Many people believe that faith and reason, or religion and science, are locked in an irreconcilable war of attrition against one another.
One must choose to be a person of learning, science, and reason, or choose to embrace religion, dogma, and faith alone. On this view, the Church opposes science, and if one embraces science, then one ought to reject the Church.
The scientific method looks to evidence to settle questions, so perhaps it would be fair to look at evidence to answer the question whether the Catholic Church is opposed to science and reason. If the Catholic Church were opposed to science, we would expect to find no or very few Catholic scientists, no sponsorship of scientific research by Catholic institutions, and an explicit distrust of reason in general and scientific reasoning in particular taught in official Catholic teaching. In fact, we find none of these things.
Historically, Catholics are numbered among the most important scientists of all time, including Rene Descartes, who discovered analytic geometry and the laws of refraction; Blaise Pascal, inventor of the adding machine, hydraulic press, and the mathematical theory of probabilities; Augustinian priest Gregor Mendel, who founded modern genetics; Louis Pasteur, founder of microbiology and creator of the first vaccine for rabies and anthrax; and cleric Nicolaus Copernicus, who first developed scientifically the view that the earth rotated around the sun. Jesuit priests in particular have a long history of scientific achievement; they
contributed to the development of pendulum clocks, pantographs, barometers, reflecting telescopes and microscopes, to scientific fields as various as magnetism, optics and electricity. They observed, in some cases before anyone else, the colored bands on Jupiter’s surface, the Andromeda nebula and Saturn’s rings. They theorized about the circulation of the blood (independently of Harvey), the theoretical possibility of flight, the way the moon affected the tides, and the wave-like nature of light. Star maps of the southern hemisphere, symbolic logic, flood-control measures on the Po and Adige rivers, introducing plus and minus signs into Italian mathematics — all were typical Jesuit achievements, and scientists as influential as Fermat, Huygens, Leibniz and Newton were not alone in counting Jesuits among their most prized correspondents. 
The scientist credited with proposing in the 1930s what came to be known as the “Big Bang theory” of the origin of the universe was Georges Lemaitre, a Belgian physicist and Roman Catholic priest. Alexander Fleming, the inventor of penicillin, shared his faith. More recently, Catholics constitute a good number of Nobel Laureates in Physics, Medicine, and Physiology, including Erwin Schrodinger, John Eccles, and Alexis Carrel. How can the achievements of so many Catholics in science be reconciled with the idea that the Catholic Church opposes scientific knowledge and progress?
One might try to explain such distinguished Catholic scientists as rare individuals who dared to rebel against the institutional Church, which opposes science. However, the Catholic Church as an institution funds, sponsors, and supports scientific research in the Pontifical Academy of Science and in the departments of science found in every Catholic university across the world, including those governed by Roman Catholic bishops, such as The Catholic University of America. This financial and institutional support of science by the Church began at the very birth of science in seventeenth-century Europe and continues today. Even Church buildings themselves were not only used for religious purposes but designed in part to foster scientific knowledge. As Thomas Woods notes:
Cathedrals in Bologna, Florence, Paris, and Rome were designed in the seventeenth and eighteenth centuries to function as world-class solar observatories. Nowhere in the world were there more precise instruments for the study of the sun. Each such cathedral contained holes through which sunlight could enter and time lines (or meridian lines) on the floor. It was by observing the path traced out by the sunlight on these lines that researchers could obtain accurate measurements of time and predict equinoxes. 
In the words of J. L. Heilbron of the University of California, Berkeley, the “Roman Catholic Church gave more financial aid and social support to the study of astronomy over six centuries, from the recovery of ancient learning during the late Middle Ages into the Enlightenment, than any other, and probably, all other institutions.”  This financial and social support extended also to other branches of scientific inquiry.
