MAKING A CASE FOR A DEVELOPMENT-DRIVEN APPROACH TO LAW AS A LINCHPIN FOR THE POST-2015 DEVELOPMENT AGENDA

O Soyeju
MAKING A CASE FOR A DEVELOPMENT-DRIVEN APPROACH TO LAW AS A LINCHPIN FOR THE POST-2015 DEVELOPMENT AGENDA
1727-37816F1DCBC9F6121EE2FFE3CB5D7201A62610.4314/pelj.v18i2.10
As stated earlier, with the target date set for reaching the MDGs in plain sight, it is obvious that the attainment of all the set goals is no longer realistic.In the face of many supervening events like the increase in conflict, insurgencies and terrorism in the developing regions of the world, the global economic crises and the menace of climate change, the prospect of realising all the set goals by the target date has disappeared.For example, much of the progress made on poverty and hunger has occurred in a few large middle-income countries.Putting this grim reality into perspective, Amina Mohammed, the UN Special Adviser on Post-2015 Development Planning, states that:More than 1 billion people still live in extreme poverty.Far too many people continue to face serious deprivations of basic human needs, including food, safe drinking water, sanitation facilities, health, shelter, and education, with progress hampered by deep inequalities linked to income, gender, ethnicity, disability, location and age.The global economic downturn and increasing conflicts of recent years have worsened poverty and inequality, while climate change threatens to reverse achievements, and undermine future gains. 2    Again, as put by Amina Mohammed:Major new challenges have emerged, while existing ones have been exacerbated since the year 2000.Inequality has deepened.Environmental degradation has increased.People across the world are demanding more responsive governments and better governance and rights at all levels.Migration challenges have grown, and young people in many countries face poor prospects for decent jobs or livelihoods.Conflicts and instability have halted or reversed progress in many countries.Our future challenges are becoming more than ever cross-regional, intergenerational and transformative. 3Similarly, in the report of the High-Level Panel of Eminent Persons on the Post-2015 Development Agenda, the Panel notes that: 4    We considered the massive changes in the world since the year 2000 and the changes that are likely to unfold by 2030.There are a billion more people today, with world 2 Mohammed 2013 http://goo.gl/TBJZjj.3 Mohammed 2013 http://goo.gl/TBJZjj.4 UN High-level Panel New Global Partnership -see "Executive Summary".The report sets out a universal agenda to eradicate extreme poverty from the face of the earth by 2030 and deliver on the promise of sustainable development, and calls upon the world to rally around a new global partnership that offers hope and a role to every person in the world.

Introduction

The Millennium Development Goals (MDGs) are "the world's time-bound and quantified targets for addressing extreme poverty in its many dimensions -incomes, poverty, hunger, disease, lack of adequate shelter, and exclusion -while promoting gender equality, education, and environmental sustainability". 1 The formulation of the goals was a multilateral response to the development challenges confronting the developing world with the objective of reducing global poverty and other sources of human deprivation like hunger, universal primary education, gender inequality and the need for the empowerment of women, child mortality, maternal health, combating HIV/AIDS, bringing about enduring environmental sustainability, and developing global partnerships for development.

However, with the deadline for meeting the quantified targets in plain sight, the prospect of realising all the set goals by this date is diminishing.There are also reasonable concerns that even if these set goals are met, there have emerged new challenges with the potential of reversing whatever progress has been made under the current development framework.

For example, governance failure, among other flaws, has been identified as one of the major reasons for the widespread shortfalls of some of these developing regions in attaining the indicative parameters for the MDGs.And of all the indicative parameters of governance failure, not upholding the rule of law and a lack of honesty and transparency in government functions seem to be the most critical."Upholding the rule of law" requires credible institutions to hold government accountable, and * Olufemi Soyeju.LLD (UP) MILD (University of Lagos) LLM (Lagos State University) BL; Post-Doctoral Fellow and Academic Coordinator, LLM (International Trade and Investment Law in Africa), International Development Law Unit, Centre for Human Rights, Faculty of Law, University of Pretoria, South Africa.Email: email@example.com SOYEJU PER / PELJ 2015(18)2 unfortunately, these "credible institutions" are unavailable in the countries in most of these regions.

The thesis in this article is that law has an inherent development function and can play a significant role in driving the proposed post-2015 development agenda.Hence, a development-driven approach to law should be at the heart of the proposed post-2015 development agenda.

A development-driven approach to law denotes approaching development from the legal perspective, using the legal rules and institutions in a legal system to guide and support the development process, to ensure that development policy, goals and objectives are implemented successfully.

In support of the thesis of the paper, the overarching questions which this paper will seek to answer are: how important is law in driving the proposed 2015 development agenda?If it is important, why, and in what respects?It is important to note from the outset that "law" in this context includes both the formal and informal legal rules and institutions.

In pursuit of this agenda, this paper is structured as follows: Section 1 sets the stage with an introduction to the discussion; Section 2 contextualises the problem which this paper seeks to address; Section 3 examines the MDGs as a linchpin for global development, their nature and the relative regional performance score-card; Section 4 discusses the imperative for the post-2015 development agenda; Section 5 interrogates the law and development as a socio-legal theory and the intrinsic relationship between legal rules and institutions and development; Section 6 takes a look at the development-driven approach to law and makes a case for its adoption as a linchpin for the post-2015 development agenda; Section 7 examines corruption as an indicative parameter of governance failure; and Section 8 makes concluding remarks.

population at seven billion, and another billion expected by 2030.More than half of us now live in cities.Private investment in developing countries now dwarfs aid flows.The number of mobile phone subscriptions has risen from fewer than one billion to more than six billion.Thanks to the internet, seeking business or information on the other side of the world is now routine for many.Yet inequality remains and opportunity is not open to all.The 1.2 billion poorest people account for only 1 per cent of world consumption while the billion richest consume 72 per cent.

It is on the back of this that there is on-going initiative for a new development framework that would take forward the spirit of the Millennium Declaration and the best of the MDGs, with a focus on pressing global issues like poverty, hunger, water, sanitation, education and healthcare.

MDGs as a linchpin for global development

The adoption of the MDGs as a development strategy was partly a response to the failure of the strong economic growth of the late 1990s to address the needs of the billions of people caught in the web of extreme poverty.These Goals are also about basic human rights like "the rights of each person on the planet to health, education, shelter, and security as pledged in the Universal Declaration on Human Rights (UDHR) and the United Nations' Millennium Declaration". 8

As succinctly put by a report to the UN Secretary-General, 9 the projection at the time of the conception of these ambitious goals was that if the Goals were achieved by

2015:

More than 500 million people will be lifted out of the web of extreme poverty.More than 300 million will no longer suffer from hunger.There will also be dramatic progress in child health.Rather than die before reaching their fifth birthdays, 30 million children will be saved.So will the lives of more than 2 million mothers.

Besides the projections above, it was also envisaged that achieving the goals would address the needs of "350 million … people [who] are without safe drinking water and 650 million … people" who "live without the benefits of basic sanitation, allowing them to lead healthier and more dignified lives" and also, "hundreds of millions more women and girls" would "go to school, access economic and political opportunity, and have greater security and safety". 10

These goals are mutually reinforcing and inter-twined.As put by Ramesh Thakur, 11 the eradication of extreme poverty would translate into the reduction of infant mortality, the improvement of maternal heath, and ensuring the sustainability of the environment.In the same vein, the attainment of universal primary education, the combating of endemic diseases and empowering women would ultimately aid in the effort to eradicate the grinding global poverty.The next two sub-sections examine why the goals are important and the performance score card of the regions regarding the attainment of these lofty goals.

Why are the goals important?

Broadly speaking, these goals are important in several ways.First, on the international political level, the goals are the fulcrum on which development policy is hinged for the billions caught in the web of extreme poverty.As a development policy, they establish "a landmark framework for global development partnership in which the developed and developing countries agreed to take joint actions" towards the reduction of extreme poverty.Second, these goals represent "capital inputs -the means to a productive life, to economic growth, and to further development," though they are ends in themselves. 12 pointed out in the report to the UN Secretary-General, a "healthier worker is a more productive worker.A better educated worker is a more productive worker.Improved water and sanitation infrastructure raises output per capita through various channels, such as reduced illness.So many of these goals are part of capital accumulation, defined broadly, as well as desirable objectives in their own right". 13ird, for every member of humanity "these goals are a linchpin to the quest for a more secure and peaceful world".As plausibly posited in the same report, the "poor and hungry societies are much more likely than high-income societies to fall into conflict over scarce vital resources, such as watering holes and arable land -and over scare natural resources, such as oil, diamonds, and timber." 14Therefore, there is a strong link between poverty reduction and global security.

