scientists under the Coastal Regions and

Small Islands Unit of UNESCO- Jakarta office. Not all essential data were gathered

because of the unavailability of technical resources from the local government of South

Maluku. The unavailability was due to the prevailing religious conflict and crisis in the

province of South Maluku.

[image:169.582.51.493.92.834.2]

600 Kilometers

Figure 3.1 The study site, Banda Islands, is located southeast of Ambon- the capital of South, Maluku, Indonesia. (prepared by the author)

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Located between 04" 31' S and 129' 54' E in the eastern part of the Banda Sea is

the Banda Islands, a small archipelago with six major islands and a number of smaller

islets.

The three largest islands are Gunung Api, Banda Neira and Banda Besar, which

form a cluster. To the west of this cluster are Run and Ai, with Hatta Island lying to the

southeast. An active volcano, Gunung Api (meaning, volcano or 'fire mountain'),

uniquely dominates the Gunung Api island. It rises 656 m above sea level, and is

considered to be the most active volcano in eastern Indonesia. (Fig.3.2)

PULAU

NUSANTARA

-'/

PULAU RHUN

[image:170.573.48.470.29.826.2]

PULAU HATTA

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3.2 Ma

Remote Sensing Application and Spatial Database Design For Sustainable Management of Coral Reefs in Banda Island, South Maluku, Indonesia

Remote Sensing Application and Spatial Database Design for

DECLARATION LETTER

Remote Sensing Application and Spatial Database Design for Sustainable Management of Coral Reefs in

Remote Sensing Application and Spatial Database Design for

Graduate Program

Dr. Ir. Handoko, M.Sc

AUTOBIOGRAPHY

CONTENTS

1. INTRODUCTION

3. MATERIALS AND METHODOLOGY

List of Figures

List of

1.2 Problem Conclusion

1.3 Framework for Solving the Problem

1.4 Objectives of the Study and Benefits

1.4.2 Benefits

Review

2.2 Genetic Diversity

QUERRY:

I. Do any SSSls occur in this region?

QUERRY:

1. Tell me about SSSI 002W2

2.4 The Concept of Database Design

3. Materials and Methodology

3.1 Study Area

3.1.1 Time and Location

600 Kilometers

PULAU