Such support is not only consistent with official Catholic teaching but is enthusiastically endorsed. On the Church’s view, science and faith are complementary to each other and mutually beneficial. In 1988, Pope John Paul II addressed a letter to the Director of the Vatican Astronomical Observatory, noting, “Science can purify religion from error and superstition; religion can purify science from idolatry and false absolutes. Each can draw the other into a wider world, a world in which both can flourish.”  As Nobel Laureate Joseph Murray notes, “Is the Church inimical to science? Growing up as a Catholic and a scientist — I don’t see it. One truth is revealed truth, the other is scientific truth. If you really believe that creation is good, there can be no harm in studying science. The more we learn about creation — the way it emerged — it just adds to the glory of God. Personally, I’ve never seen a conflict.”  In order to understand the complementarity of faith and science, indeed faith and reason more broadly, it is important to consider their relationship in greater depth.
A sign hung in Albert Einstein’s office at Princeton University that read: “Not everything that can be counted counts; not everything that counts can be counted.” Faith cannot be quantified and counted, like forces in physics or elements in chemistry, but that does not mean that faith is insignificant. Faith helps us to answer some of the most important questions facing mankind. As important as scientific discoveries can be, such discoveries do not touch on all of the inevitable questions facing us: What should I do? Whom should I love? What can I hope for? To answer questions such as these, science alone is not enough because science alone cannot answer questions that fall outside its empirical method. Rather, we need faith and reason operating together to answer such questions and to build a truly human community.
One reason that people view faith and science as in opposition is that they often view faith and reason more generally as in opposition. Our culture often pits faith against reason, as if the more faith-filled you are, the less reasonable you are. Faith and reason in the minds of so many people are polar opposites, never to be combined, and never to be reconciled. In this way, our culture often offers us false alternatives: live either by faith or by reason. To be religious is to reject reason; to be reasonable is to reject religion. But like other false alternatives, e.g., “Did you stop beating your wife this week, or last week?” such thinking artificially limits our freedom. Rather than choosing between faith and reason, the Church invites us to harmonize our faith and our reason because both are vitally important to human well-being.
A sign hung in Albert Einstein’s office at Princeton University that read: “Not everything that can be counted counts; not everything that counts can be counted.”
Developing a long tradition of Catholic reflection on the compatibility of faith and reason, Pope Benedict XVI seeks to unite what has so often become divided, by championing the full breadth of reason (including but not limited to scientific reasoning) combined with an adult faith. Rather than pitting faith against reason, the pope is calling for a reasonable faith and a faithful reason. From a Catholic perspective, the truths of faith and the truths of reason (including science) cannot in principle ever be opposed, because God is the ultimate Author of the book of Grace (revelation) as well as the book of Nature (philosophy and science). One ought not, therefore, choose between faith on the one hand and reason on the other, but rather one should seek to bring both faith and reason into a more fruitful collaboration.
In a Catholic view, since faith and reason are compatible, science — one particular kind of reasoning — and the Catholic religion are also compatible. Nevertheless, it is a commonly held view that one must choose between science and faith. Why is this? There are several core issues that drive this misunderstanding. First, Genesis claims that God created the world in seven days, but science indicates that the universe, including the earth, developed over billions of years. Secondly, Genesis talks about the first man, Adam, and the first woman, Eve, being created by God, as well as all the animals being created by God. Science indicates that all life — including human life — evolved over millions of years. Third, Bible stories are rife with miracles, but science has shown that miracles are impossible. Fourth, and most famously, the Catholic Church condemned Galileo. Finally, the Church’s opposition to stem cell research is seen as anti-science. Each of these objections is commonly used to justify the claim that the Church opposes science.
First, let’s consider the claim that in Genesis God created the world in seven days but science indicates that the universe, including the earth, developed over billions of years. In the Catholic tradition, the creation accounts in Genesis have been interpreted in a wide variety of ways. Both literal and figurative readings of Genesis are theologically acceptable for Catholics. Some theologians, such as Saint Ambrose, understood the Genesis account of creation in a literal way. But for the most part, Catholic theologians, including Saint Augustine, Saint Thomas Aquinas, Blessed John Henry Newman, Pope John Paul II, and Pope Benedict XVI, have interpreted Genesis as teaching the truth about creation in a nonliteral, nonscientific way.  Pope John Paul II puts the point as follows:
The Bible itself speaks to us of the origin of the universe and its make-up, not in order to provide us with a scientific treatise, but in order to state the correct relationships of man with God and with the universe. Sacred Scripture wishes simply to declare that the world was created by God, and in order to teach this truth it expresses itself in the terms of the cosmology in use at the time of the writer. 