The report contends further that: The 13 years since the millennium have seen the fastest reduction in poverty in human history: there are half a billion fewer people living below an international poverty line of $1.25 a day.Child death rates have fallen by more than 30%, with about three million children's lives saved each year compared to 2000.Deaths from malaria have fallen by one quarter.This unprecedented progress has been driven by a combination of economic growth, better policies, and the global commitment to the MDGs, which set out an inspirational rallying cry for the whole world.

On the back of this remarkable progress, the Panel argues that "it would be a mistake to simply tear down the MDGs and start from scratch."Hence the call for a new global partnership to eradicate poverty and transform economies through sustainable development.

The Panel further recommends that "to fulfil our vision of promoting sustainable development, we must go beyond the MDGs" and "a new development agenda should carry forward the spirit of the Millennium Declaration and the best of the MDGs, with a practical focus on things like poverty, hunger, water, sanitation, education and healthcare". 25 argued in the report of the Panel, the goals did not address the plight of the poorest and most excluded people; the impact of conflict and violence on development; the imperatives of developing good governance and institutions that guarantee the rule of law, free speech and open and accountable government; and the need for inclusive growth to provide jobs. 26ntinuing, the High-Level Panel contends that the "the MDGs fell short by not integrating the economic, social, and environmental aspects of sustainable development as envisaged in the Millennium Declaration," and accordingly "[t]he This is a report which sets out a universal agenda to eradicate extreme poverty from the face of the earth by 2030, and deliver on the promise of sustainable development.The report calls upon the world to rally around a new global partnership that offers hope and a role to every person in the world.

result was that environment and development were never properly brought together.

People were working hard -but often separately -on interlinked problems". 27Having said that, and bearing in mind the words of Seidman et al "… research without a theory apes the rat in the maze", 29 , the focus in the next segment will be to interrogate law and development as a socio-legal theory.

Law and development as a theory

Law and development is a social theory of law which has as its core the idea of legal liberalism. 30 theorists "adopted the notion that evolutionary progress [in the Third World] would ultimately result in legal ideals and institutions similar to those in the West". 35They argued that the diffusion of Western law to the Third World would aid its modernisation and that modern law was the "functional prerequisite of an industrial economy". 36The chief exponents of this school of thought, Trubeck 37 and Galanter, 38 contributed significantly to the knowledge of law and development through literature and proved, though theoretically, that law is essential to economic development in as much "as it provides the necessary support for the functioning of a market system". 39cording to their thesis, they made a prediction that when rules that are universal in Just like the fate of modernisation theory, the law and development movement was short-lived, in that it was contradicted by events in the developing countries during that period in which it held sway.By the mid-1970s it was obvious that the theory was sterile, in that law was not achieving its intended objectives and had failed to function as it was anticipated in the theory.The two leading figures in the Movement, Trubek and Galanter, signalled the death of this movement in their article published in 1974. 41cording to the duo, the movement failed because it was said to be an "ethnocentric and naïve" school of thought. 42eir judgment of its failure was based on the observation that the theory contrasted sharply with the realities in developing countries, such as their typically having authoritarian governments, and the size of the disparities between the wealthy and the extremely poor, where it seemed as if laws were made to serve the interests of the economic elite and that the courts were weak and irrelevant.Another reason for the failure of the theory was that once law as an instrument of development or social change fell into the hands of an authoritarian and weak government, it was used to set and achieve goals supported by that government. 43e decline of this school of thought could be traced to the American experiences with the civil rights movement and the Vietnam War.The experiences, most likely, must have led to an awareness of the gaps between the ideals of America and the reality of her legal system.In the words of Scheepers, the criticism of the Law and Development Movement brought to the fore five issues of utmost importance to ensure "an effective role for law in the development process in developing countries".First, there is a need for empirical knowledge about developing countries.Second, there is the realisation that the picture of legal liberalism in the United States will be at variance with the reality in the developing world.Third, there are doubts about the universality of the experiences of developed countries.Fourth, there also exists scepticism with regard to the policy objective of the advanced countries, and lastly, there is an acceptance that instrumentalism is merely an aspect "of law, "not the essence of the rule of law". 45w and development has been the subject of intense legal study and research for over three decades.There are, however, wide and varied perspectives on development that offer insights into the relationship between law and development.

These perspectives have had a considerable influence on the thinking about development in general and about the symbiotic association between law and development.These ever-evolving perspectives include: the modernisation theory, the central thesis of which was that the process of development can be fast-tracked by "transplanting legal institutions from developed Western countries to less developed countries"; 46 dependency theory, which has had much influence on the law and development theory, and where the underlying argument is that the causes of underdevelopment lie in the history and structure of global capitalism; the economic perspective, which supports economic theories of development that focus primarily on policies that seek to promote aggregated economic growth rates; the welfarist perspective, which challenges the premise of many economic theories of development that conventional measures of economic growth capture all of the important aspects of human well-being; feminism, which emphasises policies that facilitate the integration of women into the economic system and combats gender-based discrimination in the productive sphere, the promotion of self-empowerment and the enhancement of the well-being of women in both public and private spheres; and the sustainable development perspective, that emphasises the causal link between environmental quality and human well-being, in terms of both the present and the future generations.

The perspectives discussed above underscore the instrumentalist assumption that underpins the law and development movement's view about the interface between law and development and sees law as a force which could be used to alter and influence human behaviour to achieve development.

Going forward in the discussion, the next segment examines the interface between law and development.

The interface between law and development

Based on law and development theory, it is clear that law has an inherent development function, and that in every society laws are needed to ensure the institutional changes needed to implement more effective development strategies.

In every society, primitive or civilised, there must be a body of rules which members of that society must regard as the standard of behaviour without which there may be anarchy or a state of anomie.This body of rules called "law" is aimed at the social arrangement of human existence.Without law, society becomes the devil's workshop, where the logic of the criminal reigns.

Therefore law is generally multi-functional in a contemporary society in that it regulates, creates order, determines outcomes, prescribes penalties, and outlaws certain acts or actions.It could be used as a tool of administration, control, crime prevention, rehabilitation and justice, and for collecting revenue and taxes, 47 all of which are outcomes of the development process.

Seidman et al define a law as "a normative rule promulgated by the state and ultimately implemented by state officials" which "may take many forms: a statute, a local ordinance, subsidiary legislation, a ministerial rule, an administrative regulation, a military junta's decree". 48 the other hand, just like "law", there is no universally accepted precise definition of "development".The word "development" is shifty and has been shifting over time.

The preamble to the United Nations' General Assembly's Declaration on the Right to Development 49 underscores wider, all-embracing components of the term "development" by defining it as:

... a comprehensive economic, social, cultural and political process, which aims at the constant improvement of the well-being of the entire population and all individuals on the basis of active, free and meaningful participation in development and in the fair distribution of benefits resulting therefrom.

In a response "to a tendency to confine or reduce the idea of poverty to low income in the case of individuals and low GDP in the case of countries", Amartya Sen came up with a formulation about development and posits that:

Development requires the removal of major sources of un-freedom: poverty as well as tyranny, poor economic opportunities as well as systemic social deprivation, neglect of public facilities as well as intolerance or the overactivity of repressive states. 50artya Sen further explains development "as a process of expanding the real freedoms that people enjoy," and according to him, the focus "on human freedoms contrasts with narrower views of development, such as identifying development with the growth of gross national product, or with the rise in personal incomes, or with industrialization, or with technological advance, or with social modernization". 51

Theo Scheepers also defines "development" and argues that:

Development is a people-centred process of change depending for its ultimate success on the capacity of people to manage the process through a variety of critical steps and phases within the limits of an institutional and value framework that will guarantee meaningful and lasting improvement of quality of life for all in a peaceful, stable and well-governed environment. 52ading the pack of those who see the relationship between law and development in a positive light, Hernando de Soto 53 forcefully argues that "The legal system may be the main explanation of the difference in development that exists between industrialised countries and those that are not industrialized".

Commenting on the relationship between law and development, Scheepers contends that law may either promote or restrict development.This depends on its aims and objectives as well as the manner in which legal rules are implemented. 54 the topic of the institutional thesis, Trebilcock et al argue that the major preoccupation of law as a discipline is the "process and institutions by which laws and related policies are enacted, implemented and enforced". 55According to these writers, "empirical research between … a country's institutions and development outcomes" suggests that "improvements in the rule of law are likely to have dramatic impacts on development outcomes". 56milarly, Davis et al argue that though there is a paucity of conclusive proof "reforms in particular substantive areas of law such as property law, contract law and human rights law have been effective in furthering development".Nevertheless there is "evidence that enhancing the quality of institutions that enact, administer and enforce laws can have positive and significant effects". 57

In the same vein, Ulen 58 commenting in support of the link "between legal institutions and modern growth," points out that:

The broadest view holds that law is vital to national growth to the extent that it creates incentives for people to behave in a growth-enhancing manner.good by doing well".Thus, a business organisation must have the appropriate incentives to produce and market so as to make a profit, but in doing so, must respect the interests of their customers and employees in not being harmed unreasonably by the products they are purchasing or producing.And the production process must not result in unwanted and uncompensated pollution of the air or water.Those seeking to make agreements that will bind them for a period of time must have confidence that those agreements will be kept or, if broken, result in adequate compensation, Those artists and inventors who seek to create new expressive works or new, useful, and non-obvious inventions … should have reasonable expectations of being able to enjoy the economic benefits of their expressive and creative activities.Property owners should have reasonable security in their assets and know themselves to be free from unreasonable interference in the enjoyment and employment of those assets from other individuals, organizations, and the government.

In "large-scale aggregated studies" conducted to examine "the relationship between law, administration and development, essentially by examining the impact of factors such as the quality of the bureaucracy, level of corruption, likelihood of government repudiation of contracts, risk of government expropriation, and overall maintenance of the rule of law on economic development", it was established" that "these factors significantly influence levels of income and rates of growth and investment". 59And one other compelling "finding is that "common law countries have experienced faster economic growth than civil law countries in recent decades". 60guing in favour of the finding, Davis et al state that "The fact that the quality of bureaucracy and levels of corruption are significant determinants of growth rates suggests that as a general matter the way in which law is administered is important".This claim has also been reinforced by the finding that predictability on the part of the judiciary is positively correlated with growth and investment. 61e other strand of thought on economic growth is the one that finds the academic interest in institutions to be a critical determinant of national growth and development.

Leading the vanguard is Douglas North, who is renowned for his long association with the "new economics," which postulates, inter alia, "that the legally and otherwisedetermined rules that govern economic activity have a profound influence on the ability of an economy to prosper". 62Citing an example, Ulen posits that "the mechanisms by which a society encourages and rewards risk-taking will have a deep effect on investments that might be necessary for growth.If a society discourages economic risk-taking or does not have appropriate safety nets to catch those who take risks and fail, then that society may not have sufficient investment in entrepreneurial activity". 63stly, another compelling strand of scholarship in relation to the institutional thesis is the argument of the Acemoglu, Robinson, and Johnson.Acemoglu et al through their writings argue "that there is persuasive theoretical and empirical evidence that those nations that have strong legal and social institutions have prospered and that those nations that do not have strong and stable institutions have not prospered". 64ing forward, the research agenda in the next section is to provide an answer to the question: what then is a "development-driven approach to law"?

A development-driven approach to law

A development-driven approach to law denotes approaching development from the legal perspective, using the legal rules and institutions in a legal system to guide and support the development process to ensure that development policy, goals and objectives are implemented successfully.

In a way, all laws impact on the development of a country and its people in one way or another.In most cases, most laws will affect development individually; only a few laws are deliberately targeted at achieving specific development goals and objectives.The problem, however, with many developing countries is that quite a number of laws that are part of their legal systems are not specifically targeted at facilitating or promoting development.

The imperative for a development-driven approach to law to be at the heart of the post-2015 development agenda

As mentioned earlier in this paper, law may either promote or restrict development.

This depends on its aims and objectives as well as the manner in which legal rules are implemented.

Official policy is translated into written laws and policy becomes law through a lawmaking process.Development policies become development-driven laws through a similar channel or process.Typical development-driven laws include the laws that protect the vulnerable in society like women, children, the disabled, minority groups, the racially disadvantaged and the down-trodden or the "poorest of the poor". 71For example, the law provides the platform by which governments regulate and ensure the provision of public services to the public and offer protection of rights for all citizens alike.

From the above it may be seen that laws are critical in ensuring the institutional changes needed to implement more effective development strategies.Besides the enactment of appropriate laws, there is a need for availability of a well-functioning court system.Reasonably, a country with a well-functioning court system will be able to attract investment into the economy.Related to this is the capacity to enforce contracts.Where enforceability is a problem, this raises the risk of capital loss and hinders the flow of capital for economic development. 72 underscoring the importance of legal rules and institutions in the development process, scholars have identified governance failure as one of the reasons for the widespread shortfall from most of the MDGs in low-income countries.

According to the report of the UN Secretary-General:

Economic development stalls when governments do not uphold the rule of law, pursue sound economic policy, make appropriate public investments, manage a 71 Scheepers Practical Guide to Law and Development 18.

public administration, protect basic human rights, and support civil society organizations-including those representing poor people-in national decision making. 73 other words, the following have been identified as the indicative parameters of governance failure in low-income countries of the world: not upholding the rule of law; a lack of the pursuit of sound economic policy; inappropriate public investment;

bad management of public a lack of protection of basic human rights;

and a lack of support for civil society organisations. 74 plausibly argued, political and social rights would "ensure equality before the law and fairness in the society across groups".By this, the vulnerable groups in the society would "be assured freedom from violence and from legal, economic, and social discrimination". 75e pursuit of sound economic policies entails "a natural balance of responsibilities between the private sector and the public sector to secure sustained and widespread economic progress". 76As the private sector remains the engine of growth in production, "the public sector establishes the framework and enabling environment for growth by setting sound macro-economic policies and providing such public goods as infrastructure, public health and education, and support for science and technology". 77

In the area of appropriate public investments, there is a need for heavy public sector investment in critical sectors of the economy, economic and social infrastructure in particular.Importantly, too, it must be noted that this public spending is the main driver of a private sector-driven market economy.The management of public administration needs to be efficient and transparent and driven by "administrators who are qualified, motivated, and adequately paid".In many of the low-income countries, especially in SSA, because of lack of adequate resources to incentivise the public sector, these countries suffer "from large-scale inefficiencies" and wastages.Also critical to effective governance is virile civil society engagement and participation.

Civil society participation ensures good governance, accountability and efficient development-driven public investments, which are products of well-informed decisions taken in the best interest of the generality of the citizens or the governed.In other words, "a vibrant civil society plays the role of watchdogs for the development and implementation of government policies". 79e rule of law entails "security of private property and tenure rights, safety from violence and physical abuse, honesty and transparency in government functions, and predictability of government's behaviour according to law". 80However, many of these countries have failed to achieve these minimum standards, more often than not because "upholding the rule of law requires institutions for government accountability', and unfortunately, "these institutions are missing". 81

Under the failure of governance, a lack of honesty and transparency in government functions or corruption seems to be one of the greatest reasons for the wide-spread shortfall from most of the MDGs in most low-income countries.

This takes the discussion in the next section to the issue of corruption as an indicative parameter of governance failure in low-income countries, using SSA as an example.

Corruption as an indicative parameter of governance failure in SSA

Corruption as a notion is generally surrounded by a great deal of confusion.Many definitions have been formulated over the years and none of them seems to have captured all the ingredients. 82However, Transparency International (hereafter TI) 83 defines corruption as "the abuse of entrusted power for private gain".Boersma pointed out that this definition "entails three elements: an abuse of power; a power that is entrusted; and a private benefit". 84The World Bank too, an international financial 79 Scheepers Practical Guide to Law and Development 18. institution which has lately been in the vanguard of the anti-corruption crusade, characterises "corruption" as "the abuse of public office for private gain". 85ough the two definitions contain the same three elements, there is a divergence between them in that "the World Bank's definition only covers corruption in the public sector" and "not corruption in the private sector".This dichotomy presupposes that there are two major types corruption -public and private sector corruption.While public sector corruption happens in the public sector of a country, the private sector corruption happens "within and between non-State actors, such as corporations, nongovernmental organizations and other private institutions". 86

For the purposes of this paper however, the word "corruption" denotes the "abuse of public office for private gains".