Dr. Scott Hahn has pointed out that we might misunderstand the point of the seven days spoken about in Genesis, if we do not understand that the ancient Hebrew word for seven is the same word used for “making a covenant”. So, when it is said that God created the world in seven days, the text is communicating to its original readers that God has created the world in a covenantal relationship with the Divine.  Indeed, it was this idea — that the world is an orderly creation from an intelligent God — that led to the beginnings of science. For if the world is not intelligible and orderly, there would be no point in trying to understand its laws of operation, the laws of nature which scientific investigation seeks to discover.
Secondly, the incompatibility of Genesis and the evolution of species causes some people to think that religious belief is incompatible with science. If the first man, Adam, and the first woman, Eve, were created by God, as well as all the animals, then all life — including human life — did not evolve over millions of years. If all life evolved over millions of years, then there could not be a first man, Adam, a first woman, Eve, or a creation of animals directly by God. As noted, the Catholic Church does not generally require that individual Scripture verses be interpreted in one sense rather than another. Individual believers and theologians may come to different understandings of a particular passage but remain Catholics in good standing. So, one could believe with Saint Ambrose that Genesis provides a play-by-play account of exactly how God did things over seven 24-hour days. Or, one could believe with Saint Augustine, Saint Thomas Aquinas, Blessed John Henry Newman, Pope John Paul II, and Pope Benedict XVI that Genesis is not properly interpreted in this literalistic way. If one interprets Genesis in the ways suggested by the nonliteral view, then there is no contradiction in believing both in Genesis and in evolution as a way for accounting for the physical development of man provided one believes in a first man and first woman, from whom mankind descended and inherited original sin (see Humani Generis, no. 27).  Of course, the Catholic Church does not require that Catholics believe in evolution or any other view taught by any given scientist. However, if one believes in evolution, then one can also — as did Pope John Paul II — remain a faithful Catholic. 
A third problem that gives rise to difficulties for some people is that miracles are found in the Bible, but science is incompatible with belief in miracles. By miracle, I mean a supernatural intervention by God into the normal course of events. Is belief in miracles incompatible with science? To answer this question, it is important to distinguish science or the scientific method from what is called philosophical naturalism. The scientific method looks for natural causes to explain things that have happened. Philosophical naturalism, a philosophical theory, not a scientifically justified view, holds that there are only natural causes and no supernatural (divine) causes. Scientists can conduct their scientific investigations with or without a belief in philosophical naturalism. If God the Creator exists, then naturalism is false because a Creator God is a supernatural cause. If there is a Creator with power over the entire universe, then miracles are possible, for God could intervene in his creation. Indeed, science could only prove that miracles cannot happen, if it proved that there is no God. But science has not and cannot prove such a claim, since the realm of science is limited to the empirically verifiable, and God — at least as understood by most believers — is not a material being but a spiritual being.
On the one hand, we have the many Catholic scientists of distinction, from the beginning of the use of the scientific method until now, who argue that there is no conflict between their faith and their pursuit of science. We have the institutional Church sponsoring scientific endeavors of all kinds, at Catholic universities around the world, in the construction of cathedrals, and at the Vatican itself. We also have the explicit Catholic teaching that faith and reason are not opposed but rather complementary, and that scientific reasoning and faith are mutually enriching.