Corruption manifests in a wide variety of forms such as bribery, embezzlement, trading in influence, the abuse of functions, and illicit enrichment. 87s virulence also manifests in various ways and is more felt in the developing world especially SSA "because it undermines economic growth, discourages foreign investment and reduces the resources available for infrastructure, public services and anti-poverty programmes". 88Besides, it also undermines democratic institutions in that it weakens "legitimacy and accountability of governments" in power.Boersma, the phrase "abuse of functions" is a catch-phrase for other forms of conducts "that cannot be qualified as either bribery, embezzlement or trading in influence".He then classifies patronage and nepotism as manifestations of "abuse of functions".As argued by him, though such "practices are not included in the anti-corruption treaty … they are generally regarded as types of corruption".The Oxford Dictionaries http://www.oxforddictionaries.com/definition/ english/patronage defines "patronage" as "the power or right to control appointments to public office or the right to privileges".According to Boersma, in the modern use it connotes the abuse of this power by the appointing to office of political allies (Boersma Corruption 25).Nepotism, on the other hand, though not made mentioned of in any international and regional legal frameworks, is defined in the Oxford English Dictionary as "the showing of special favour or unfair preference to a relative in conferring a position, job, privilege, etc".Also, Robinson points out that corruption "also reduce[s] the effectiveness of aidfunded development projects and weaken[s] public support for development assistance in donor countries". 90He then concludes that corruption "is inimical to sustainable development, poverty reduction and good governance" and that it "not only affects poor people most directly, through the misallocation of public resources (including those derived from foreign aid) and routine exactions on the part of corrupt local officials, but it also keeps poor countries from becoming richer". 91mmenting on the poverty-outcomes of corruption in Africa, TI indicates that corruption is one of the factors perpetuating poverty, and that about 80% of Africans live on less than US$ 2 a day. 92 his part, Kututwa 93 writes that:

Corruption erodes the ability of a state to provide social services to its citizenry.The state's failure in this regard threatens human security because individuals' choices become limited.Much of the poverty in Africa can be traced to poor governance.Poor governance itself is caused by, among other things, corruption coupled with bad policies formulated and implemented by governments.Poverty in turn leads to instability and instability increases the insecurity of persons at the individual and national levels.Human security can only be achieved where public participation and accountability by the government to the citizenry are held as paramount and reinforced through building transparent and accountable systems.

Based on the foregoing, it may be concluded that corruption affects development in many ways.

First, it distorts public spending.As noted by Heymans and Lipietz, 94 "Distortions arise in three ways: from shaping the official priorities of government, by deflecting allocated resources away from their original purpose, and by undermining the tax base of government". 95As they rightly argue, "Priorities are distorted and public resources deflected in corrupt regimes, because allocations go where corrupt officials and politicians personally gain the most" and "Corrupt officials also deflect funds that have been earmarked specifically for developmental goals away from their original purpose". 96cond, it also undermines efficiency."Time and money wasted through corrupt activities come at the expense of productive activities.This impacts both on public administration and private enterprise". 97ird, corruption also discourages investment and growth.As explained by Heymans and Lipietz, "While some investors might well conduct their business through bribes, the overall implication of notoriously corrupt environments is that many potential investors avoid them.Incidents of corruption deter investment because higher bribes imply declining profitability on productive investments relative to rent-seeking investments, thus tending to crowd out the former". 98urth, corruption undermines the quality of governance.It diminishes "governance, public trust in the state's credibility and the ethics of government and society". 99sides, one other area in which the menace of corruption also manifests is the area of the huge funds being illicitly taken out of the African continent, especially out of SSA.SSA as a region is going through a huge "financial haemorrhage".According to former president Thabo Mbeki, who is the head of the UN High Level Panel on Illicit Financial Flows from Africa, the continent of Africa, SSA in particular, "is presently losing at least $50 billion every year through illicit fund flows". 100ving examined corruption and its virulent effects, this paper moves on in the next segment to gauge the effects of corruption on the realisation of the MDGs.

The effects of corruption on MDGs

Corruption as an outcome of poor governance has been identified as a major In a report commenting on the negative impact of corruption on the attainment of MDGs, 102 TI contends that "there is clear evidence that corruption has proven to be a major obstacle for countries and regions to reach the MDGs by 2015 as pledged".The report goes on to argue that "The costs of corruption can be explicit, implicit and hidden.Decision-makers must recognise these problems and find solutions that integrate the MDGs and anti-corruption agendas" and that "such measures need to be systematically built into development initiatives". 103re directly, the report avers that:

There is ample evidence of the value of designing MDG action plans that adequately integrate governance and anti-corruption mechanisms.New analysis by TI demonstrates a strong and positive correlation between increased transparency, accountability and integrity and better MDG outcomes on education, health and water in more than 48 countries.In practice, country-level work shows how anti-corruption approaches have an MDG payoff: examples are drawn from Ghana and Liberia, among others. 104r example, research "from across 50 countries shows that there is a clear, positive correlation between increased corruption and the reduced quality and quantity of education in a country". 105e TI states that the "global Corruption Barometer confirms that corruption hits the poor people hardest -with devastating consequences". 106Corroborating this view in another report, the TI argues that "When corruption plagues education, health or access to water, it is the poor who suffer the most.Poor families, when compared to other income groups, are especially burdened by demands for petty bribes.Corruption is turned into a regressive tax on needy households that sabotages attempts to eradicate poverty as part of meeting the MDGs". 107According to the report, "Corruption exacts a high cost on development" and "Abuses in one sector do not spare the others from collateral damage". 108e report also suggests that "While statistical and empirical evidence reveals corruption's high price in development, other findings show that preventing the problem has a clear 'MDG payoff'.Data analysis and country examples provide the proof that transparency, accountability and integrity produce positive changes that promote MDG achievement". 109milarly, the UN Global Compact 110 is of the opinion that corruption is one of the greatest challenges to the realisation of global development as it impedes "sustainable development with a disproportionate impact on poor countries and is corrosive on the very fabric of society". 111Continuing, the same organisation contends that "the impact on the private sector is also considerable -it impedes economic growth, distorts competition and represents serious legal and reputational risks", and that "corruption is also very costly for business, with the extra financial burden estimated to add 10% or more to the costs of doing business in many parts of the world". 112 rightly pointed out by Ramesh Thakur, 113 corruption is more of a governance issue.

According to him, corruption is a failure of institutions and stewardship in public life, a lack of capacity to manage social, economic and political affairs by the rules of the game and with the help of effective checks and balances.In eradicating high levels of corruption, the appropriate policy would be to criminalise corruption and impose adequate penalties through the instrument of appropriate laws.Going further, the  The United Nations Global Compact is a platform for business and non-business entities to proactively network and engage in areas of human rights, labour, environment, anti-corruption and contributing to UN goals in order to achieve the common objectives of building a sustainable and inclusive global economy.UN Global Compact 2015 https://goo.gl/EczxZd.In conclusion, though it may be argued that the rule of law is not the only requirement for the attainment of the time-bound development goals, to drive the post-2015 development agenda for optimal results a development-driven approach to law is very critical.As Twining rightly argues, "In this cause law has a largely unobtrusive, but significant role to play". 115Steps should be taken to encourage the emergence of the legal institutions that will promote development in most of the developing world, especially the countries of SSA, where such pro-development or development-driven institutions do not exist.

115

1UNDP

As a way forward, beginning with the present development framework the Panel came up with questions like: "what to keep, what to amend and what to add" to the current MDGs, and after wide and varied global consultations with all stakeholders, the Panel recommended a new development framework that "needs to be driven by five big, transformative shifts: leave no one behind; put sustainable development at the core; transform economies for jobs and inclusive growth; build peace and effective, open and accountable institutions for all; and forge a new global partnerships". 28This author agrees with the recommendations and conclusions of the High-Level Panel of Eminent Persons regarding the need to advance the development agenda beyond 2015.However, this writer argues that law has a critical role to play, should be at the heart of the architecture of the post-2015 development agenda, and that law can be a transformative force in the realisation of the post-2015 development goals.

It views law as a means of social engineering and as a veritable tool for the attainment of development aspirations and objectives.The theory explores the interface between law and development or social change in a given society and the development functions of law, and argues that laws and legal institutions can play an independent instrumental role in achieving development or bringing about a social change.27 UN High-level Panel New Global Partnership -see -see "Executive Summary".28 UN High-level Panel New Global Partnership.29 Seidmann and Seidmann State and Law 354.Commenting on the evolutionary trend of legal liberalism, Lawan 31 remarked that legal liberalism "came in three phases: the Law and Development Movement (LDM) of the 1970s, the legal reforms under the Structural Adjustment Programme (SAP) of the 1980s, and the World Bank's rule of law project, which started in 1990".According to him, "the last phase was introduced as one of the four elements of good governance which the World Bank identified as relevant for development.The other three elements are public sector management, accountability and transparency and information". 32Law and development started as a specialised academic study in the United States primarily concerning the relationship between the legal systems and development, that is, the social, economic and political changes taking place in the developing countries. 33Relying on modernisation theory, 34 the Law and Development Movement emerged and gained acceptance in the United States in the 1960s.The law and development

Such laws are referred to as laws that have a development function or developmentdriven.These laws provide the legal framework within which development within a particular country is driven, and these are generally called "development law" 65 or "development-driven law".62NorthUnderstanding the Process of Economic Change 185.63Ulen "Role of Law in EconomicGrowth and Development" 185.64   Ulen "Role of Law in EconomicGrowth and Development" 202.65   Ulen "Role of Law in Economic Growth and Development" 18. as an instrument of social change in a book, scholars are unanimous as to its facilitative role and explain that development implies social change, which in turn implies institutional change.They submit that "to bring about social change, government has no other instrument than the law, broadly conceived" and "to transform an institution that perpetuates a social problem a government can only use law".66Two reasons for this are: first, with the complexity of present society it is imperative for the government to "promulgate and effectively implement rules that … prescribe and contribute to shaping the relevant social actors' behaviours in desirable ways"; second, with the recognition of the doctrine of ultra vires as an integral part of the rule of law, "a government official has no power except what the law permits".67Development-driven law is based on development policy; development policy comes into existence through a policy-making process.This process starts when political leaders decide to respond to the needs, problems, ideals and aspirations of the citizens of a particular country.These issues and problems are identified by way of research inquiries and a consultation process in response to which a general discussion document is drafted.68Policy becomes law; and in order to make laws effective, people become involved in the implementation process, and the implementation of law and policy always depends for its validity and successful implementation on being constantly in congruence with what the people need. 69However, policy, no matter how well-researched and drafted, cannot bring about development alone.Policies and laws will bring about the desired change only when they have been implemented effectively.70

70

73

77

78

80

Scheepers Practical Guide to Law and Development 18. 81 Scheepers Practical Guide to Law and Development 18. 82 Boersma Corruption 25. 83 Transparency International is the main non-governmental organisation working in the field of anticorruption.Boersma Corruption 25.

impediment hindering the attainment of the current development goals."Corruption 96 Heymans and Lipietz Corruption and Development 14-15.97 Heymans and Lipietz Corruption and Development 17. 98 Heymans and Lipietz Corruption and Development 18. 99 Heymans and Lipietz Corruption and Development 19. 100 Anon 2013 http://goo.gl/2PTsbE.distorts the development process and overall actualization of the development agenda". 101

101

111 UN Global Compact 2015 https://goo.gl/ohsNkg.112 See http://www.transparency.org/topic/detail/poverty_and_development.113 Thakur "From the Millennium to Global Development Goals" 70.address this insidious eveil should include a well-resourced, well paid and well trained police force, civil service and judiciary. 1148 Concluding remarks The core thesis of this paper is that with the deadline in plain sight, the prospect of realizing all the MDGs by the target date is very slim.The progress made so far under the current development framework has been examined and the reasons why most of the developing regions of the world are off track in achieving the set under the eight development goals have been unpacked.However, as pointed out earlier on in the paper, there are concerns that even if the current set goals under the MDGs framework are met, there has been an emergence of new challenges which have the potential of reversing whatever progress has been made under the current development framework.This underscores the imperative need for the post-2015 development agenda and the need to adopt a development-driven approach to law in that agenda.Law can play a significant role in the global development process and become a linchpin for the post-2015 development agenda.

4 Imperatives for the post-2015 development agenda

the Report of the High-Level Panel of Eminent Persons on the Post-2015 Development Agenda, 23 the Panel reviewed the MDGs and concluded that: 24
O SOYEJU O SOYEJUPER / PELJ 2015(18)2 PER / PELJ 2015(18)2the wake of diminishing rainfall. Without productive alternatives, young people may the targets for gender parity, child mortality, maternal mortality, and access to safeturn to violence for material gain, or feel a sense of hopelessness, despair, and rage. Poor farmers who lack basic infrastructure and access to agricultural markets may water". 19turn in desperation to narcotics production and trade, such as growing poppy inAfghanistan or coca in the Andes. Many slums are controlled by gangs of drug traffickers and traders, who create a vicious cycle of insecurity and poverty. The lack Then, why is SSA the least developed of all the regions?of economically viable options other than criminal activity creates the seedbed of instability-and increases the potential for violence. 15 According to the UN Report, the region has become the epicenter of all kinds of3.2 Performance score card development-related crises like "food insecurity, a rise of extreme poverty, stunninglyhigh child and maternal mortality, and large numbers of people living in slums",As things stand now and with the target date set for reaching the MDGs in plain sight, coupled with the pernicious impact of climate change, all of which translate intoit is obvious that the attainment of these lofty goals is no longer feasible. Nevertheless, widespread shortfalls in all the indicative parameters for the MDGs. 20 For example,progress has been made and the progress is "diverse across goals and regions". 16 while the proportion of undernourished people is falling slowly in most regions of thePutting the progress made across goals and regions in perspective, the Global world, the over-all proportions remain high with little change in countries in SSA. 21Monitoring Report 2013 states that:Global estimates indicate that targets such as the reduction of extreme poverty (MDG1.a), gender equality in primary education (MDG 3.a), access to safe drinking One of the key negotiated outcomes of the United Nations Conference on Sustainablewater (MDG 7.c), and improved lives for at least 100 million slum dwellers (MDG 7.d) Development (Rio+20) which took place in Rio de Janeiro, Brazil in June 2012, washave been reached. The proportion of people whose income is less than $1.25 a day fell from 43.1 percent in 1990 to below 20.6 percent in 2010, leaving 1.2 billion people the decision of the Member States to launch a process to develop a set of Sustainablein extreme poverty. Gender equality in primary school enrolments was also achieved Development Goals (SDGs), which will build upon the MDGs and converge with thein 2010. Similarly, the goal of halving the proportion of people without sustainable access to safe drinking water has already been reached. At the same time, progress post-2015 development agenda.on the remaining MDGs has been lagging, especially for education and health-relatedMDGs. Global targets for infant, under-five, and maternal mortality (MDGs 4.a and 5.a), and to a lesser extent, access to basic sanitation (MDG 7.c) are significantly The UN Secretary-General's report on accelerating progress toward the MDGs and thebehind, and progress needs to be greatly accelerated if all of the goals are to be issues for advancing the UN development agenda beyond 2015 22 contends that "theachieved by 2015. The goal for primary school completion should have been within sight by 2011, but only half the progress needed has been made. 17 post-2015 development framework is likely to have the best development impact if itUsing SSA as an example, the region is lagging furthest behind and seems to be off-emerges from an inclusive, open and transparent process with multiple stakeholdertrack in meeting these goals. While other regions of the world have made significant participation".progress in achieving many of the goals, there is a widespread shortfall for most ofthe MDGs in SSA countries. 18 As pointed out in the Global Monitoring Report 2013,Poverty increases the risks of conflict through multiple paths. Poor countries are more "SSA has achieved more than 40 percent of the progress required to reach, by 2015,likely to have weak governments, making it easier for would-be rebels to grab landand vital resources. Resource scarcity can provoke population migrations anddisplacements that result in conflicts between social groups, as in Darfur, Sudan, in19Global Monitoring Report 2013 24.15 20UNDP Investing in Development 6, 8. UNDP Investing in Development 9.12 16 21UNDP Investing in Development 4. Global Monitoring Report 2013 22. UNDP Investing in Development 9.13 17UNDP Investing in Development 4. Global Monitoring Report 2013 22.14 18UNDP Investing in Development 6. Global Monitoring Report 2013 24.

are uniformly applied, they would give birth to predictability and make room for planning.They gave examples: contract law would secure expectation; property law would protect assets, and in theory would assist political development by providing the support required for a politically democratic state.Besides, government would be able to achieve its vision through law and the rule of law would prevent arbitrariness and oppression on the part of the government.40
33Zagaris 1988 U Miami Inter-Am L Rev 551.34Modernisation theorists contended that a society's underdevelopment was both caused by andreflected in its traditional (as opposed to its modern) economic, political, social and culturalcharacteristics or structures; and that in order to develop, underdeveloped societies would haveto undergo the same process of transition from traditionalism to modernity previously experiencedby more developed societies.

UN High-level Panel New Global Partnership -see "Executive Summary".
UN High-level Panel New Global Partnership -see "Executive Summary".
UN High-level Panel New Global Partnership -see "Executive Summary".
Simon 2004 Wm & Mary L Rev 127.
Galanter "Modernization of Law" 156.
Davis and Trebilcock "What Role Do Legal Institutions Play in Development?" 14.
Scheepers Practical Guide to Law and Development 118.
Ulen "Role of Law in Economic Growth and Development" 202.
Davis and Tebilcock 2001 Third World Quarterly 26. 60 Davis and Tebilcock 2001 Third World Quarterly 26. 61 Davis and Tebilcock 2001 Third World Quarterly 26.
Scheepers Practical Guide to Law and Development 18.
Robinson Corruption and Development 2.
BIBLIOGRAPHY
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Optimizing substitution matrix choice and gap parameters for sequence alignment

Robert C Edgar firstname.lastname@example.com
BMC Bioinformatics
45 Monterey Dr94920TiburonCAUSA