Fourth, and most famously, many people believe that the Catholic Church is antagonistic to science because of the condemnation of Galileo Galilei. This notorious and complicated conflict — the subject of many scholarly books — is partially based on scientific disputes but also has much to do with the conflicts of personality, politics, and theology of the time. Galileo’s view that the earth rotated around the sun was not the central issue. Heliocentrism was held by many people of the time, including Jesuit priests in good standing. More central to the Galileo controversy was whether Galileo broke agreements he had made about in what manner to teach his views. Through his polemical writings, Galileo alienated one-time friends and gave rivals an opportunity to undermine him. His work Dialogue Concerning the Two Chief World Systems was widely understood to mock the pope, a onetime friend and sponsor. Galileo did not limit himself to scientific claims on the basis of a view at the time lacking conclusive proof, but also insisted on challenging the dominant interpretations of Scripture at the time, which held that the sun rotated around the earth.  Thus, both influential theologians as well as scientists turned against Galileo. If Galileo had presented his views with greater modesty about his claims, it is likely that there would have been no condemnation.
Nevertheless, it is true that ecclesial authorities wrongly condemned Galileo’s heliocentricism, which was in 1633 not yet scientifically demonstrated. Galileo’s view was condemned because of an overly literal interpretation of a certain passage in Scripture. This erroneous condemnation could have been avoided if the theologians involved had remembered the methods of biblical interpretation propounded by Saint Augustine and Saint Thomas Aquinas, who recognized that Scripture often speaks the truth about creation in a nonliteral, nonscientific way. Pope John Paul II wrote:
Thanks to his intuition as a brilliant physicist and by relying on different arguments, Galileo, who practically invented the experimental method, understood why only the sun could function as the centre of the world, as it was then known, that is to say, as a planetary system. The error of the theologians of the time, when they maintained the centrality of the Earth, was to think that our understanding of the physical world’s structure was, in some way, imposed by the literal sense of Sacred Scripture. 
Indeed, even today people still speak, as does Scripture, about “the sun rising”, even though strictly speaking it is not the sun that rises but the earth that turns, causing it to appear that the sun rises.
In any case, Pope John Paul II acknowledged that the ecclesial judicial authorities in the trial of Galileo were wrong. These errors of a disciplinary and judicial nature were not a formal part of Catholic teaching. Then, as now, Church officials can and do make errors — unfortunately sometimes serious errors — in terms of discipline and order within the Church community. Church infallibility only applies to official teachings of faith and morals, not to assigning the best bishop to a particular place, nor to making wise decisions about political matters, nor to determining who can and ought to teach certain topics. The condemnation of Galileo was an erroneous decision in a matter of judicial order in the Christian community, but it does not have to do with official teaching of faith and morals.
One final controversy is the alleged opposition to science seen by Richard Dawkins. Dawkins writes, “He [Pope Benedict] is an enemy of science, obstructing vital stem cell research, on grounds not of morality but of pre-scientific superstition.”  In other words, the Church opposes science because she opposes embryonic stem cell research that involves destroying human embryos. Stem cell research is viewed as a promising means of fighting disease and promoting human well-being, but the Church, in Dawkins’ view, stands in the way of this progress.
It is important to begin responding to Dawkins’ accusation with the common ground shared by all people of good will. Indeed, everyone agrees, including Dawkins, that we should not kill innocent people, even if killing them might benefit other people or bring about an advance in scientific knowledge. The Tuskegee experiment in which African-American males were research subjects without their consent and to their detriment is universally condemned. Similarly, the research done by Dr. Josef Mengele on various human patients, or rather victims, in Auschwitz cannot be justified regardless of the scientific progress that was an alleged goal of the experiments. It is a basic principle of ethics that persons should not be harmed without their consent in scientific research in order potentially to benefit other people.
It is this principle, together with modern science, that has led the Catholic Church to oppose embryo research that kills human embryos. If human embryos have basic human rights as do other human persons, then embryonic research that involves killing human embryos is wrong. It was actually science overcoming “pre-scientific superstition” that brought the Catholic Church to the defense of human life from conception. In ancient times, Aristotle taught that the human person arose only 40 to 90 days after the union of the man and the woman in sexual intercourse. Aristotle thought, and this view was a common one until the nineteenth century, that the menses of the woman was “worked on” by the fluid ejaculated by the man to form a human being, some 40 days after the sexual union in the case of a male and 90 days in the case of a female.