Optimizing substitution matrix choice and gap parameters for sequence alignment
10.1186/1471-2105-10-396BioMed Central Page 1 of 11 (page number not for citation purposes) Research article
Background: While substitution matrices can readily be computed from reference alignments, it is challenging to compute optimal or approximately optimal gap penalties. It is also not well understood which substitution matrices are the most effective when alignment accuracy is the goal rather than homolog recognition. Here a new parameter optimization procedure, POP, is described and applied to the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global protein alignments.Results: POP is compared to a recent method due to Kim and Kececioglu and found to achieve from 0.2% to 1.3% higher accuracies on pair-wise benchmarks extracted from BALIBASE. The VTML matrix series is shown to be the most accurate on several global pair-wise alignment benchmarks, with VTML200 giving best or close to the best performance in all tests. BLOSUM matrices are found to be slightly inferior, even with the marginal improvements in the bug-fixed RBLOSUM series. The PAM series is significantly worse, giving accuracies typically 2% less than VTML. Integer rounding is found to cause slight degradations in accuracy. No evidence is found that selecting a matrix based on sequence divergence improves accuracy, suggesting that the use of this heuristic in CLUSTALW may be ineffective. Using VTML200 is found to improve the accuracy of CLUSTALW by 8% on BALIBASE and 5% on PREFAB.Conclusion:The hypothesis that more accurate alignments of distantly related sequences may be achieved using low-identity matrices is shown to be false for commonly used matrix types. Source code and test data is freely available from the author's web site at

Background

Sequence alignment is a fundamental tool in contemporary biology. Most algorithmic formulations of the problem seek an alignment maximizing a function known as the objective score. Objective scores are usually defined as a sum of terms for matching pairs of letters (tabulated in a substitution matrix) and penalties for gaps. While the effects of different substitution matrices and gap parameters have been extensively studied in the context of local alignment and homolog recognition (see for example [1] and references therein), their effects on alignment accuracy, especially for global alignment, are not so well understood. Several heuristics are in common use, for example CLUSTALW's choice of low-identity matrices for aligning low-identity sequences [2], which have not to the best of my knowledge been empirically tested. One factor impeding such testing is the lack of effective automated methods for optimizing parameters for a given objective function. Previous work in this area has included unsupervised expectation maximization [3], discriminative train-ing [4], inverse parametric alignment [5][6][7][8][9] and maximum-margin structured learning [10,11]. Katoh et al. [12] reported using golden section search to optimize gap penalties, but this generally assumes a unimodal function which does not hold in this case. Exhaustive search has been attempted several times, for examples see [1,13].

In this work I describe a new parameter optimization procedure, POP, compare it with the IPA method of [6], and use it to investigate a number of questions related to global protein alignment accuracy, including: which is the best substitution matrix, do the best choices of matrix and gap penalties vary with sequence identity, should terminal gaps be penalized differently from internal gaps, and does the loss of precision due to integer rounding in substitution matrices degrade alignment accuracy? IPA was chosen for comparison because it is a recently published method, code was readily available, and because it optimizes parameters exactly equivalent to those studied in this work. To the best of my knowledge there has been no prior comparative study of alternative gap optimization methods, so IPA's effectiveness relative to other approaches is not known. In the tests performed here, POP was shown to achieve from 0.2% to 1.3% higher training-set accuracy than IPA, and evidence is presented that POP finds parameters within about 0.1% of the true optimum, i.e. an improvement in training set error of up to an order of magnitude. Differences of a fraction of a percent will be shown to be informative in assessing differences between substitution matrices, for which a method with the improved precision of POP is required. POP, like IPA, is designed to maximize training set accuracy, which may be achieved at some cost in generalization error, i.e. worse performance on novel data. In the case of POP this is by design: the problem of minimizing training set error is simpler than minimizing generalization error and the experiments reported here were not designed to compute the most biologically appropriate parameters for a given algorithm but rather to compare models with small and equal numbers of free parameters. It is then reasonable to assume that training set accuracy is a good measure of the relative performance of those models.

Let w = w i , i = 1...N be the parameters of interest (e.g., gap open and extend penalties), and Q(w) be the function to be optimized (e.g., an alignment accuracy or homolog recognition measure on some benchmark). The goal is to find values w OPT = argmax(w) Q(w) that maximize Q. This optimization problem is challenging for several reasons. Sufficiently small changes in w will leave all alignments unchanged and hence most Q functions of interest have zero partial derivatives almost everywhere. Also, Q is typically expensive to compute, requiring seconds to hours to evaluate at a single point, and is non-convex with many local maxima (Fig. 1).

Methods

IPA

Kim and Kececioglu [6] described an inverse parametric alignment method that can be trained on so-called "partial examples" such as those found in BALIBASE [14] in which only a subset of columns are annotated as reliably aligned. Eagu Kim (personal communication) kindly provided a software implementation of this algorithm (IPA). This implementation extended the method to allow separate terminal and internal gap penalties to be learned.

POP

The central idea in POP is to search for changes in parameters that result in "Goldilocks" changes in Q--not too big, not too small, but changes in just of the right size to have a good chance of indicating coarse trends rather than small-scale noise. This approach can be regarded as a generalization of line search optimization (see for example [15]). As theoretical and empirical methods for dealing with non-convex, non-continuous Q functions are currently limited, practical experience, especially examination of plots such as Fig. 1, is the best guide to determining the size of a "just right" change. In the experiments reported here, values around 0.5% were most effective.

POP proceeds in three stages. In the first stage, an Ndimensional hypercuboid is explored by evaluating Q(w) at each point in a regularly spaced grid. Local maxima are identified as points at which Q is greater than all neighboring points, and the best of these are used as starting points for the second stage. (It is important to do this rather than to use the best Q values found in the grid because these will tend to cluster around the same maxima and it is better to find a diverse set of starting points to avoid local maxima.) The second and third stages use a hill-climbing strategy to approach a local maximum given a starting point. The second stage uses a faster but less accurate variant of the hill-climbing method than the third stage, which starts from the best local optima found in the second stage. The final result is the best maximum found by the third stage. To save computation time, the three stages typically use increasingly large subsets of the training samples, with the first two stages using randomly chosen subsets and the third stage the entire training set.

Hill-climbing

Hill climbing repeats the following procedure until no improvement is found. Starting from a point w, each axis i is explored in both the positive and negative direction;

i.e., all parameters are held fixed but one (w i ). Let δ be a proposed change in w i ,
= w i + δ, w' = {w j , j ≠ i, }, Q' = Q(w'), i.e. Q'
is the value of Q after a proposed move along one axis, and Δ = Q' -Q. In each direction a δ is found that gives Δ > 0 (improves Q), or, failing that, a δ that reduces Q by an amount that is small, but not too small, say in the range 0.1% to 1%. Very small changes are undesirable because they will tend to be dominated by "noise" (Fig 1) rather than indicating a systematic trend. Large reductions in Q will tend to take w i out of the range where it might make an improvement when combined with a change along another axis (further discussed below). A heuristic designed to minimize these problems introduces a maximum (μ) and minimum (λ) reduction in Q (i.e., λ ≤ -Δ ≤ μ). After computing the proposed changes, a new w is determined as described in Making a move below.

Proposed changes

A proposed change δ is determined as follows. In the first iteration δ is set to a small fraction (say, 10%) of the absolute value of w i or a small value (say, 0 "hint" value set by the user. In subsequent iterations the initial value of δ is its final value from the previous iteration. Having set the initial value, the following procedure is then repeated. The value of Δ is computed. If Δ = 0, δ is multiplied by 4. If Δ < 0 and -Δ <λ, i.e. Q is reduced by too small an amount, δ is doubled. If Δ < 0 and -Δ >μ, i.e. Q is reduced by too much, δ is halved. Otherwise, Δ > 0 (Q is improved) and further exploration is tried. First, smaller values of δ (specifically, mδ/4 for m = 1, 2 and 3) are evaluated in an attempt to discover an intermediate maximum; if one is found this is repeated to investigate increasingly small changes. If smaller values give no further improvement, larger values are tried (mδ/4 for m = 5, 6, 7 and 8) in a similar way. A maximum improvement in Q, denoted Γ, is imposed in order to avoid extreme changes in a single parameter when far from an optimum (except when the smallest improvement found gives Δ >Γ, in which case it is accepted).
.1) if w i is zero, or a ′ w i ′ w i A typical Q function

Making a move

The search for proposed changes yields a set of 2N values
{δ i +, δ i -, i = 1 .
.. N} where the + and -superscripts indicate moves in the positive and negative directions respectively. All moves are considered that apply the proposed changes on from k = 1, 2 ... K axes simultaneously, where K is a user-settable parameter may be 1, 2 ... N. When k > 1, new evaluations of Q are required. For example, K = 2 considers eight moves for each pair of parameters: (+, +), (+, 0), (+, -), (-, +), (-, 0), (-, -), (0, +), and (0, -) where + or -indicates an increase or decrease in the parameter and 0 indicates no change. The move giving the best improvement in Q is accepted, otherwise the routine terminates. Naively, one might expect that consideration of singleaxis moves only (K = 1) would suffice, but in practice it turns out that allowing moves on two or more axes sometimes gives a significantly better final result, with K = 2 sufficient in most cases. It is desirable to keep K small as the number d of evaluated moves per iteration grows very rapidly with K:

It also turns out that allowing moves along axes that reduce Q can, when combined with moves on other axes, improve Q and that allowing this possibility also gives significantly improved optimization in some cases. For example, a small increase in the gap open penalty and a small decrease in the gap extend penalty might each reduce Q, but increase Q when both changes are made simultaneously.