Contemporary biology has shown that this understanding of how human reproduction takes place is radically mistaken. Sperm and egg are the gametes of sexual reproduction, not the menses and the entire ejaculated fluid. There is not a different time period for the formation of male and female children, nor does the seminal fluid continue to work for weeks and weeks to inform the menses. Rather, egg and sperm unite so as to create a new, individual, living, whole human person which passes through various stages — zygotic, fetal, infant, toddler, adolescent, adult — of human development.
Is there any reason to think that the human embryo is alive? To live is to have self-generated activities. The activities of proportionate growth and increase of specialization of cells contributing to the good of the whole organism indicate that the embryo is a living being. Further, it is clear that the embryo can die, but only living things can die, so the embryo must be living.
Is the living embryo also human? Since the embryo arises from a human mother and a human father, what species could it be other than human? Coming as it does from a human mother and a human father, made of human genetic tissues organized as a living being, and progressing along the trajectory of human development, the newly conceived human embryo is biologically and genetically one of us. This new living, growing being is a member of the species homo sapiens, a member of the human family. This human being is genetically new, that is, distinct from both mother and father. The embryo is not a part of the mother (as is obvious when the embryo is in a petri dish and not in utero), but rather is made from part of the mother (her ovum) and part of the father (his sperm). This new person is an individual whose genetic makeup and very existence is not the same as the mother’s or father’s or anyone else’s. There is nothing “pre-scientific” about the Church’s view that the human embryo is a human being; indeed, this view is confirmed by the findings of science which overturned the long-accepted prescientific views of Aristotle on reproduction.
Now, should very young human persons, including human embryos, be protected by law and welcomed in life? This is a moral question, not a scientific question. Science attempts to discover what is the case; ethics attempts to discover what should be the case in terms of human choices. Should the human embryo be protected as are human persons at later stages of development? I have explored this question at great length in a book called The Ethics of Abortion: Women’s Rights, Human Life, and the Question of Justice. Looking at every single pro-choice objection of which I was aware, I found that there is no rational justification for not according every human — including those in the embryonic stage of development — equal basic rights, including the right not to be intentionally killed in the hopes of benefiting other people’s health. By contrast, defenders of abortion and lethal embryonic stem cell research hold that it is permissible to kill some human beings in order to benefit others. However, neither view is “scientific”. Science qua science cannot settle the question of which human beings should be accorded human rights and welcomed into the human community.
Dawkins is also mistaken that the Church obstructs vital stem cell research. The Church opposes research — stem cell or otherwise — that involves the intentional killing of human embryos. Stem cell research that does not involve killing embryos is not only permitted by the Church but even funded by the Church, which has held at least two international conferences on stem cell research and has also funded research on adult stem cells undertaken at the University of Maryland School of Medicine. This research, using stem cells from adults or umbilical cords, has actually been developed into treatments that have already saved human lives. To date, despite billions of dollars, embryonic stem cell research has not led to one cure or a single effective treatment. The Church does not oppose stem cell research as such, but only opposes any kind of research that involves killing humans.
At this point, we are in a position to come to a prima facie judgment about the question of whether the Church opposes science. On the one hand, we have the many Catholic scientists of distinction, from the beginning of the use of the scientific method until now, who argue that there is no conflict between their faith and their pursuit of science. We have the institutional Church sponsoring scientific endeavors of all kinds, at Catholic universities around the world, in the construction of cathedrals, and at the Vatican itself. We also have the explicit Catholic teaching that faith and reason are not opposed but rather complementary, and that scientific reasoning and faith are mutually enriching. On the other hand, we have the trial and condemnation of Galileo. The Galileo case appears, against the larger background of Catholic teaching and practice, as an unfortunate aberration from the norm. However, both Galileo himself — who remained a faithful Catholic all his life — and those involved in his trial, such as Saint Robert Bellarmine, agreed that there can never be a true conflict between science and faith. Apparent but not real conflicts can arise through a mistaken interpretation of faith (as was made by those who condemned Galileo), a misunderstanding of science (e.g., that science requires denying miracles), or both. It is therefore a myth — albeit a persistent myth — that the Church opposes science.