Fast hill-climbing

A "fast" variant of the hill-climbing procedure sets K = 1 (no multi-axis moves) and immediately applies any proposed move that is found to improve Q. Speed is also improved by increasing μ, λ and Γ. These modifications reduce the number of times the Q function is invoked, saving execution time but sometimes yielding significantly inferior parameters. Directions to try, and the sign (+ or -) first tried, may be selected at random or cycled to minimize systematic bias.

Gap models and substitution matrices

Let a model be the set of parameters associated with a given objective function. In this work the substitution matrix is regarded as fixed; only gap penalty parameters are included. A gap is a series of indel symbols; formally, a maximal consecutive sequence of indels. If a gap includes the first or last column of an alignment it is described as terminal; all other gaps are internal. While POP has been implemented for a wide variety of models, most of these are works in progress and I will therefore report results for just two models: g2, in which the same affine penalties are applied to all gaps, and g4, in which internal and terminal gaps have different open and extend penalties. The parameters are g, e, G and E; the penalty for an internal gap of length L is g + (L -1) e and G + (L -1) E for a terminal gap. Thus g2 is a special case of g4 in which G = g and E = e. The objective score is then the sum of substitution scores minus gap penalties; a maximum-scoring global alignment is found using standard dynamic programming techniques.

The following substitution matrix types are considered: BLOSUM [16], RBLOSUM [17], PAM [18], JTT [19] and VT/VTML [20,21]. The RBLOSUM matrices were constructed using a bug-fixed version of the program used to compute BLOSUM matrices from the BLOCKS database [22]. Surprisingly, the corrected BLOSUM62 matrix was found to slightly degrade performance in homolog recognition [17]. Each matrix family is a series with members defined by a measure of evolutionary distance: percent identity cutoff in the case of BLOSUM and RBLOSUM, PAM distance for the rest. Conventionally, integer valued matrices are used in which log-odds scores in fractional bits have been rounded to one or two significant figures. Presumably this is for historical reasons: in older computer processors integer arithmetic was faster than floating point. This is no longer the case for many general-purpose processors, and regardless it is of interest to investigate whether the loss of precision due to integer rounding has an effect on alignment accuracy. Unless otherwise stated, full precision, one bit unit matrices were used.
d N K K = ⎛ ⎝ ⎜ ⎞ ⎠ ⎟ ⎧ ⎨ ⎪ ⎩ ⎪ ⎫ ⎬ ⎪ ⎭ ⎪ − 3 1 .

Benchmark data

Reference data was taken from three protein alignment benchmarks: PREFAB [23]

Accuracy measure

The accuracy measure (q) for a single pair is the number of correctly aligned residue pairs divided by the number of residue pairs in the reference alignment. The total accuracy score (Q) is the weighted average of q over all pairs, where the weighting is uniform in the case of PREFAB and the inverse of the number of pairs in the original multiple alignment in the case of BALIBASE. It would have been desirable to estimate error bars using a method such as the Bayesian bootstrap [1]; however this proved to be infeasible due to limitations in available computer time (a CPU year was needed to generate the results reported here). For brevity, the reference sets will be denoted Bali (all-pairs from BALIBASE v2), Prefab (all-pairs from PREFAB v4), TermGaps (1,000 randomly selected pairs from BALIBASE v3, subset 4), and IntGaps (1,000 randomly selected pairs from BALIBASE v3, subset 5). To investigate the effects of evolutionary distance three subsets of BALIBASE v3 pairs were constructed: 1,000 randomly selected pairs with identities in the range 0-33% (Id0_33), 33-66% (Id33_66) and 66-99% (Id66_99), respectively. These were selected from the full-length rather than domaintrimmed sequences.

Results

Comparison of POP and IPA

I compared POP and IPA using the TermGaps set, where the biggest difference between g2 and g4 might be expected, and on Bali. The BLOSUM62 matrix in 1/3 bit units was used as this was hardcoded into IPA. Results are shown in Table 1. POP was found to be from 0.2% to 1.3% more accurate than IPA; these improvements are typical (additional results not shown). Fig. 2 shows the results of optimizing model g2 on the Bali and Prefab sets. The results are qualitatively similar on the two sets, giving confidence that they indicate general trends rather than artifacts of benchmark construction, of overtraining or of significantly suboptimal local maxima. This is further confirmed by cross-training (Fig.  3), which again gives similar, albeit noisier, results, as would be expected. The results show VTML to be the best matrix series, with VTML > VT > BLOSUM > JTT > PAM holding for most members, though the differences between VTML, VT and BLOSUM are small except at the extreme high and low-distance ends of the series. The PAM series is significantly inferior to VTML, giving accuracy scores around 2% lower.

Substitution matrix family

Matrix selection by evolutionary distance

It has been suggested that different substitution matrices might be more effective at different evolutionary distances. For example, CLUSTALW uses more distant matrices to align more distant sequences, and Lassmann and Sonhammer [24] report that "softer", i.e. more distant, matrices are better at aligning more more distant sequences while are equally good with more closely related sequences. To investigate this, I optimized g2 on the Id0_33, Id33_66 and Id66_99 sets, with the results shown in Fig, 4. Interestingly, the plots are qualitatively similar for the three sets despite increasing pair-wise identity and the increasingly narrow variation in optimal Q. Remarkably, in the case of Id66_99 accuracies are all above 99.5% and the difference between the best matrix (VT50) and worst (BLOSUM30) is only 0.17%, yet trends observed at lower identities are still clearly discernible. The peak in each curve that identifies the best matrix in each family is at approximately the same evolutionary distance on each set, showing that the best choice of matrix is almost independent of sequence divergence. Similar results are found with g4 (not shown), suggesting that the best matrix is also approximately independent of the gap model, as might be expected.

Recommended matrix choice

In all the tests reported here, and others not shown, VTML200 is the best or close to best choice and is recommended as the general-purpose choice. In the VT and BLOSUM series, VT200 and BLOSUM70 respectively are recommended. In the clearly inferior PAM series, PAM100 to PAM150 appear to be best.

Improving CLUSTALW accuracy

The above results lead to the conclusion that CLUSTALW's heuristic use of distance-dependent matrices is probably not effective and suggest that a superior strategy would be to use a single high-accuracy matrix. I tested this in CLUS-TALW v2.0.9 [25] by setting the matrix to VTML200. This was necessarily an integer-rounded version as floatingpoint matrices are not supported by the software; I chose to use 1/3-bit units. The gap-open penalty was set to 2.0 and gap-extend to 0.1. These penalties were chosen after trying a few reasonable values; no attempt was made at systematic optimization. Results are shown in Table 2. An 8% improvement is seen in the column score on BALI-BASE v3. This suggests that a small reduction in pair-wise alignment errors due to a better choice of substitution matrix can have a cumulative effect in a multiple alignment and yield a substantial improvement. However, it is not sufficient to raise the accuracy of CLUSTALW to those of more recent methods such as MUSCLE [23,26] or PROBCONS [3], as shown in Table 2. Figure 2 Matrix accuracy. Optimal accuracy (Q) according to POP for the VTML, VT, BLOSUM, JTT and PAM series using the g2 model on the Bali (upper) and Prefab (lower) training sets. The horizontal axis is the evolutionary distance of a matrix; the correspondence between PAM and BLOSUM distance is arbitrary.

Matrix accuracy

Terminal gaps

The g4 model allows terminal gaps to be assigned different open and extend penalties versus internal gaps (see results in Table 3). On Bali and Prefab optimized terminal gap open penalties are roughly half those of internal penalties, validating the scheme used in MAFFT [12] and MUSCLE in which terminal gaps have the same extension penalty as internal gaps and half the open penalty. However, these results should be interpreted with caution since sequences in both Bali and Prefab are trimmed to domain boundaries. Multi-domain proteins are common, and different parameters and indeed different alignment algorithms may be appropriate when sequences have different domain organizations and are thus not globally alignable [27].

Random element

POP has a random element due to the selection of random subsets of the training data in its first two stages. It is therefore of interest to investigate how results vary for the same training data when different random number seeds are used. I chose to do this using the TermGaps set as practical experience shows it to have the most challenging parameter landscape of the sets considered here. I ran POP ten times for the g4 model on this set and found the following characteristics of the resulting Q values: mean 0.8412, standard deviation 5.3 × 10-4, maximum 0.8419, minimum 0.8401. These results suggest a low sensitivity to subset selection and are consistent with finding the global optimum to within approximately three significant figures. Figure 3 Cross-training results. Cross-trained results in which g2 parameters optimized for Bali were used to compute alignments on Prefab.

Cross-training results

Subsets by sequence identity Figure 4 Subsets by sequence identity. Results for the Id0_33 (top), Id33_66 (middle) and Id33_99 (bottom) sets. Observe that the curves on the three sets are qualitatively similar with no evident trend for the peak in a given family to move towards higher or lower identities.

Integer rounding

Integer rounding causes a small, but consistent, degradation in accuracy of around 0.1% to 0.3% in VTML and 0.05% to 0.1% in BLOSUM (detailed results not shown).

Corrected BLOSUM matrices

RBLOSUM gave a small but again consistent improvement in accuracy over BLOSUM of around 0.1%. This result is surprising considering that the opposite effect was found when testing homolog recognition [17].

Discussion

POP is an ad hoc algorithm without a strong theoretical foundation and has more heuristic parameters than one would ideally like. It does not scale well to larger numbers of parameters. Implementing and using POP requires an understanding of the input data and some trial and error. However, consistency of trends across different benchmarks, even when differences are very small, and consistency when run with different random number seeds combine to suggest that POP may find a global optimum to within approximately three significant figures on the pair-wise global alignment tests considered here, and regardless provide strong evidence that POP provides a sensitive test of differences between models with the same number of parameters. It is also readily parallelized and, unlike some other approaches, can easily be applied to multiple alignment. The hill-climbing in POP can start from parameters proposed by some other method, such as IPA, providing a lower bound on the training set error. It should be noted that the reduced training set error achieved by POP may come at some cost in generalization error; this is a topic for further study. Defaults is the accuracies using default parameters, VTML200 with that matrix and gap parameters given in the main text, and >Acc is the improvement due to VTML200. Accuracies of the more recent methods MUSCLE v3.7 and PROBCONS v1.12 are given for comparison.   Table 3.

Compute resources required by POP are relatively modest (Table 4), needing memory well within the range of current commodity computers and times (including alignments) ranging from minutes to hours on the tests considered here. The modern VTML matrices proved to give the best accuracy, in agreement with studies of homolog recognition [1]. The VT and BLOSUM series were not far behind, except for low-identity BLOSUMs which performed relatively poorly on all tests, even when aligning low-identity sequences. The RBLOSUM series (bug-fixed BLOSUM) was marginally better, but still inferior to VTML. Full-precision matrices were also marginally better than the integer-rounded versions in common use. It is natural to expect that improved pair-wise alignment accuracy will lead to improved multiple alignments, and this is a direction that deserves further exploration. The accuracy of CLUSTALW was significantly improved by using VTML200. It is therefore of interest to review the matrices employed by other multiple aligners. MUSCLE uses VTML240, which is close to VTML200 on most tests and therefore appears to have been a fortuitous choice. MAFFT v2 used PAM250, a clearly suboptimal choice; possibly this partly explains the lower accuracy of MAFFT v2 relative to the similar algorithm of MUSCLE v3. It is not clear to me which matrices are used in more recent versions of MAFFT, though the authors report testing members of the BLOSUM and JTT series [12]. ALIGN-M [28] uses BLOSUM35. Given the rapid drop in accuracy observed between BLOSUM40 and BLOSUM30 on all benchmark tests, it seems likely that a significant improvement would result from using a different matrix. KALIGN [24] uses GONNET250 [29] which I found to perform comparably with VTML200 (results not shown). MUM-MALS [30] and PROBCONS use BLOSUM matrices, suggesting the possibility of a small improvement in those programs by using VTML instead.

An examination of Fig. 2 shows that BLOSUM60-70 achieves almost the same accuracy as VTML150-200 on BALIBASE but is roughly 1% worse on PREFAB. This suggests that BALIBASE may be biased towards BLOSUM62 due to the use of sequence methods in alignment construction (87% of BALIBASE sequences have unknown structure, so are necessarily aligned by sequence alone). The source code for an example implementation of POP is available from the author's web site at http:// www.drive5.com/pop. This is designed for optimization of the g2 and g4 models described here, but can be modified relatively easily for other models by replacing the appropriate Q and alignment functions.

As I can attest from an abundance of personal experience, manual optimization of alignment parameters is a tedious process that rarely leaves the practitioner feeling confident in the results. Having an automated method at one's experimentation with new and modified algorithms by enabling a relatively trustworthy and painless evaluation of their relative effectiveness. I plan to use POP to explore ideas for improved pair-wise and multiple global alignment algorithms.

Conclusion

On the basis of this analysis, the VTML200 matrix is recommended as the most appropriate in general when global alignment accuracy is desired. My results suggest a bias in BALIBASE towards the BLOSUM series of matrices of around 1% in accuracy. While the effect is small, a bias of this magnitude could be significant in validations of multiple alignment methods because differences between the better methods on BALIBASE are of comparable size. Bias towards substitution matrices or gap penalty functions is not unexpected as only 13% of BALIBASE sequences have solved structures, and its alignments were therefore constructed mostly by the use of sequence rather than structure methods. Future studies of alignment accuracy should use data derived independently of sequence in order to avoid such biases.

Figure 1 A
1typical Q function. The graphs show alignment accuracy (vertical axis) on all pairs in BALIBASE v2 as a function of extension penalty e (horizontal axis) with fixed gap-open penalty g = 6.5 and the BLOSUM70 matrix. The interval outlined in the dashed box on the left is expanded on the right. Note the many local maxima, and that trends are apparent with changes in Q of around 0.01 (left), while smaller changes are typically "noise". (right).

Table 1 :
1Training set accuracySet
Model
POP
IPA
>Acc

Bali
g2
80.3%
80.0%
0.4%

Bali
g4
80.6%
79.6%
1.3%

TermGaps
g2
80.2%
79.7%
0.6%

TermGaps
g4
84.0%
83.8%
0.2%

Training set accuracy (Q) for the g2 and g4 models on Bali and
TermGaps using BLOSUM62 1/3-bit units. in The numbers in the POP
and IPA columns are the Q values achieved by the gap para-meters
reported by each method. In all cases, POP achieves higher accuracy,
the >Acc column shows the amount by which the POP accuracy is
better than IPA.

Table 2 :
2Improvement in CLUSTALW using VTML200Test
Defaults
VTML200
>Acc
MUSCLE
PROBCONS

B3 TC
44.8%
48.4%
8%
53.2%
61.3%

B3 SPS
78.6%
80.9%
3%
84.4%
88.3%

P4 SPS
61.7%
64.6%
5%
67.7%
71.7%

Improvement in accuracy of CLUSTALW v2.0.9 by using the VTML200 matrix. B3 is BALIBASE v3, P4 is PREFAB v4. TC and SPS are the average
fraction of correctly aligned columns and residue pairs, respectively. In PREFAB reference alignments are pair-wise so SPS and TC are equivalent.

Table 3 :
3Example parametersOptimized gap parameters reported by POP for the Bali, Prefab, TermGaps and IntGaps sets. Models are g2 (affine gaps) and g4 (different affine penalties for internal and terminal gaps). Penalties are g (gap-open), e (gap-extend), G (terminal gap-open) and E (terminal gap-extend). Q is the accuracy score. The matrix was the fullprecision, one-bit unit version of VTML200, one of the best matrices according to the tests reported here.Set
Model
g
e
G
E
Q

Bali
g2 5.370 0.423
80.7%

Bali
g4 5.874 0.473
2.332 1.488 81.0%

Prefab
g2 6.914 0.320
61.2%

Prefab
g4 6.742 0.476
3.964 0.322 62.3%

TermGaps
g2 6.508 0.133
80.8%

TermGaps
g4 5.010 0.635
15.507 0.026 84.2%

IntGaps
g2 5.725 0.304
78.3%

IntGaps
g4 5.725 0.304
6.419 3.343 78.4%

Table 4 :
4Typical compute resources required by POP.This following table shows the CPU time (minutes on a 2.2 GHz 64bit Athlon processor) and memory (Mb) used to compute the results shown inSet
Model
Time (mins.)
Memory (Mb)

Bali
g2
135
72

Bali
g4
840
72

Prefab
g2
27
24

Prefab
g4
68
24

TermGaps
g2
55
26

TermGaps
g4
192
27

IntGaps
g2
13
12

IntGaps
g4
61
25

(page number not for citation purposes)
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AcknowledgementsI am indebted to Chuong B. Do for many helpful discussions and to Eagu Kim for assistance with IPA.
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